Starting phenix.real_space_refine
on Thu Mar 13 10:42:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ia8_35298/03_2025/8ia8_35298_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ia8_35298/03_2025/8ia8_35298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ia8_35298/03_2025/8ia8_35298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ia8_35298/03_2025/8ia8_35298.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ia8_35298/03_2025/8ia8_35298_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ia8_35298/03_2025/8ia8_35298_neut.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    5620      2.51       5
     N    1506      2.21       5
     O    1616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8810
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "L"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 56
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
    Chain: "A"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2255
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 15, 'TRANS': 270}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1716
          Classifications: {'peptide': 216}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 2580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2580
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 431
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 5.55, per 1000 atoms: 0.63
  Number of scatterers: 8810
  At special positions: 0
  Unit cell: (91.8, 123.25, 125.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      68     16.00
     O    1616      8.00
     N    1506      7.00
     C    5620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.93
  Conformation dependent library (CDL) restraints added in 952.0 milliseconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 15 sheets defined
      35.9% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 51
      removed outlier: 3.745A  pdb=" N   SER A  26 " --> pdb=" O   PRO A  22 " (cutoff:3.500A)
      Proline residue:  A  39  - end of helix
    Processing helix  chain 'A' and resid 55 through 74
      removed outlier: 3.540A  pdb=" N   SER A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 84
      removed outlier: 3.946A  pdb=" N   SER A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 114
      removed outlier: 3.547A  pdb=" N   ILE A 102 " --> pdb=" O   ILE A  98 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE A 111 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 126
    Processing helix  chain 'A' and resid 126 through 134
    Processing helix  chain 'A' and resid 135 through 153
      removed outlier: 3.573A  pdb=" N   ALA A 139 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP A 147 " --> pdb=" O   CYS A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 161
    Processing helix  chain 'A' and resid 330 through 343
    Processing helix  chain 'A' and resid 345 through 363
      removed outlier: 3.653A  pdb=" N   ILE A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR A 356 " --> pdb=" O   MET A 352 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE A 359 " --> pdb=" O   CYS A 355 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 379
    Processing helix  chain 'A' and resid 384 through 390
    Processing helix  chain 'A' and resid 390 through 396
      removed outlier: 3.541A  pdb=" N   HIS A 394 " --> pdb=" O   TRP A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 416
    Processing helix  chain 'A' and resid 416 through 427
      removed outlier: 3.731A  pdb=" N   CYS A 420 " --> pdb=" O   TRP A 416 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
    Processing helix  chain 'A' and resid 440 through 454
    Processing helix  chain 'C' and resid 6 through 30
      removed outlier: 3.800A  pdb=" N   ALA C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL C  13 " --> pdb=" O   ASP C   9 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LYS C  29 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 53
    Processing helix  chain 'C' and resid 207 through 212
      removed outlier: 4.077A  pdb=" N   TRP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 216
    Processing helix  chain 'C' and resid 242 through 255
      removed outlier: 3.515A  pdb=" N   SER C 246 " --> pdb=" O   ARG C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 278
    Processing helix  chain 'C' and resid 282 through 286
    Processing helix  chain 'C' and resid 295 through 309
      removed outlier: 3.664A  pdb=" N   ALA C 301 " --> pdb=" O   GLU C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 351
      removed outlier: 3.680A  pdb=" N   CYS C 351 " --> pdb=" O   ASN C 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 22
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.604A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.753A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.508A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.613A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.965A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166
    Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 191
      removed outlier: 6.161A  pdb=" N   VAL C  34 " --> pdb=" O   LYS C 197 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   PHE C 199 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU C  36 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 8.971A  pdb=" N   ALA C 220 " --> pdb=" O   GLU C  33 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.558A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.780A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.983A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.604A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.755A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.563A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.722A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.871A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.409A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.678A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.678A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   THR S 238 " --> pdb=" O   GLN S 231 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1116 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: 2.59

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2822
        1.34 -     1.46: 2081
        1.46 -     1.58: 3998
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 8997
  Sorted by residual:
  bond pdb=" C   PRO A  21 "
       pdb=" N   PRO A  22 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 1.51e-02 4.39e+03 2.33e+00
  bond pdb=" C   VAL S   2 "
       pdb=" O   VAL S   2 "
    ideal  model  delta    sigma   weight residual
    1.236  1.219  0.017 1.19e-02 7.06e+03 1.99e+00
  bond pdb=" C   ILE A 116 "
       pdb=" O   ILE A 116 "
    ideal  model  delta    sigma   weight residual
    1.239  1.224  0.015 1.13e-02 7.83e+03 1.82e+00
  bond pdb=" C   ILE A  98 "
       pdb=" N   PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.031 2.34e-02 1.83e+03 1.71e+00
  bond pdb=" C   MET A 138 "
       pdb=" N   ALA A 139 "
    ideal  model  delta    sigma   weight residual
    1.335  1.319  0.016 1.31e-02 5.83e+03 1.52e+00
  ... (remaining 8992 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 11685
        1.38 -     2.77: 415
        2.77 -     4.15: 62
        4.15 -     5.54: 23
        5.54 -     6.92: 5
  Bond angle restraints: 12190
  Sorted by residual:
  angle pdb=" N   GLY L  13 "
        pdb=" CA  GLY L  13 "
        pdb=" C   GLY L  13 "
      ideal   model   delta    sigma   weight residual
     112.60  106.66    5.94 1.53e+00 4.27e-01 1.51e+01
  angle pdb=" N   SER A 117 "
        pdb=" CA  SER A 117 "
        pdb=" C   SER A 117 "
      ideal   model   delta    sigma   weight residual
     113.88  109.22    4.66 1.23e+00 6.61e-01 1.43e+01
  angle pdb=" CA  GLY L  13 "
        pdb=" C   GLY L  13 "
        pdb=" N   LEU L  14 "
      ideal   model   delta    sigma   weight residual
     114.78  118.92   -4.14 1.16e+00 7.43e-01 1.27e+01
  angle pdb=" N   CYS A  95 "
        pdb=" CA  CYS A  95 "
        pdb=" C   CYS A  95 "
      ideal   model   delta    sigma   weight residual
     112.72  108.02    4.70 1.36e+00 5.41e-01 1.19e+01
  angle pdb=" CA  GLY B 330 "
        pdb=" C   GLY B 330 "
        pdb=" N   SER B 331 "
      ideal   model   delta    sigma   weight residual
     114.74  118.43   -3.69 1.13e+00 7.83e-01 1.07e+01
  ... (remaining 12185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.14: 4692
       14.14 -    28.29: 479
       28.29 -    42.43: 121
       42.43 -    56.57: 27
       56.57 -    70.72: 8
  Dihedral angle restraints: 5327
    sinusoidal: 2054
      harmonic: 3273
  Sorted by residual:
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.05   27.95     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  LEU B  51 "
           pdb=" C   LEU B  51 "
           pdb=" N   ARG B  52 "
           pdb=" CA  ARG B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.08  -20.92     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.73   18.27     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5324 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 770
       0.031 -    0.062: 409
       0.062 -    0.093: 136
       0.093 -    0.125: 67
       0.125 -    0.156: 8
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CG  LEU A  75 "
            pdb=" CB  LEU A  75 "
            pdb=" CD1 LEU A  75 "
            pdb=" CD2 LEU A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.06e-01
  chirality pdb=" CB  THR S  91 "
            pdb=" CA  THR S  91 "
            pdb=" OG1 THR S  91 "
            pdb=" CG2 THR S  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CB  ILE A 163 "
            pdb=" CA  ILE A 163 "
            pdb=" CG1 ILE A 163 "
            pdb=" CG2 ILE A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.72e-01
  ... (remaining 1387 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 287 "   -0.051 5.00e-02 4.00e+02   7.77e-02 9.65e+00
        pdb=" N   PRO C 288 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C 288 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 288 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  21 "    0.037 5.00e-02 4.00e+02   5.53e-02 4.90e+00
        pdb=" N   PRO A  22 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A  22 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  22 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.72e+00
        pdb=" N   PRO S  75 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 217
        2.70 -     3.25: 8268
        3.25 -     3.80: 12831
        3.80 -     4.35: 17619
        4.35 -     4.90: 30675
  Nonbonded interactions: 69610
  Sorted by model distance:
  nonbonded pdb=" O   GLY C  45 "
            pdb=" OG1 THR C  48 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD2 ASP B  76 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   LEU A 387 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   VAL A  23 "
            pdb=" OG  SER A  26 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NH2 ARG L  16 "
            pdb=" O   TYR A 393 "
     model   vdw
     2.227 3.120
  ... (remaining 69605 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:             12.920
  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:                    0.080
  Process input model:                     22.080
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:11.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8997  Z= 0.332
  Angle     :  0.632   6.920  12190  Z= 0.363
  Chirality :  0.045   0.156   1390
  Planarity :  0.004   0.078   1537
  Dihedral  : 12.725  70.718   3206
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  0.21 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -1.21 (0.24), residues: 1114
  helix: -0.34 (0.27), residues: 375
  sheet: -0.21 (0.32), residues: 280
  loop : -1.48 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.002   PHE A 164 
 TYR   0.014   0.001   TYR B 105 
 ARG   0.005   0.000   ARG S 160 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 0.899 
Fit side-chains
REVERT: S    1 ASP cc_start: 0.7641 (t70) cc_final: 0.7426 (t70)
  outliers start: 4
  outliers final: 0
  residues processed: 144
  average time/residue: 1.7968
  time to fit residues: 270.5611
Evaluate side-chains
  111 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.126799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.082684 restraints weight = 11320.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.55
r_work: 0.2722 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2588 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8997  Z= 0.338
  Angle     :  0.641   7.260  12190  Z= 0.340
  Chirality :  0.047   0.354   1390
  Planarity :  0.005   0.062   1537
  Dihedral  :  4.734  25.842   1218
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  8.79 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: 1114
  helix:  0.47 (0.27), residues: 377
  sheet:  0.14 (0.32), residues: 280
  loop : -1.42 (0.26), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.002   PHE S  29 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.005   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7539 (ptm160)
REVERT: C  330 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7885 (mtpt)
REVERT: B   42 ARG cc_start: 0.8117 (tpt170) cc_final: 0.7730 (tmt170)
REVERT: B   46 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7147 (mmp80)
REVERT: B  198 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8350 (pp)
REVERT: B  217 MET cc_start: 0.8327 (ptt) cc_final: 0.8075 (ptt)
REVERT: G   42 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: G   58 GLU cc_start: 0.8515 (pm20) cc_final: 0.7965 (pm20)
REVERT: S    1 ASP cc_start: 0.7609 (t70) cc_final: 0.7258 (t0)
  outliers start: 20
  outliers final: 7
  residues processed: 126
  average time/residue: 1.7184
  time to fit residues: 227.2324
Evaluate side-chains
  121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ARG
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 85 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 93 optimal weight:    0.2980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 427 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.129836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.086013 restraints weight = 11552.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.55
r_work: 0.2762 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8997  Z= 0.187
  Angle     :  0.556   9.291  12190  Z= 0.292
  Chirality :  0.044   0.354   1390
  Planarity :  0.004   0.065   1537
  Dihedral  :  4.361  22.305   1218
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 10.56 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.23 (0.25), residues: 1114
  helix:  0.95 (0.28), residues: 379
  sheet:  0.24 (0.31), residues: 279
  loop : -1.32 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE S  29 
 TYR   0.014   0.001   TYR S 190 
 ARG   0.005   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8429 (mt) cc_final: 0.7915 (tp)
REVERT: A  151 PHE cc_start: 0.8008 (t80) cc_final: 0.7753 (t80)
REVERT: A  365 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7752 (ptm160)
REVERT: A  442 PHE cc_start: 0.7508 (t80) cc_final: 0.7305 (t80)
REVERT: C  313 ARG cc_start: 0.8170 (pmm-80) cc_final: 0.7826 (pmm-80)
REVERT: B   42 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7763 (tmt170)
REVERT: B  198 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8387 (pp)
REVERT: B  217 MET cc_start: 0.8373 (ptt) cc_final: 0.8142 (ptt)
REVERT: G   42 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8102 (mm-30)
REVERT: G   58 GLU cc_start: 0.8554 (pm20) cc_final: 0.7982 (pm20)
REVERT: S    1 ASP cc_start: 0.7472 (t70) cc_final: 0.7084 (t0)
  outliers start: 22
  outliers final: 10
  residues processed: 132
  average time/residue: 1.6507
  time to fit residues: 228.7430
Evaluate side-chains
  124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   16 ARG
Chi-restraints excluded: chain A residue   54 ARG
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   52 GLN
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.130144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.086391 restraints weight = 11332.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.53
r_work: 0.2777 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8997  Z= 0.187
  Angle     :  0.543   8.490  12190  Z= 0.286
  Chirality :  0.043   0.258   1390
  Planarity :  0.004   0.064   1537
  Dihedral  :  4.201  21.533   1218
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.34 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.02 (0.25), residues: 1114
  helix:  1.19 (0.29), residues: 377
  sheet:  0.24 (0.31), residues: 282
  loop : -1.18 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 297 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE A 107 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.006   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8459 (mt) cc_final: 0.7973 (tp)
REVERT: A  151 PHE cc_start: 0.8027 (t80) cc_final: 0.7821 (t80)
REVERT: A  155 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7012 (mp)
REVERT: A  365 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7786 (ptm160)
REVERT: A  442 PHE cc_start: 0.7531 (t80) cc_final: 0.7310 (t80)
REVERT: C  313 ARG cc_start: 0.8157 (pmm-80) cc_final: 0.7708 (pmm-80)
REVERT: B   23 LYS cc_start: 0.8443 (tttp) cc_final: 0.7989 (tppt)
REVERT: B   42 ARG cc_start: 0.8190 (tpt170) cc_final: 0.7767 (tmt170)
REVERT: B  198 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8378 (pp)
REVERT: B  217 MET cc_start: 0.8358 (ptt) cc_final: 0.8136 (ptt)
REVERT: G   42 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8008 (mm-30)
REVERT: G   58 GLU cc_start: 0.8573 (pm20) cc_final: 0.7967 (pm20)
REVERT: S    1 ASP cc_start: 0.7237 (t70) cc_final: 0.7016 (t70)
  outliers start: 22
  outliers final: 11
  residues processed: 126
  average time/residue: 1.6244
  time to fit residues: 214.9723
Evaluate side-chains
  126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ARG
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   52 GLN
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  347 ASN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    0.1980
   chunk 14 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
A 427 ASN
B 259 GLN
S  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.131384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.087651 restraints weight = 11330.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 2.53
r_work: 0.2795 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8997  Z= 0.164
  Angle     :  0.527   8.474  12190  Z= 0.277
  Chirality :  0.042   0.206   1390
  Planarity :  0.004   0.061   1537
  Dihedral  :  4.080  20.441   1218
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.55 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.20 (0.26), residues: 1114
  helix:  1.40 (0.29), residues: 377
  sheet:  0.30 (0.31), residues: 281
  loop : -1.03 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.010   0.001   PHE S 110 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.006   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8463 (mt) cc_final: 0.7963 (tp)
REVERT: A   98 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6658 (tt)
REVERT: A  155 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7030 (mp)
REVERT: A  365 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7872 (ptm160)
REVERT: A  442 PHE cc_start: 0.7515 (t80) cc_final: 0.7257 (t80)
REVERT: C  313 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7669 (pmm-80)
REVERT: B   19 ARG cc_start: 0.8323 (tmm160) cc_final: 0.8119 (tmm160)
REVERT: B   23 LYS cc_start: 0.8389 (tttp) cc_final: 0.7935 (tppt)
REVERT: B  198 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8358 (pp)
REVERT: B  217 MET cc_start: 0.8321 (ptt) cc_final: 0.8117 (ptt)
REVERT: G   42 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8010 (mm-30)
REVERT: G   58 GLU cc_start: 0.8569 (pm20) cc_final: 0.7982 (pm20)
  outliers start: 30
  outliers final: 13
  residues processed: 133
  average time/residue: 1.7404
  time to fit residues: 242.5745
Evaluate side-chains
  130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ARG
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  313 ARG
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 56 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0370
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.131707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.087966 restraints weight = 11394.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.55
r_work: 0.2813 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8997  Z= 0.152
  Angle     :  0.511   8.532  12190  Z= 0.267
  Chirality :  0.041   0.140   1390
  Planarity :  0.003   0.038   1537
  Dihedral  :  3.945  19.279   1218
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.60 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.36 (0.26), residues: 1114
  helix:  1.53 (0.28), residues: 381
  sheet:  0.35 (0.31), residues: 286
  loop : -0.94 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.009   0.001   PHE S 110 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.006   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8491 (mt) cc_final: 0.7992 (tp)
REVERT: A   98 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6663 (tt)
REVERT: A  155 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7090 (mp)
REVERT: C  242 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7802 (ttm-80)
REVERT: C  245 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7950 (mp0)
REVERT: C  313 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7710 (pmm-80)
REVERT: B   23 LYS cc_start: 0.8341 (tttp) cc_final: 0.7923 (tppt)
REVERT: B  198 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (pp)
REVERT: B  215 GLU cc_start: 0.8529 (mp0) cc_final: 0.7695 (mp0)
REVERT: B  217 MET cc_start: 0.8281 (ptt) cc_final: 0.8076 (ptt)
REVERT: B  254 ASP cc_start: 0.8061 (t70) cc_final: 0.7814 (t70)
REVERT: G   42 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7997 (mm-30)
REVERT: G   58 GLU cc_start: 0.8569 (pm20) cc_final: 0.7968 (pm20)
REVERT: S   39 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8375 (tt0)
  outliers start: 22
  outliers final: 12
  residues processed: 132
  average time/residue: 1.6262
  time to fit residues: 225.4844
Evaluate side-chains
  126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ARG
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  313 ARG
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.129937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.085964 restraints weight = 11473.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.56
r_work: 0.2784 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2650 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8997  Z= 0.205
  Angle     :  0.539   8.772  12190  Z= 0.283
  Chirality :  0.043   0.161   1390
  Planarity :  0.004   0.038   1537
  Dihedral  :  4.027  20.688   1218
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.85 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: 1114
  helix:  1.52 (0.28), residues: 381
  sheet:  0.39 (0.31), residues: 283
  loop : -0.98 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.009   0.001   PHE C 189 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.007   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8548 (mt) cc_final: 0.8032 (tp)
REVERT: A   98 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6632 (tt)
REVERT: A  155 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7153 (mp)
REVERT: C   24 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6632 (mtt90)
REVERT: C  242 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7889 (ttm-80)
REVERT: C  245 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7955 (mp0)
REVERT: C  313 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7736 (pmm-80)
REVERT: B   23 LYS cc_start: 0.8337 (tttp) cc_final: 0.7931 (tppt)
REVERT: B  198 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8377 (pp)
REVERT: B  215 GLU cc_start: 0.8541 (mp0) cc_final: 0.7707 (mp0)
REVERT: B  217 MET cc_start: 0.8330 (ptt) cc_final: 0.8093 (ptt)
REVERT: B  254 ASP cc_start: 0.8203 (t70) cc_final: 0.7905 (t70)
REVERT: G   42 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7991 (mm-30)
REVERT: G   58 GLU cc_start: 0.8551 (pm20) cc_final: 0.7948 (pm20)
REVERT: S   39 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8484 (tt0)
  outliers start: 26
  outliers final: 14
  residues processed: 125
  average time/residue: 1.6742
  time to fit residues: 219.4114
Evaluate side-chains
  128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  313 ARG
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0470
   chunk 73 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.087492 restraints weight = 11505.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.56
r_work: 0.2804 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8997  Z= 0.155
  Angle     :  0.517   8.979  12190  Z= 0.269
  Chirality :  0.041   0.137   1390
  Planarity :  0.004   0.038   1537
  Dihedral  :  3.922  19.184   1218
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.00 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.45 (0.26), residues: 1114
  helix:  1.64 (0.28), residues: 381
  sheet:  0.44 (0.32), residues: 271
  loop : -0.92 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.000   HIS S  35 
 PHE   0.009   0.001   PHE S 110 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.008   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.894 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8546 (mt) cc_final: 0.8029 (tp)
REVERT: A   98 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6598 (tt)
REVERT: A  155 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7183 (mp)
REVERT: A  365 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7771 (ptp-110)
REVERT: C   24 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6525 (mtt90)
REVERT: C  242 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7931 (ttm-80)
REVERT: C  245 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7923 (mp0)
REVERT: C  313 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7764 (pmm-80)
REVERT: B   23 LYS cc_start: 0.8330 (tttp) cc_final: 0.7916 (tppt)
REVERT: B  198 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8381 (pp)
REVERT: B  215 GLU cc_start: 0.8519 (mp0) cc_final: 0.7707 (mp0)
REVERT: B  217 MET cc_start: 0.8267 (ptt) cc_final: 0.8054 (ptt)
REVERT: B  234 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8610 (m-80)
REVERT: B  254 ASP cc_start: 0.8192 (t70) cc_final: 0.7895 (t70)
REVERT: G   42 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7999 (mm-30)
REVERT: G   58 GLU cc_start: 0.8539 (pm20) cc_final: 0.7903 (pm20)
REVERT: S    7 SER cc_start: 0.8905 (t) cc_final: 0.8437 (p)
REVERT: S   39 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8495 (tt0)
REVERT: S   76 LYS cc_start: 0.7924 (mtmm) cc_final: 0.7667 (pmtt)
  outliers start: 20
  outliers final: 10
  residues processed: 130
  average time/residue: 1.6106
  time to fit residues: 219.9565
Evaluate side-chains
  128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  313 ARG
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0070
   chunk 87 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 101 optimal weight:    0.3980
   chunk 80 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.0400

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  13 GLN
S  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.129081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.084864 restraints weight = 11547.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 2.56
r_work: 0.2747 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8997  Z= 0.240
  Angle     :  0.560   9.256  12190  Z= 0.293
  Chirality :  0.043   0.137   1390
  Planarity :  0.004   0.049   1537
  Dihedral  :  4.111  21.944   1218
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.00 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.39 (0.25), residues: 1114
  helix:  1.59 (0.28), residues: 380
  sheet:  0.44 (0.31), residues: 273
  loop : -0.98 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE A 164 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.014   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8548 (mt) cc_final: 0.8026 (tp)
REVERT: A   98 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6600 (tt)
REVERT: A  155 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7213 (mp)
REVERT: A  162 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5644 (pp20)
REVERT: C   24 ARG cc_start: 0.7064 (mtp180) cc_final: 0.6618 (mtt90)
REVERT: C  242 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7959 (ttm-80)
REVERT: C  245 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7920 (mp0)
REVERT: C  313 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7786 (pmm-80)
REVERT: B   23 LYS cc_start: 0.8340 (tttp) cc_final: 0.7921 (tppt)
REVERT: B  198 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8363 (pp)
REVERT: B  215 GLU cc_start: 0.8517 (mp0) cc_final: 0.7713 (mp0)
REVERT: B  217 MET cc_start: 0.8326 (ptt) cc_final: 0.8060 (ptt)
REVERT: B  234 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8687 (m-80)
REVERT: B  254 ASP cc_start: 0.8230 (t70) cc_final: 0.7873 (t70)
REVERT: G   42 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: G   58 GLU cc_start: 0.8552 (pm20) cc_final: 0.7941 (pm20)
REVERT: S    7 SER cc_start: 0.8909 (t) cc_final: 0.8486 (p)
REVERT: S   39 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8541 (tt0)
REVERT: S  116 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8505 (t)
  outliers start: 24
  outliers final: 12
  residues processed: 129
  average time/residue: 1.5785
  time to fit residues: 214.1072
Evaluate side-chains
  134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  313 ARG
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    0.0970
   chunk 109 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 95 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.087087 restraints weight = 11472.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 2.56
r_work: 0.2796 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8997  Z= 0.167
  Angle     :  0.527   9.146  12190  Z= 0.274
  Chirality :  0.042   0.136   1390
  Planarity :  0.004   0.056   1537
  Dihedral  :  3.970  20.083   1218
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.42 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.50 (0.25), residues: 1114
  helix:  1.70 (0.28), residues: 382
  sheet:  0.47 (0.31), residues: 273
  loop : -0.93 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.011   0.001   PHE A 164 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.014   0.000   ARG B 134 

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A   84 LEU cc_start: 0.8535 (mt) cc_final: 0.8003 (tp)
REVERT: A   98 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6591 (tt)
REVERT: A  155 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7217 (mp)
REVERT: A  365 ARG cc_start: 0.7924 (ptp-110) cc_final: 0.7723 (ptp-110)
REVERT: C  245 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7908 (mp0)
REVERT: C  313 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7795 (pmm-80)
REVERT: B   23 LYS cc_start: 0.8346 (tttp) cc_final: 0.7933 (tppt)
REVERT: B  198 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8391 (pp)
REVERT: B  215 GLU cc_start: 0.8501 (mp0) cc_final: 0.7704 (mp0)
REVERT: B  217 MET cc_start: 0.8259 (ptt) cc_final: 0.8051 (ptt)
REVERT: B  234 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8603 (m-80)
REVERT: B  254 ASP cc_start: 0.8224 (t70) cc_final: 0.7879 (t70)
REVERT: G   42 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8030 (mm-30)
REVERT: G   58 GLU cc_start: 0.8557 (pm20) cc_final: 0.7920 (pm20)
REVERT: S    7 SER cc_start: 0.8873 (t) cc_final: 0.8406 (p)
REVERT: S   39 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8496 (tt0)
  outliers start: 21
  outliers final: 13
  residues processed: 127
  average time/residue: 1.8659
  time to fit residues: 248.4612
Evaluate side-chains
  132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  305 CYS
Chi-restraints excluded: chain C residue  313 ARG
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  216 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.130674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.086583 restraints weight = 11366.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 2.53
r_work: 0.2775 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8997  Z= 0.209
  Angle     :  0.550   9.204  12190  Z= 0.286
  Chirality :  0.042   0.136   1390
  Planarity :  0.004   0.054   1537
  Dihedral  :  4.040  21.175   1218
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.32 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.25), residues: 1114
  helix:  1.66 (0.28), residues: 382
  sheet:  0.47 (0.31), residues: 273
  loop : -0.95 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE A 164 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.015   0.000   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7598.07 seconds
wall clock time: 130 minutes 59.75 seconds (7859.75 seconds total)