Starting phenix.real_space_refine
on Sun May 18 04:18:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sp3_40673/05_2025/8sp3_40673_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sp3_40673/05_2025/8sp3_40673.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sp3_40673/05_2025/8sp3_40673.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sp3_40673/05_2025/8sp3_40673.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sp3_40673/05_2025/8sp3_40673_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sp3_40673/05_2025/8sp3_40673_neut.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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: 6
    Type Number    sf(0)   Gaussians
     P      82      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C   10228      2.51       5
     N    2708      2.21       5
     O    3206      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16270
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 3494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3494
          Classifications: {'peptide': 419}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406}
    Chain: "B"
      Number of atoms: 3787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3787
          Classifications: {'peptide': 469}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 444}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 442
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 18}
    Chain: "D"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 411
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "E"
      Number of atoms: 3494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3494
          Classifications: {'peptide': 419}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406}
    Chain: "F"
      Number of atoms: 3787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3787
          Classifications: {'peptide': 469}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 444}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 442
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 18}
    Chain: "H"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 411
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 10.13, per 1000 atoms: 0.62
  Number of scatterers: 16270
  At special positions: 0
  Unit cell: (106.4, 171, 131.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P      82     15.00
     Mg      2     11.99
     O    3206      8.00
     N    2708      7.00
     C   10228      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.89
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3384

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 21 sheets defined
      35.5% alpha, 21.9% beta
      18 base pairs and 48 stacking pairs defined.
    Time for finding SS restraints: 5.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 29
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 3.559A  pdb=" N   ASP A  56 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 89
    Processing helix  chain 'A' and resid 123 through 139
    Processing helix  chain 'A' and resid 149 through 157
      removed outlier: 3.804A  pdb=" N   ILE A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 203
      removed outlier: 3.564A  pdb=" N   LEU A 203 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 247
    Processing helix  chain 'A' and resid 257 through 280
      removed outlier: 3.982A  pdb=" N   VAL A 266 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 353 through 365
    Processing helix  chain 'A' and resid 369 through 384
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 31
    Processing helix  chain 'B' and resid 46 through 60
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 97 through 105
    Processing helix  chain 'B' and resid 109 through 131
      removed outlier: 3.930A  pdb=" N   LYS B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ILE B 125 " --> pdb=" O   PHE B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 149
      removed outlier: 3.584A  pdb=" N   TYR B 148 " --> pdb=" O   PRO B 144 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS B 149 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 144 through 149'
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.686A  pdb=" N   LEU B 214 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 331 through 351
      removed outlier: 3.663A  pdb=" N   GLN B 349 " --> pdb=" O   SER B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 373
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 478 through 491
      removed outlier: 3.731A  pdb=" N   ALA B 483 " --> pdb=" O   THR B 479 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ASP B 484 " --> pdb=" O   LEU B 480 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE B 489 " --> pdb=" O   LYS B 485 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 14 through 28
    Processing helix  chain 'E' and resid 46 through 56
    Processing helix  chain 'E' and resid 71 through 89
    Processing helix  chain 'E' and resid 104 through 108
      removed outlier: 4.044A  pdb=" N   ILE E 108 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 113
      removed outlier: 3.660A  pdb=" N   VAL E 113 " --> pdb=" O   ILE E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 138
    Processing helix  chain 'E' and resid 146 through 158
      removed outlier: 4.419A  pdb=" N   SER E 150 " --> pdb=" O   ASP E 146 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
    Processing helix  chain 'E' and resid 234 through 236
      No H-bonds generated for 'chain 'E' and resid 234 through 236'
    Processing helix  chain 'E' and resid 243 through 249
    Processing helix  chain 'E' and resid 257 through 280
    Processing helix  chain 'E' and resid 300 through 302
      No H-bonds generated for 'chain 'E' and resid 300 through 302'
    Processing helix  chain 'E' and resid 353 through 365
    Processing helix  chain 'E' and resid 369 through 385
      removed outlier: 3.599A  pdb=" N   LEU E 384 " --> pdb=" O   PHE E 380 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER E 385 " --> pdb=" O   ILE E 381 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 15 through 17
      No H-bonds generated for 'chain 'F' and resid 15 through 17'
    Processing helix  chain 'F' and resid 22 through 30
    Processing helix  chain 'F' and resid 46 through 60
    Processing helix  chain 'F' and resid 77 through 83
    Processing helix  chain 'F' and resid 97 through 105
      removed outlier: 3.555A  pdb=" N   ILE F 101 " --> pdb=" O   THR F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 131
      removed outlier: 4.272A  pdb=" N   LYS F 124 " --> pdb=" O   LEU F 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 144 through 151
      removed outlier: 4.055A  pdb=" N   TYR F 150 " --> pdb=" O   GLU F 146 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   CYS F 151 " --> pdb=" O   ILE F 147 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 213
    Processing helix  chain 'F' and resid 214 through 218
      removed outlier: 3.526A  pdb=" N   HIS F 217 " --> pdb=" O   LEU F 214 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR F 218 " --> pdb=" O   LEU F 215 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 214 through 218'
    Processing helix  chain 'F' and resid 226 through 230
    Processing helix  chain 'F' and resid 248 through 264
    Processing helix  chain 'F' and resid 331 through 350
    Processing helix  chain 'F' and resid 366 through 376
      removed outlier: 3.625A  pdb=" N   VAL F 376 " --> pdb=" O   ALA F 372 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 451 through 462
    Processing helix  chain 'F' and resid 463 through 465
      No H-bonds generated for 'chain 'F' and resid 463 through 465'
    Processing helix  chain 'F' and resid 478 through 488
      removed outlier: 3.855A  pdb=" N   ALA F 483 " --> pdb=" O   THR F 479 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP F 484 " --> pdb=" O   LEU F 480 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 502 through 506
      removed outlier: 3.608A  pdb=" N   TYR F 505 " --> pdb=" O   ALA F 502 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33
      removed outlier: 5.901A  pdb=" N   ILE A   5 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LYS A   4 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   LEU A  61 " --> pdb=" O   LYS A   4 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   PHE A   6 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   VAL A  63 " --> pdb=" O   PHE A   6 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   SER A   8 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   PHE A  60 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   LEU A  97 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LEU A  62 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
      removed outlier: 8.696A  pdb=" N   ILE A 118 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 310 through 316
      removed outlier: 3.671A  pdb=" N   GLY B 310 " --> pdb=" O   ASP B 306 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ARG B 295 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   LEU B 305 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL B 278 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   GLY B 385 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   SER B 417 " --> pdb=" O   VAL B 413 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL B 413 " --> pdb=" O   SER B 417 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   VAL B 412 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   GLU B   3 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ASN A 413 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   TYR B   6 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
      removed outlier: 10.519A  pdb=" N   SER A 415 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A 414 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   LYS A 167 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177
      removed outlier: 4.785A  pdb=" N   GLY A 325 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   THR A 291 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.593A  pdb=" N   ARG A 186 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 241 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 394
    Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13
      removed outlier: 3.760A  pdb=" N   CYS B  20 " --> pdb=" O   ILE B  12 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 95
      removed outlier: 6.755A  pdb=" N   GLY B  42 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   ILE B 142 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE B  44 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   TRP B 139 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   PHE B 224 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   VAL B 141 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 425 through 426
    Processing sheet with id=AB1, first strand: chain 'E' and resid 32 through 33
      removed outlier: 6.070A  pdb=" N   ILE E   5 " --> pdb=" O   TRP E  33 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   PHE E   6 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL E  63 " --> pdb=" O   PHE E   6 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   SER E   8 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   ILE E 118 " --> pdb=" O   ILE E  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 3
      removed outlier: 3.993A  pdb=" N   GLY E 412 " --> pdb=" O   GLU E 169 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 175 through 177
      removed outlier: 4.054A  pdb=" N   LEU E 176 " --> pdb=" O   LEU E 335 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE E 323 " --> pdb=" O   TYR E 293 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TYR E 293 " --> pdb=" O   ILE E 323 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   GLY E 325 " --> pdb=" O   THR E 291 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   THR E 291 " --> pdb=" O   GLY E 325 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 175 through 177
      removed outlier: 4.054A  pdb=" N   LEU E 176 " --> pdb=" O   LEU E 335 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 208 through 210
      removed outlier: 4.174A  pdb=" N   ILE E 239 " --> pdb=" O   PHE E 187 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 304 through 305
    Processing sheet with id=AB7, first strand: chain 'E' and resid 390 through 394
    Processing sheet with id=AB8, first strand: chain 'F' and resid 5 through 6
      removed outlier: 5.617A  pdb=" N   ILE F 443 " --> pdb=" O   SER F 389 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   SER F 389 " --> pdb=" O   ILE F 443 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ILE F 445 " --> pdb=" O   THR F 387 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   THR F 387 " --> pdb=" O   ILE F 445 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 5 through 6
      removed outlier: 5.617A  pdb=" N   ILE F 443 " --> pdb=" O   SER F 389 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   SER F 389 " --> pdb=" O   ILE F 443 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   ILE F 445 " --> pdb=" O   THR F 387 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   THR F 387 " --> pdb=" O   ILE F 445 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 20
      removed outlier: 3.739A  pdb=" N   CYS F  20 " --> pdb=" O   ILE F  12 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 94
      removed outlier: 6.755A  pdb=" N   SER F  41 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   LYS F  94 " --> pdb=" O   SER F  41 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL F  43 " --> pdb=" O   LYS F  94 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   GLY F  42 " --> pdb=" O   PHE F 140 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ILE F 142 " --> pdb=" O   GLY F  42 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ILE F  44 " --> pdb=" O   ILE F 142 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   TRP F 139 " --> pdb=" O   GLN F 222 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   PHE F 224 " --> pdb=" O   TRP F 139 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   VAL F 141 " --> pdb=" O   PHE F 224 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'F' and resid 425 through 426
      removed outlier: 3.849A  pdb=" N   THR F 431 " --> pdb=" O   VAL F 426 " (cutoff:3.500A)

    626 hydrogen bonds defined for protein.
    1770 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      48 stacking parallelities
  Total time for adding SS restraints: 5.42

  Time building geometry restraints manager: 4.54 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3862
        1.33 -     1.45: 3970
        1.45 -     1.57: 8780
        1.57 -     1.70: 160
        1.70 -     1.82: 66
  Bond restraints: 16838
  Sorted by residual:
  bond pdb=" N   ASN F 293 "
       pdb=" CA  ASN F 293 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 8.30e-03 1.45e+04 1.59e+01
  bond pdb=" N   PRO F  10 "
       pdb=" CA  PRO F  10 "
    ideal  model  delta    sigma   weight residual
    1.466  1.419  0.047 1.19e-02 7.06e+03 1.53e+01
  bond pdb=" N   ARG A 186 "
       pdb=" CA  ARG A 186 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.26e-02 6.30e+03 1.01e+01
  bond pdb=" N   ARG A 257 "
       pdb=" CA  ARG A 257 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.17e-02 7.31e+03 8.48e+00
  bond pdb=" N   LYS B  11 "
       pdb=" CA  LYS B  11 "
    ideal  model  delta    sigma   weight residual
    1.453  1.493 -0.040 1.37e-02 5.33e+03 8.33e+00
  ... (remaining 16833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 22494
        1.67 -     3.34: 550
        3.34 -     5.00: 60
        5.00 -     6.67: 19
        6.67 -     8.34: 5
  Bond angle restraints: 23128
  Sorted by residual:
  angle pdb=" N   THR F 491 "
        pdb=" CA  THR F 491 "
        pdb=" C   THR F 491 "
      ideal   model   delta    sigma   weight residual
     114.56  107.31    7.25 1.27e+00 6.20e-01 3.26e+01
  angle pdb=" C   PRO F  10 "
        pdb=" CA  PRO F  10 "
        pdb=" CB  PRO F  10 "
      ideal   model   delta    sigma   weight residual
     110.98  103.64    7.34 1.31e+00 5.83e-01 3.14e+01
  angle pdb=" N   LEU A 185 "
        pdb=" CA  LEU A 185 "
        pdb=" C   LEU A 185 "
      ideal   model   delta    sigma   weight residual
     109.72  101.38    8.34 1.60e+00 3.91e-01 2.72e+01
  angle pdb=" N   GLU A 260 "
        pdb=" CA  GLU A 260 "
        pdb=" C   GLU A 260 "
      ideal   model   delta    sigma   weight residual
     112.38  106.80    5.58 1.22e+00 6.72e-01 2.09e+01
  angle pdb=" CA  LEU A 185 "
        pdb=" C   LEU A 185 "
        pdb=" O   LEU A 185 "
      ideal   model   delta    sigma   weight residual
     121.11  116.26    4.85 1.13e+00 7.83e-01 1.84e+01
  ... (remaining 23123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 9706
       35.61 -    71.22: 286
       71.22 -   106.83: 20
      106.83 -   142.44: 1
      142.44 -   178.05: 11
  Dihedral angle restraints: 10024
    sinusoidal: 4786
      harmonic: 5238
  Sorted by residual:
  dihedral pdb=" O4'   U C  17 "
           pdb=" C1'   U C  17 "
           pdb=" N1    U C  17 "
           pdb=" C2    U C  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   18.05 -178.05     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U G  17 "
           pdb=" C1'   U G  17 "
           pdb=" N1    U G  17 "
           pdb=" C2    U G  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.42 -176.42     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U G  13 "
           pdb=" C1'   U G  13 "
           pdb=" N1    U G  13 "
           pdb=" C2    U G  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   14.27 -174.27     1      1.50e+01 4.44e-03 8.51e+01
  ... (remaining 10021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 2207
       0.061 -    0.121: 302
       0.121 -    0.182: 23
       0.182 -    0.243: 4
       0.243 -    0.303: 2
  Chirality restraints: 2538
  Sorted by residual:
  chirality pdb=" CA  LEU A 185 "
            pdb=" N   LEU A 185 "
            pdb=" C   LEU A 185 "
            pdb=" CB  LEU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  PRO F  10 "
            pdb=" N   PRO F  10 "
            pdb=" C   PRO F  10 "
            pdb=" CB  PRO F  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    3.01   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  LEU E 185 "
            pdb=" N   LEU E 185 "
            pdb=" C   LEU E 185 "
            pdb=" CB  LEU E 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 2535 not shown)

  Planarity restraints: 2632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 186 "    0.479 9.50e-02 1.11e+02   2.15e-01 2.82e+01
        pdb=" NE  ARG E 186 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 186 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 186 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 186 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  11 "    0.027 2.00e-02 2.50e+03   1.34e-02 4.93e+00
        pdb=" N9    A C  11 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8    A C  11 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A C  11 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    A C  11 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A C  11 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A C  11 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A C  11 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A C  11 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    A C  11 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A C  11 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A G  11 "   -0.027 2.00e-02 2.50e+03   1.34e-02 4.93e+00
        pdb=" N9    A G  11 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    A G  11 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A G  11 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A G  11 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A G  11 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A G  11 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A G  11 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A G  11 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A G  11 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A G  11 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2629 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 15
        2.29 -     2.94: 6763
        2.94 -     3.59: 22375
        3.59 -     4.25: 36407
        4.25 -     4.90: 60991
  Nonbonded interactions: 126551
  Sorted by model distance:
  nonbonded pdb=" CE  LYS B  11 "
            pdb=" CG2 THR B  21 "
     model   vdw
     1.632 3.860
  nonbonded pdb=" CD2 LEU A 185 "
            pdb=" CE1 PHE A 217 "
     model   vdw
     1.829 3.760
  nonbonded pdb=" CG2 ILE B  12 "
            pdb=" O   LYS B 270 "
     model   vdw
     1.914 3.460
  nonbonded pdb=" CD2 LEU A 185 "
            pdb=" CZ  PHE A 217 "
     model   vdw
     1.944 3.760
  nonbonded pdb=" OP2   U G   1 "
            pdb="MG    MG F 601 "
     model   vdw
     1.950 2.170
  ... (remaining 126546 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.840
  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:          0.660
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     40.100
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.070
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16838  Z= 0.189
  Angle     :  0.616   8.341  23128  Z= 0.368
  Chirality :  0.043   0.303   2538
  Planarity :  0.006   0.215   2632
  Dihedral  : 17.323 178.055   6640
  Min Nonbonded Distance : 1.632

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.38 (0.20), residues: 1764
  helix:  1.54 (0.23), residues: 553
  sheet:  0.03 (0.29), residues: 355
  loop : -1.65 (0.20), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 319 
 HIS   0.007   0.001   HIS F 207 
 PHE   0.015   0.001   PHE B 313 
 TYR   0.014   0.001   TYR B 397 
 ARG   0.004   0.000   ARG E 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16216 (  614)
  hydrogen bonds       : angle       6.38401 ( 1858)
  covalent geometry    : bond        0.00328 (16838)
  covalent geometry    : angle       0.61562 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 373
  time to evaluate  : 1.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6623 (mp) cc_final: 0.6341 (mp)
REVERT: A   35 ASP cc_start: 0.6205 (t70) cc_final: 0.5984 (t70)
REVERT: A  209 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6741 (mtp85)
REVERT: A  210 TYR cc_start: 0.7093 (t80) cc_final: 0.6824 (t80)
REVERT: A  213 TYR cc_start: 0.6375 (m-80) cc_final: 0.6067 (m-80)
REVERT: A  255 PHE cc_start: 0.8377 (t80) cc_final: 0.8163 (t80)
REVERT: A  263 ARG cc_start: 0.7372 (ttp80) cc_final: 0.6908 (ttp80)
REVERT: A  267 GLN cc_start: 0.8156 (tt0) cc_final: 0.7802 (tt0)
REVERT: A  349 LYS cc_start: 0.7219 (ttpp) cc_final: 0.6822 (ttpp)
REVERT: A  399 GLU cc_start: 0.7572 (mp0) cc_final: 0.7254 (mp0)
REVERT: B  115 TYR cc_start: 0.7436 (t80) cc_final: 0.7102 (t80)
REVERT: B  132 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7529 (mt-10)
REVERT: B  138 VAL cc_start: 0.8560 (t) cc_final: 0.8273 (m)
REVERT: B  254 TRP cc_start: 0.7502 (m100) cc_final: 0.7126 (m100)
REVERT: B  309 ASP cc_start: 0.4368 (m-30) cc_final: 0.3691 (m-30)
REVERT: B  321 TYR cc_start: 0.7834 (m-80) cc_final: 0.7325 (m-10)
REVERT: B  417 SER cc_start: 0.8107 (t) cc_final: 0.7668 (m)
REVERT: E    4 LYS cc_start: 0.6764 (mttm) cc_final: 0.6443 (mtpp)
REVERT: E   15 ASN cc_start: 0.5140 (m-40) cc_final: 0.4615 (m-40)
REVERT: E   59 LYS cc_start: 0.7732 (tppt) cc_final: 0.7413 (tppt)
REVERT: E   93 PHE cc_start: 0.6583 (t80) cc_final: 0.6217 (t80)
REVERT: E  208 VAL cc_start: 0.7249 (t) cc_final: 0.6976 (t)
REVERT: E  286 GLU cc_start: 0.5179 (tp30) cc_final: 0.4930 (tp30)
REVERT: E  360 SER cc_start: 0.7501 (m) cc_final: 0.7201 (p)
REVERT: F   16 HIS cc_start: 0.6018 (m-70) cc_final: 0.5724 (m-70)
REVERT: F   37 TYR cc_start: 0.7710 (m-80) cc_final: 0.7382 (m-80)
REVERT: F   56 TYR cc_start: 0.5739 (t80) cc_final: 0.5281 (t80)
REVERT: F   91 ILE cc_start: 0.8396 (mt) cc_final: 0.8168 (tt)
REVERT: F   94 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7083 (mmtm)
REVERT: F  115 TYR cc_start: 0.7589 (t80) cc_final: 0.7384 (t80)
REVERT: F  142 ILE cc_start: 0.7393 (mm) cc_final: 0.7036 (mt)
REVERT: F  272 SER cc_start: 0.7836 (t) cc_final: 0.7634 (p)
REVERT: F  285 TYR cc_start: 0.7145 (m-80) cc_final: 0.6890 (m-80)
REVERT: F  287 LYS cc_start: 0.7309 (mttm) cc_final: 0.7014 (mtmt)
REVERT: F  336 LYS cc_start: 0.7855 (mttp) cc_final: 0.7533 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 373
  average time/residue: 0.2972
  time to fit residues: 160.3066
Evaluate side-chains
  295 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 153 optimal weight:    0.9990
   chunk 137 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0070
   chunk 93 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0870
   chunk 142 optimal weight:    0.0570
   chunk 55 optimal weight:    0.1980
   chunk 86 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 165 optimal weight:    0.7980
   overall best weight:    0.2294

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
F 468 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.194181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.160444 restraints weight = 24294.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.164732 restraints weight = 13865.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.167466 restraints weight = 9692.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16838  Z= 0.120
  Angle     :  0.560  12.379  23128  Z= 0.294
  Chirality :  0.041   0.171   2538
  Planarity :  0.004   0.046   2632
  Dihedral  : 18.047 177.329   3014
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.48 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.13 (0.21), residues: 1764
  helix:  1.77 (0.23), residues: 559
  sheet:  0.06 (0.28), residues: 374
  loop : -1.52 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  86 
 HIS   0.004   0.001   HIS E 340 
 PHE   0.023   0.001   PHE B  30 
 TYR   0.016   0.001   TYR B   6 
 ARG   0.006   0.000   ARG B 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04099 (  614)
  hydrogen bonds       : angle       4.67832 ( 1858)
  covalent geometry    : bond        0.00262 (16838)
  covalent geometry    : angle       0.55970 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 306
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6545 (mp) cc_final: 0.6242 (mp)
REVERT: A    8 SER cc_start: 0.8105 (t) cc_final: 0.7674 (p)
REVERT: A  209 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6703 (mtp85)
REVERT: A  210 TYR cc_start: 0.7156 (t80) cc_final: 0.6796 (t80)
REVERT: A  213 TYR cc_start: 0.6491 (m-80) cc_final: 0.6065 (m-80)
REVERT: A  246 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8202 (tp)
REVERT: A  255 PHE cc_start: 0.8431 (t80) cc_final: 0.8148 (t80)
REVERT: A  263 ARG cc_start: 0.7378 (ttp80) cc_final: 0.6984 (ttp80)
REVERT: A  279 ASP cc_start: 0.7904 (t70) cc_final: 0.7659 (t0)
REVERT: A  399 GLU cc_start: 0.7608 (mp0) cc_final: 0.7257 (mp0)
REVERT: B  115 TYR cc_start: 0.7431 (t80) cc_final: 0.7012 (t80)
REVERT: B  132 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7554 (mt-10)
REVERT: B  254 TRP cc_start: 0.7504 (m100) cc_final: 0.7068 (m100)
REVERT: B  321 TYR cc_start: 0.7813 (m-80) cc_final: 0.7314 (m-80)
REVERT: B  417 SER cc_start: 0.8114 (t) cc_final: 0.7725 (m)
REVERT: E    4 LYS cc_start: 0.6829 (mttm) cc_final: 0.6550 (mtpp)
REVERT: E   15 ASN cc_start: 0.5305 (m-40) cc_final: 0.4746 (m-40)
REVERT: E   59 LYS cc_start: 0.7742 (tppt) cc_final: 0.7407 (tppt)
REVERT: E   93 PHE cc_start: 0.6567 (t80) cc_final: 0.6231 (t80)
REVERT: E  128 LEU cc_start: 0.7206 (tp) cc_final: 0.6992 (tp)
REVERT: E  286 GLU cc_start: 0.5170 (tp30) cc_final: 0.4949 (tp30)
REVERT: E  290 LYS cc_start: 0.8186 (pttt) cc_final: 0.7809 (ptpp)
REVERT: E  364 GLN cc_start: 0.6476 (tt0) cc_final: 0.6156 (tm-30)
REVERT: F    5 ILE cc_start: 0.7924 (pt) cc_final: 0.7690 (pt)
REVERT: F   16 HIS cc_start: 0.6045 (m-70) cc_final: 0.5790 (m-70)
REVERT: F   19 LYS cc_start: 0.7776 (mttp) cc_final: 0.7560 (mttt)
REVERT: F   37 TYR cc_start: 0.7685 (m-80) cc_final: 0.7432 (m-80)
REVERT: F   56 TYR cc_start: 0.5642 (t80) cc_final: 0.5153 (t80)
REVERT: F  115 TYR cc_start: 0.7693 (t80) cc_final: 0.7358 (t80)
REVERT: F  142 ILE cc_start: 0.7375 (mm) cc_final: 0.6895 (mt)
REVERT: F  247 LYS cc_start: 0.7191 (mtpt) cc_final: 0.6931 (mtpp)
REVERT: F  278 VAL cc_start: 0.8472 (t) cc_final: 0.8225 (p)
REVERT: F  287 LYS cc_start: 0.7263 (mttm) cc_final: 0.6751 (mtmm)
REVERT: F  311 THR cc_start: 0.8101 (t) cc_final: 0.7716 (p)
REVERT: F  316 GLU cc_start: 0.6763 (tp30) cc_final: 0.6365 (tp30)
REVERT: F  336 LYS cc_start: 0.8030 (mttp) cc_final: 0.7716 (mtmm)
REVERT: F  342 SER cc_start: 0.8348 (m) cc_final: 0.8113 (t)
  outliers start: 20
  outliers final: 10
  residues processed: 311
  average time/residue: 0.3095
  time to fit residues: 139.2377
Evaluate side-chains
  308 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 297
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  391 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 161 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 142 optimal weight:    7.9990
   chunk 139 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9980
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
E 188 HIS
F 360 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.188399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.155029 restraints weight = 24243.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.158983 restraints weight = 14175.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.161597 restraints weight = 10132.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  16838  Z= 0.222
  Angle     :  0.636   7.116  23128  Z= 0.338
  Chirality :  0.044   0.172   2538
  Planarity :  0.004   0.052   2632
  Dihedral  : 18.285 179.085   3014
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 11.01 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.48 (0.20), residues: 1764
  helix:  1.31 (0.23), residues: 566
  sheet: -0.05 (0.28), residues: 383
  loop : -1.68 (0.20), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 269 
 HIS   0.008   0.001   HIS E 358 
 PHE   0.024   0.002   PHE B  93 
 TYR   0.026   0.002   TYR B 321 
 ARG   0.005   0.001   ARG B 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05351 (  614)
  hydrogen bonds       : angle       4.89389 ( 1858)
  covalent geometry    : bond        0.00497 (16838)
  covalent geometry    : angle       0.63586 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 309
  time to evaluate  : 1.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6711 (mp) cc_final: 0.6388 (mp)
REVERT: A  126 ARG cc_start: 0.6214 (tpm170) cc_final: 0.5917 (tpm170)
REVERT: A  209 ARG cc_start: 0.7055 (mtp85) cc_final: 0.6796 (mtp85)
REVERT: A  213 TYR cc_start: 0.6617 (m-80) cc_final: 0.6150 (m-80)
REVERT: A  222 ASP cc_start: 0.6124 (m-30) cc_final: 0.5890 (m-30)
REVERT: A  246 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8342 (tp)
REVERT: A  263 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7088 (ttp80)
REVERT: A  279 ASP cc_start: 0.8012 (t70) cc_final: 0.7719 (t0)
REVERT: A  399 GLU cc_start: 0.7717 (mp0) cc_final: 0.7294 (mp0)
REVERT: A  400 LYS cc_start: 0.7493 (mttt) cc_final: 0.7209 (mttp)
REVERT: B  226 GLU cc_start: 0.7599 (mp0) cc_final: 0.7265 (mp0)
REVERT: B  254 TRP cc_start: 0.7669 (m100) cc_final: 0.7386 (m100)
REVERT: B  270 LYS cc_start: 0.5959 (ttpt) cc_final: 0.5534 (tttm)
REVERT: B  321 TYR cc_start: 0.8017 (m-80) cc_final: 0.7729 (m-80)
REVERT: B  412 VAL cc_start: 0.8297 (t) cc_final: 0.8030 (p)
REVERT: B  417 SER cc_start: 0.8035 (t) cc_final: 0.7669 (m)
REVERT: E    4 LYS cc_start: 0.6852 (mttm) cc_final: 0.6526 (mtpp)
REVERT: E   15 ASN cc_start: 0.5457 (m-40) cc_final: 0.4876 (m-40)
REVERT: E   59 LYS cc_start: 0.7828 (tppt) cc_final: 0.7459 (tppt)
REVERT: E   93 PHE cc_start: 0.6630 (t80) cc_final: 0.6230 (t80)
REVERT: E  119 ASP cc_start: 0.7986 (t0) cc_final: 0.7640 (t70)
REVERT: E  128 LEU cc_start: 0.7135 (tp) cc_final: 0.6874 (tp)
REVERT: F   16 HIS cc_start: 0.6172 (m-70) cc_final: 0.5882 (m-70)
REVERT: F   54 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5916 (mpp80)
REVERT: F   74 MET cc_start: 0.3434 (ptm) cc_final: 0.3097 (ptm)
REVERT: F  115 TYR cc_start: 0.7966 (t80) cc_final: 0.7628 (t80)
REVERT: F  142 ILE cc_start: 0.7440 (mm) cc_final: 0.7085 (mm)
REVERT: F  247 LYS cc_start: 0.7326 (mtpt) cc_final: 0.7116 (mtpp)
REVERT: F  287 LYS cc_start: 0.7452 (mttm) cc_final: 0.6874 (mtmm)
REVERT: F  306 ASP cc_start: 0.6352 (p0) cc_final: 0.6102 (p0)
REVERT: F  311 THR cc_start: 0.8210 (t) cc_final: 0.7921 (p)
REVERT: F  316 GLU cc_start: 0.6873 (tp30) cc_final: 0.6574 (tp30)
REVERT: F  336 LYS cc_start: 0.8169 (mttp) cc_final: 0.7910 (mttp)
REVERT: F  342 SER cc_start: 0.8415 (m) cc_final: 0.8109 (t)
  outliers start: 40
  outliers final: 28
  residues processed: 320
  average time/residue: 0.2931
  time to fit residues: 136.6858
Evaluate side-chains
  321 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 291
  time to evaluate  : 1.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  122 MET
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  392 TYR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   54 ARG
Chi-restraints excluded: chain F residue   88 SER
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  368 GLN
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  459 ILE
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 86 optimal weight:    0.2980
   chunk 83 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 169 optimal weight:    0.0980
   chunk 179 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 146 optimal weight:    0.5980
   chunk 164 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
B  61 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.190204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.156388 restraints weight = 24307.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.160595 restraints weight = 13983.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.163299 restraints weight = 9825.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6481
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16838  Z= 0.152
  Angle     :  0.580   9.065  23128  Z= 0.306
  Chirality :  0.042   0.170   2538
  Planarity :  0.004   0.053   2632
  Dihedral  : 18.166 179.441   3014
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.77 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.38 (0.20), residues: 1764
  helix:  1.54 (0.23), residues: 559
  sheet: -0.04 (0.28), residues: 373
  loop : -1.67 (0.20), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 319 
 HIS   0.005   0.001   HIS F 207 
 PHE   0.027   0.002   PHE B  93 
 TYR   0.019   0.001   TYR A 251 
 ARG   0.006   0.000   ARG B 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04371 (  614)
  hydrogen bonds       : angle       4.62062 ( 1858)
  covalent geometry    : bond        0.00341 (16838)
  covalent geometry    : angle       0.57959 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 299
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6541 (mp) cc_final: 0.6206 (mp)
REVERT: A  126 ARG cc_start: 0.6228 (tpm170) cc_final: 0.5887 (tpm170)
REVERT: A  209 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6800 (mtp85)
REVERT: A  213 TYR cc_start: 0.6558 (m-80) cc_final: 0.6174 (m-80)
REVERT: A  246 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8362 (tp)
REVERT: A  263 ARG cc_start: 0.7480 (ttp80) cc_final: 0.6986 (ttp80)
REVERT: A  279 ASP cc_start: 0.8044 (t70) cc_final: 0.7758 (t0)
REVERT: A  366 LYS cc_start: 0.7951 (tttm) cc_final: 0.7498 (ttpt)
REVERT: A  399 GLU cc_start: 0.7696 (mp0) cc_final: 0.7259 (mp0)
REVERT: A  416 TYR cc_start: 0.6904 (p90) cc_final: 0.6649 (p90)
REVERT: B  270 LYS cc_start: 0.5944 (ttpt) cc_final: 0.5501 (tttm)
REVERT: B  417 SER cc_start: 0.8055 (t) cc_final: 0.7679 (m)
REVERT: E    4 LYS cc_start: 0.6890 (mttm) cc_final: 0.6544 (mtpp)
REVERT: E   15 ASN cc_start: 0.5415 (m-40) cc_final: 0.4857 (m-40)
REVERT: E   59 LYS cc_start: 0.7872 (tppt) cc_final: 0.7495 (tppt)
REVERT: E   93 PHE cc_start: 0.6612 (t80) cc_final: 0.6228 (t80)
REVERT: E  119 ASP cc_start: 0.7991 (t0) cc_final: 0.7625 (t0)
REVERT: E  128 LEU cc_start: 0.7196 (tp) cc_final: 0.6906 (tp)
REVERT: E  210 TYR cc_start: 0.7205 (t80) cc_final: 0.6923 (t80)
REVERT: F    5 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7880 (pt)
REVERT: F   16 HIS cc_start: 0.6184 (m-70) cc_final: 0.5889 (m-70)
REVERT: F   54 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5983 (mpp80)
REVERT: F   56 TYR cc_start: 0.5446 (t80) cc_final: 0.4896 (t80)
REVERT: F   74 MET cc_start: 0.3354 (ptm) cc_final: 0.3098 (ptm)
REVERT: F  115 TYR cc_start: 0.7981 (t80) cc_final: 0.7713 (t80)
REVERT: F  142 ILE cc_start: 0.7412 (mm) cc_final: 0.7056 (mm)
REVERT: F  247 LYS cc_start: 0.7333 (mtpt) cc_final: 0.7094 (mtpp)
REVERT: F  278 VAL cc_start: 0.8551 (t) cc_final: 0.8282 (p)
REVERT: F  287 LYS cc_start: 0.7416 (mttm) cc_final: 0.6866 (mtmm)
REVERT: F  311 THR cc_start: 0.8215 (t) cc_final: 0.7894 (p)
REVERT: F  316 GLU cc_start: 0.6743 (tp30) cc_final: 0.6508 (tp30)
REVERT: F  336 LYS cc_start: 0.7921 (mttp) cc_final: 0.7684 (mtmm)
REVERT: F  342 SER cc_start: 0.8419 (m) cc_final: 0.8144 (t)
  outliers start: 44
  outliers final: 31
  residues processed: 319
  average time/residue: 0.2866
  time to fit residues: 132.5712
Evaluate side-chains
  324 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 290
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  392 TYR
Chi-restraints excluded: chain E residue  401 VAL
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   54 ARG
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  463 THR
Chi-restraints excluded: chain F residue  465 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 34 optimal weight:    0.1980
   chunk 153 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   chunk 157 optimal weight:    2.9990
   chunk 150 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0030
   overall best weight:    0.3990

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.191284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.157330 restraints weight = 24790.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.161537 restraints weight = 14168.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.164270 restraints weight = 9952.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16838  Z= 0.137
  Angle     :  0.570  10.653  23128  Z= 0.299
  Chirality :  0.041   0.168   2538
  Planarity :  0.004   0.040   2632
  Dihedral  : 18.123 179.802   3014
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.53 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.20), residues: 1764
  helix:  1.53 (0.23), residues: 572
  sheet:  0.04 (0.28), residues: 373
  loop : -1.66 (0.20), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 319 
 HIS   0.004   0.001   HIS F 207 
 PHE   0.030   0.002   PHE E 343 
 TYR   0.021   0.001   TYR A 251 
 ARG   0.004   0.000   ARG F  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  614)
  hydrogen bonds       : angle       4.52185 ( 1858)
  covalent geometry    : bond        0.00307 (16838)
  covalent geometry    : angle       0.57021 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 293
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6445 (mp) cc_final: 0.6132 (mp)
REVERT: A  126 ARG cc_start: 0.6261 (tpm170) cc_final: 0.5828 (tpm170)
REVERT: A  209 ARG cc_start: 0.7062 (mtp85) cc_final: 0.6798 (mtp85)
REVERT: A  213 TYR cc_start: 0.6545 (m-80) cc_final: 0.6158 (m-80)
REVERT: A  279 ASP cc_start: 0.8082 (t70) cc_final: 0.7788 (t0)
REVERT: A  321 PHE cc_start: 0.7155 (t80) cc_final: 0.6937 (t80)
REVERT: A  399 GLU cc_start: 0.7706 (mp0) cc_final: 0.7229 (mp0)
REVERT: A  416 TYR cc_start: 0.6898 (p90) cc_final: 0.6663 (p90)
REVERT: B   37 TYR cc_start: 0.5999 (m-80) cc_final: 0.5687 (m-80)
REVERT: B  254 TRP cc_start: 0.7650 (m100) cc_final: 0.7178 (m100)
REVERT: B  417 SER cc_start: 0.8062 (t) cc_final: 0.7780 (m)
REVERT: E    4 LYS cc_start: 0.6892 (mttm) cc_final: 0.6474 (mtpp)
REVERT: E   15 ASN cc_start: 0.5456 (m-40) cc_final: 0.4884 (m-40)
REVERT: E   59 LYS cc_start: 0.7903 (tppt) cc_final: 0.7462 (tppt)
REVERT: E   93 PHE cc_start: 0.6618 (t80) cc_final: 0.6026 (t80)
REVERT: E  119 ASP cc_start: 0.8005 (t0) cc_final: 0.7636 (t70)
REVERT: E  128 LEU cc_start: 0.7169 (tp) cc_final: 0.6915 (tt)
REVERT: E  222 ASP cc_start: 0.5545 (t0) cc_final: 0.5341 (t0)
REVERT: F   16 HIS cc_start: 0.6197 (m-70) cc_final: 0.5883 (m-70)
REVERT: F   40 LYS cc_start: 0.7553 (mmmt) cc_final: 0.7161 (mptt)
REVERT: F   54 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5527 (mpp80)
REVERT: F   74 MET cc_start: 0.3323 (ptm) cc_final: 0.3065 (ptm)
REVERT: F  115 TYR cc_start: 0.7980 (t80) cc_final: 0.7710 (t80)
REVERT: F  142 ILE cc_start: 0.7426 (mm) cc_final: 0.7040 (mm)
REVERT: F  247 LYS cc_start: 0.7339 (mtpt) cc_final: 0.7059 (mtpp)
REVERT: F  287 LYS cc_start: 0.7406 (mttm) cc_final: 0.6891 (mtmm)
REVERT: F  311 THR cc_start: 0.8272 (t) cc_final: 0.7935 (p)
REVERT: F  316 GLU cc_start: 0.6683 (tp30) cc_final: 0.6412 (tp30)
REVERT: F  336 LYS cc_start: 0.7904 (mttp) cc_final: 0.7701 (mttp)
REVERT: F  342 SER cc_start: 0.8438 (m) cc_final: 0.8153 (t)
REVERT: F  480 LEU cc_start: 0.8078 (tp) cc_final: 0.7771 (tp)
  outliers start: 45
  outliers final: 29
  residues processed: 312
  average time/residue: 0.2879
  time to fit residues: 131.2340
Evaluate side-chains
  308 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 278
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  348 LYS
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   54 ARG
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 149 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 153 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 162 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 76 optimal weight:    0.3980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.185719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.151907 restraints weight = 24628.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.155955 restraints weight = 14600.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.158567 restraints weight = 10438.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  16838  Z= 0.210
  Angle     :  0.630  11.009  23128  Z= 0.333
  Chirality :  0.044   0.168   2538
  Planarity :  0.004   0.039   2632
  Dihedral  : 18.247 176.919   3014
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.86 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.48 (0.20), residues: 1764
  helix:  1.45 (0.23), residues: 545
  sheet: -0.05 (0.28), residues: 373
  loop : -1.69 (0.20), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 319 
 HIS   0.007   0.001   HIS F 207 
 PHE   0.037   0.002   PHE F  93 
 TYR   0.021   0.002   TYR A 171 
 ARG   0.005   0.000   ARG B 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05072 (  614)
  hydrogen bonds       : angle       4.75282 ( 1858)
  covalent geometry    : bond        0.00476 (16838)
  covalent geometry    : angle       0.62997 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 283
  time to evaluate  : 1.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6590 (mp) cc_final: 0.6253 (mp)
REVERT: A   94 ILE cc_start: 0.8417 (mt) cc_final: 0.8144 (mm)
REVERT: A  126 ARG cc_start: 0.6249 (tpm170) cc_final: 0.5807 (tpm170)
REVERT: A  174 ASN cc_start: 0.8011 (p0) cc_final: 0.7649 (p0)
REVERT: A  209 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6805 (mtp180)
REVERT: A  213 TYR cc_start: 0.6610 (m-80) cc_final: 0.6019 (m-80)
REVERT: A  222 ASP cc_start: 0.6119 (m-30) cc_final: 0.5864 (m-30)
REVERT: A  279 ASP cc_start: 0.8083 (t70) cc_final: 0.7793 (t0)
REVERT: A  321 PHE cc_start: 0.7348 (t80) cc_final: 0.7114 (t80)
REVERT: A  399 GLU cc_start: 0.7722 (mp0) cc_final: 0.7265 (mp0)
REVERT: A  400 LYS cc_start: 0.7366 (mttt) cc_final: 0.6796 (mttm)
REVERT: A  411 LYS cc_start: 0.5520 (tttp) cc_final: 0.5138 (ttpp)
REVERT: A  416 TYR cc_start: 0.6918 (p90) cc_final: 0.6704 (p90)
REVERT: B    3 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6140 (mm-30)
REVERT: B  254 TRP cc_start: 0.7742 (m100) cc_final: 0.7482 (m100)
REVERT: B  417 SER cc_start: 0.8007 (t) cc_final: 0.7643 (m)
REVERT: E    4 LYS cc_start: 0.6933 (mttm) cc_final: 0.6493 (mtpp)
REVERT: E   15 ASN cc_start: 0.5416 (m-40) cc_final: 0.4852 (m-40)
REVERT: E   59 LYS cc_start: 0.7950 (tppt) cc_final: 0.7546 (tppt)
REVERT: E   63 VAL cc_start: 0.7485 (t) cc_final: 0.7249 (p)
REVERT: E   93 PHE cc_start: 0.6679 (t80) cc_final: 0.5951 (t80)
REVERT: E  119 ASP cc_start: 0.8072 (t0) cc_final: 0.7716 (t0)
REVERT: E  128 LEU cc_start: 0.7186 (tp) cc_final: 0.6904 (tt)
REVERT: E  222 ASP cc_start: 0.5678 (t0) cc_final: 0.5472 (t0)
REVERT: F    6 TYR cc_start: 0.7666 (t80) cc_final: 0.7447 (t80)
REVERT: F   16 HIS cc_start: 0.6189 (m-70) cc_final: 0.5884 (m-70)
REVERT: F   74 MET cc_start: 0.3552 (ptm) cc_final: 0.3320 (ptm)
REVERT: F  115 TYR cc_start: 0.8065 (t80) cc_final: 0.7778 (t80)
REVERT: F  142 ILE cc_start: 0.7466 (mm) cc_final: 0.7083 (mm)
REVERT: F  287 LYS cc_start: 0.7441 (mttm) cc_final: 0.7216 (ttmt)
REVERT: F  311 THR cc_start: 0.8266 (t) cc_final: 0.7931 (p)
REVERT: F  316 GLU cc_start: 0.6769 (tp30) cc_final: 0.6488 (tp30)
REVERT: F  342 SER cc_start: 0.8429 (m) cc_final: 0.8108 (t)
REVERT: F  356 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7120 (tm-30)
REVERT: F  480 LEU cc_start: 0.8047 (tp) cc_final: 0.7793 (tp)
  outliers start: 47
  outliers final: 41
  residues processed: 297
  average time/residue: 0.2850
  time to fit residues: 123.9662
Evaluate side-chains
  321 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 280
  time to evaluate  : 1.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  267 LYS
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  122 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  392 TYR
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue  133 ASP
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  375 GLU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  388 ILE
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 146 optimal weight:    0.0980
   chunk 166 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 158 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 151 optimal weight:    0.3980
   chunk 152 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0770
   chunk 91 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3276

-------------------------------------------------------------------------------
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 = 0.4331 r_free = 0.4331 target = 0.189543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.156297 restraints weight = 24387.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.160366 restraints weight = 14310.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.162978 restraints weight = 10177.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6459
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16838  Z= 0.126
  Angle     :  0.561   9.181  23128  Z= 0.295
  Chirality :  0.041   0.169   2538
  Planarity :  0.004   0.042   2632
  Dihedral  : 18.117 179.806   3014
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.61 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.33 (0.20), residues: 1764
  helix:  1.63 (0.23), residues: 558
  sheet: -0.06 (0.28), residues: 375
  loop : -1.64 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP F 370 
 HIS   0.004   0.001   HIS F 207 
 PHE   0.036   0.001   PHE F  93 
 TYR   0.022   0.001   TYR A 251 
 ARG   0.006   0.000   ARG B 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03949 (  614)
  hydrogen bonds       : angle       4.44169 ( 1858)
  covalent geometry    : bond        0.00282 (16838)
  covalent geometry    : angle       0.56074 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 284
  time to evaluate  : 1.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6511 (mp) cc_final: 0.6166 (mp)
REVERT: A   94 ILE cc_start: 0.8411 (mt) cc_final: 0.8120 (mm)
REVERT: A  126 ARG cc_start: 0.6208 (tpm170) cc_final: 0.5797 (tpm170)
REVERT: A  209 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6806 (mtp180)
REVERT: A  213 TYR cc_start: 0.6460 (m-80) cc_final: 0.6170 (m-80)
REVERT: A  279 ASP cc_start: 0.8110 (t70) cc_final: 0.7785 (t0)
REVERT: A  321 PHE cc_start: 0.7116 (t80) cc_final: 0.6892 (t80)
REVERT: A  399 GLU cc_start: 0.7685 (mp0) cc_final: 0.7198 (mp0)
REVERT: A  416 TYR cc_start: 0.6903 (p90) cc_final: 0.6678 (p90)
REVERT: B  417 SER cc_start: 0.7992 (t) cc_final: 0.7702 (m)
REVERT: E    4 LYS cc_start: 0.6926 (mttm) cc_final: 0.6481 (mtpp)
REVERT: E   15 ASN cc_start: 0.5518 (m-40) cc_final: 0.5004 (m-40)
REVERT: E   59 LYS cc_start: 0.7955 (tppt) cc_final: 0.7575 (tppt)
REVERT: E   93 PHE cc_start: 0.6646 (t80) cc_final: 0.5933 (t80)
REVERT: E  119 ASP cc_start: 0.8081 (t0) cc_final: 0.7722 (t0)
REVERT: E  222 ASP cc_start: 0.5705 (t0) cc_final: 0.5480 (t0)
REVERT: E  246 ILE cc_start: 0.7024 (mt) cc_final: 0.6802 (mt)
REVERT: F    6 TYR cc_start: 0.7612 (t80) cc_final: 0.7341 (t80)
REVERT: F   16 HIS cc_start: 0.6171 (m-70) cc_final: 0.5853 (m-70)
REVERT: F  115 TYR cc_start: 0.8011 (t80) cc_final: 0.7759 (t80)
REVERT: F  142 ILE cc_start: 0.7433 (mm) cc_final: 0.7065 (mm)
REVERT: F  287 LYS cc_start: 0.7365 (mttm) cc_final: 0.7121 (mtmt)
REVERT: F  311 THR cc_start: 0.8269 (t) cc_final: 0.7976 (p)
REVERT: F  316 GLU cc_start: 0.6664 (tp30) cc_final: 0.6413 (tp30)
REVERT: F  342 SER cc_start: 0.8400 (m) cc_final: 0.8130 (t)
REVERT: F  356 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7050 (tm-30)
REVERT: F  436 GLU cc_start: 0.4626 (mt-10) cc_final: 0.4379 (mt-10)
  outliers start: 42
  outliers final: 35
  residues processed: 301
  average time/residue: 0.2864
  time to fit residues: 126.5532
Evaluate side-chains
  315 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 280
  time to evaluate  : 1.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  303 ASP
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue  133 ASP
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 138 optimal weight:    0.0980
   chunk 92 optimal weight:    0.0370
   chunk 151 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.190078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.156892 restraints weight = 24368.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.161003 restraints weight = 14316.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.163624 restraints weight = 10126.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6468
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16838  Z= 0.136
  Angle     :  0.567   9.235  23128  Z= 0.299
  Chirality :  0.041   0.167   2538
  Planarity :  0.004   0.039   2632
  Dihedral  : 18.132 178.526   3014
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.48 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 (0.20), residues: 1764
  helix:  1.61 (0.23), residues: 562
  sheet: -0.03 (0.28), residues: 375
  loop : -1.69 (0.20), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 319 
 HIS   0.004   0.001   HIS F 207 
 PHE   0.034   0.002   PHE F  93 
 TYR   0.019   0.001   TYR A 251 
 ARG   0.005   0.000   ARG B 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  614)
  hydrogen bonds       : angle       4.45263 ( 1858)
  covalent geometry    : bond        0.00306 (16838)
  covalent geometry    : angle       0.56687 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 279
  time to evaluate  : 1.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6480 (mp) cc_final: 0.6150 (mp)
REVERT: A   94 ILE cc_start: 0.8406 (mt) cc_final: 0.8119 (mm)
REVERT: A  213 TYR cc_start: 0.6526 (m-80) cc_final: 0.6183 (m-80)
REVERT: A  240 ARG cc_start: 0.6391 (mtt180) cc_final: 0.6062 (mtt180)
REVERT: A  245 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6712 (tm-30)
REVERT: A  279 ASP cc_start: 0.8093 (t70) cc_final: 0.7785 (t0)
REVERT: A  321 PHE cc_start: 0.7205 (t80) cc_final: 0.6953 (t80)
REVERT: A  415 SER cc_start: 0.8559 (p) cc_final: 0.8263 (m)
REVERT: A  416 TYR cc_start: 0.6881 (p90) cc_final: 0.6660 (p90)
REVERT: B  417 SER cc_start: 0.7957 (t) cc_final: 0.7650 (m)
REVERT: E    4 LYS cc_start: 0.6925 (mttm) cc_final: 0.6478 (mtpp)
REVERT: E   59 LYS cc_start: 0.7956 (tppt) cc_final: 0.7615 (tppt)
REVERT: E   93 PHE cc_start: 0.6633 (t80) cc_final: 0.5880 (t80)
REVERT: E  119 ASP cc_start: 0.8191 (t0) cc_final: 0.7824 (t70)
REVERT: E  222 ASP cc_start: 0.5637 (t0) cc_final: 0.5415 (t0)
REVERT: E  233 TYR cc_start: 0.6741 (t80) cc_final: 0.6489 (t80)
REVERT: E  246 ILE cc_start: 0.7039 (mt) cc_final: 0.6817 (mt)
REVERT: F    6 TYR cc_start: 0.7642 (t80) cc_final: 0.7352 (t80)
REVERT: F   16 HIS cc_start: 0.6208 (m-70) cc_final: 0.5883 (m-70)
REVERT: F  115 TYR cc_start: 0.8020 (t80) cc_final: 0.7712 (t80)
REVERT: F  142 ILE cc_start: 0.7428 (mm) cc_final: 0.7075 (mm)
REVERT: F  287 LYS cc_start: 0.7392 (mttm) cc_final: 0.7130 (mtmt)
REVERT: F  311 THR cc_start: 0.8268 (t) cc_final: 0.7976 (p)
REVERT: F  316 GLU cc_start: 0.6671 (tp30) cc_final: 0.6416 (tp30)
REVERT: F  342 SER cc_start: 0.8396 (m) cc_final: 0.8129 (t)
REVERT: F  356 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7080 (tm-30)
REVERT: F  436 GLU cc_start: 0.4703 (mt-10) cc_final: 0.4439 (mt-10)
  outliers start: 39
  outliers final: 35
  residues processed: 294
  average time/residue: 0.2812
  time to fit residues: 120.9849
Evaluate side-chains
  315 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 279
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  303 ASP
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue  133 ASP
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  388 ILE
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  459 ILE
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 155 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 135 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 126 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.188100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.154823 restraints weight = 24399.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.158857 restraints weight = 14375.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.161437 restraints weight = 10263.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  16838  Z= 0.191
  Angle     :  0.620   9.729  23128  Z= 0.328
  Chirality :  0.043   0.171   2538
  Planarity :  0.004   0.040   2632
  Dihedral  : 18.205 177.099   3014
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.86 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.42 (0.21), residues: 1764
  helix:  1.51 (0.23), residues: 553
  sheet: -0.03 (0.28), residues: 375
  loop : -1.70 (0.21), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 319 
 HIS   0.006   0.001   HIS F 207 
 PHE   0.038   0.002   PHE F  93 
 TYR   0.019   0.002   TYR B 411 
 ARG   0.003   0.000   ARG B 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04862 (  614)
  hydrogen bonds       : angle       4.64873 ( 1858)
  covalent geometry    : bond        0.00434 (16838)
  covalent geometry    : angle       0.62036 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 285
  time to evaluate  : 1.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6513 (mp) cc_final: 0.6192 (mp)
REVERT: A   94 ILE cc_start: 0.8395 (mt) cc_final: 0.8103 (mm)
REVERT: A  174 ASN cc_start: 0.8018 (p0) cc_final: 0.7684 (p0)
REVERT: A  189 GLU cc_start: 0.6601 (tm-30) cc_final: 0.5691 (tp30)
REVERT: A  213 TYR cc_start: 0.6605 (m-80) cc_final: 0.5963 (m-80)
REVERT: A  222 ASP cc_start: 0.5993 (m-30) cc_final: 0.5765 (m-30)
REVERT: A  279 ASP cc_start: 0.8055 (t70) cc_final: 0.7772 (t0)
REVERT: A  321 PHE cc_start: 0.7234 (t80) cc_final: 0.7014 (t80)
REVERT: A  400 LYS cc_start: 0.7498 (mttt) cc_final: 0.7214 (mttt)
REVERT: A  411 LYS cc_start: 0.6030 (ttpt) cc_final: 0.5670 (ttpp)
REVERT: B  254 TRP cc_start: 0.7738 (m100) cc_final: 0.7229 (m100)
REVERT: B  417 SER cc_start: 0.7992 (t) cc_final: 0.7638 (m)
REVERT: E    4 LYS cc_start: 0.6936 (mttm) cc_final: 0.6485 (mtpp)
REVERT: E   59 LYS cc_start: 0.7979 (tppt) cc_final: 0.7631 (tppt)
REVERT: E   63 VAL cc_start: 0.7674 (t) cc_final: 0.7395 (p)
REVERT: E   93 PHE cc_start: 0.6676 (t80) cc_final: 0.5893 (t80)
REVERT: E  119 ASP cc_start: 0.8222 (t0) cc_final: 0.7855 (t70)
REVERT: E  222 ASP cc_start: 0.5767 (t0) cc_final: 0.5557 (t0)
REVERT: E  233 TYR cc_start: 0.6780 (t80) cc_final: 0.6525 (t80)
REVERT: E  246 ILE cc_start: 0.7048 (mt) cc_final: 0.6823 (mt)
REVERT: F    6 TYR cc_start: 0.7665 (t80) cc_final: 0.7418 (t80)
REVERT: F   14 PHE cc_start: 0.7417 (m-80) cc_final: 0.7160 (m-80)
REVERT: F   16 HIS cc_start: 0.6220 (m-70) cc_final: 0.5942 (m-70)
REVERT: F  115 TYR cc_start: 0.8057 (t80) cc_final: 0.7780 (t80)
REVERT: F  142 ILE cc_start: 0.7442 (mm) cc_final: 0.7063 (mm)
REVERT: F  247 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6994 (mtpp)
REVERT: F  287 LYS cc_start: 0.7417 (mttm) cc_final: 0.7184 (mtmt)
REVERT: F  311 THR cc_start: 0.8284 (t) cc_final: 0.7985 (p)
REVERT: F  316 GLU cc_start: 0.6788 (tp30) cc_final: 0.6507 (tp30)
REVERT: F  342 SER cc_start: 0.8447 (m) cc_final: 0.8139 (t)
REVERT: F  356 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7177 (tm-30)
REVERT: F  409 ASN cc_start: 0.7791 (m-40) cc_final: 0.7584 (m-40)
REVERT: F  436 GLU cc_start: 0.4908 (mt-10) cc_final: 0.4539 (mt-10)
  outliers start: 40
  outliers final: 36
  residues processed: 298
  average time/residue: 0.2919
  time to fit residues: 127.9369
Evaluate side-chains
  320 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 283
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  303 ASP
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  122 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  375 THR
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue  133 ASP
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  388 ILE
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  459 ILE
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 178 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 137 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 141 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0060
   chunk 161 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
B 107 ASN
** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.189701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.156759 restraints weight = 24463.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.160819 restraints weight = 14280.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.163466 restraints weight = 10124.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16838  Z= 0.159
  Angle     :  0.597   9.159  23128  Z= 0.316
  Chirality :  0.042   0.168   2538
  Planarity :  0.004   0.040   2632
  Dihedral  : 18.179 177.992   3014
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.92 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: -0.38 (0.21), residues: 1764
  helix:  1.62 (0.23), residues: 550
  sheet: -0.05 (0.28), residues: 375
  loop : -1.69 (0.20), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 319 
 HIS   0.005   0.001   HIS F 207 
 PHE   0.033   0.002   PHE F  93 
 TYR   0.023   0.001   TYR E 210 
 ARG   0.004   0.000   ARG B 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  614)
  hydrogen bonds       : angle       4.54697 ( 1858)
  covalent geometry    : bond        0.00361 (16838)
  covalent geometry    : angle       0.59745 (23128)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 275
  time to evaluate  : 1.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ILE cc_start: 0.6503 (mp) cc_final: 0.6185 (mp)
REVERT: A   94 ILE cc_start: 0.8393 (mt) cc_final: 0.8105 (mm)
REVERT: A  174 ASN cc_start: 0.7985 (p0) cc_final: 0.7649 (p0)
REVERT: A  189 GLU cc_start: 0.6570 (tm-30) cc_final: 0.5689 (tp30)
REVERT: A  213 TYR cc_start: 0.6571 (m-80) cc_final: 0.5968 (m-80)
REVERT: A  222 ASP cc_start: 0.5901 (m-30) cc_final: 0.5685 (m-30)
REVERT: A  240 ARG cc_start: 0.6465 (mtt180) cc_final: 0.6030 (mtt-85)
REVERT: A  279 ASP cc_start: 0.8062 (t70) cc_final: 0.7761 (t0)
REVERT: A  321 PHE cc_start: 0.7158 (t80) cc_final: 0.6943 (t80)
REVERT: A  400 LYS cc_start: 0.7342 (mttt) cc_final: 0.6708 (mttm)
REVERT: A  411 LYS cc_start: 0.6016 (ttpt) cc_final: 0.5615 (ttpp)
REVERT: A  415 SER cc_start: 0.8499 (p) cc_final: 0.8255 (m)
REVERT: B  417 SER cc_start: 0.8002 (t) cc_final: 0.7715 (m)
REVERT: E    4 LYS cc_start: 0.6904 (mttm) cc_final: 0.6456 (mtpp)
REVERT: E   63 VAL cc_start: 0.7617 (t) cc_final: 0.7359 (p)
REVERT: E   93 PHE cc_start: 0.6646 (t80) cc_final: 0.5930 (t80)
REVERT: E  119 ASP cc_start: 0.8218 (t0) cc_final: 0.7842 (t70)
REVERT: E  233 TYR cc_start: 0.6682 (t80) cc_final: 0.6451 (t80)
REVERT: E  246 ILE cc_start: 0.6980 (mt) cc_final: 0.6367 (tp)
REVERT: F    6 TYR cc_start: 0.7646 (t80) cc_final: 0.7417 (t80)
REVERT: F   16 HIS cc_start: 0.6272 (m-70) cc_final: 0.5980 (m-70)
REVERT: F  115 TYR cc_start: 0.8026 (t80) cc_final: 0.7700 (t80)
REVERT: F  142 ILE cc_start: 0.7470 (mm) cc_final: 0.7120 (mm)
REVERT: F  247 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6958 (mtpp)
REVERT: F  287 LYS cc_start: 0.7413 (mttm) cc_final: 0.7178 (mtmt)
REVERT: F  311 THR cc_start: 0.8258 (t) cc_final: 0.7977 (p)
REVERT: F  316 GLU cc_start: 0.6753 (tp30) cc_final: 0.6485 (tp30)
REVERT: F  342 SER cc_start: 0.8441 (m) cc_final: 0.8153 (t)
REVERT: F  356 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7210 (tm-30)
REVERT: F  436 GLU cc_start: 0.4856 (mt-10) cc_final: 0.4540 (mt-10)
  outliers start: 39
  outliers final: 35
  residues processed: 291
  average time/residue: 0.2908
  time to fit residues: 124.4462
Evaluate side-chains
  311 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 275
  time to evaluate  : 1.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  303 ASP
Chi-restraints excluded: chain A residue  363 ARG
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  369 GLU
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain E residue  122 MET
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  224 THR
Chi-restraints excluded: chain E residue  282 VAL
Chi-restraints excluded: chain E residue  339 SER
Chi-restraints excluded: chain E residue  408 VAL
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue  219 ILE
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain F residue  307 ASN
Chi-restraints excluded: chain F residue  330 LEU
Chi-restraints excluded: chain F residue  374 LEU
Chi-restraints excluded: chain F residue  377 THR
Chi-restraints excluded: chain F residue  388 ILE
Chi-restraints excluded: chain F residue  391 THR
Chi-restraints excluded: chain F residue  459 ILE
Chi-restraints excluded: chain F residue  463 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 173 optimal weight:    0.0970
   chunk 115 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 111 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9990
   chunk 138 optimal weight:    0.2980
   chunk 151 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.190558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.157501 restraints weight = 24378.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.161584 restraints weight = 14259.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.164195 restraints weight = 10135.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16838  Z= 0.136
  Angle     :  0.579   8.880  23128  Z= 0.305
  Chirality :  0.041   0.168   2538
  Planarity :  0.004   0.040   2632
  Dihedral  : 18.156 178.212   3014
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.62 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 (0.21), residues: 1764
  helix:  1.59 (0.23), residues: 562
  sheet: -0.03 (0.28), residues: 375
  loop : -1.70 (0.20), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E  20 
 HIS   0.004   0.001   HIS F 207 
 PHE   0.032   0.002   PHE F  93 
 TYR   0.025   0.001   TYR E 210 
 ARG   0.004   0.000   ARG B 364 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  614)
  hydrogen bonds       : angle       4.47075 ( 1858)
  covalent geometry    : bond        0.00308 (16838)
  covalent geometry    : angle       0.57872 (23128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5507.60 seconds
wall clock time: 97 minutes 30.56 seconds (5850.56 seconds total)