Starting phenix.real_space_refine
on Wed May 14 12:10:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eao_47838/05_2025/9eao_47838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eao_47838/05_2025/9eao_47838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eao_47838/05_2025/9eao_47838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eao_47838/05_2025/9eao_47838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eao_47838/05_2025/9eao_47838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eao_47838/05_2025/9eao_47838.cif"
  }
  resolution = 2.6
  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=   0.003 sd=   0.475
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      48      5.16       5
     C    7602      2.51       5
     N    1941      2.21       5
     O    2204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 11798
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 3949
          Classifications: {'peptide': 514}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 467}
    Chain: "B"
      Number of atoms: 3963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 3963
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 470}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 3883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3883
          Classifications: {'peptide': 504}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.71, per 1000 atoms: 0.82
  Number of scatterers: 11798
  At special positions: 0
  Unit cell: (119.9, 116.6, 123.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      48     16.00
     O    2204      8.00
     N    1941      7.00
     C    7602      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: 2.74
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2842

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 19 sheets defined
      10.6% alpha, 32.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.500A  pdb=" N   ALA A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 54 through 58
      removed outlier: 4.164A  pdb=" N   ASN A  58 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 96
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 140 through 144
      removed outlier: 3.779A  pdb=" N   PHE A 144 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 240
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.569A  pdb=" N   TRP A 285 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 282 through 286'
    Processing helix  chain 'A' and resid 368 through 371
    Processing helix  chain 'B' and resid 37 through 45
      removed outlier: 3.854A  pdb=" N   ALA B  42 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      Proline residue:  B  43  - end of helix
    Processing helix  chain 'B' and resid 54 through 58
      removed outlier: 4.102A  pdb=" N   ASN B  58 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 88
      removed outlier: 3.657A  pdb=" N   LEU B  88 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 85 through 88'
    Processing helix  chain 'B' and resid 89 through 96
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 140 through 144
      removed outlier: 3.818A  pdb=" N   PHE B 144 " --> pdb=" O   ILE B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 240
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.615A  pdb=" N   TRP B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 282 through 286'
    Processing helix  chain 'B' and resid 368 through 371
    Processing helix  chain 'B' and resid 454 through 465
    Processing helix  chain 'C' and resid 37 through 42
      removed outlier: 3.543A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 52 through 58
      removed outlier: 3.784A  pdb=" N   ASN C  58 " --> pdb=" O   ILE C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 88
    Processing helix  chain 'C' and resid 89 through 96
    Processing helix  chain 'C' and resid 97 through 99
      No H-bonds generated for 'chain 'C' and resid 97 through 99'
    Processing helix  chain 'C' and resid 139 through 144
      removed outlier: 3.775A  pdb=" N   THR C 142 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE C 144 " --> pdb=" O   ILE C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 240
    Processing helix  chain 'C' and resid 282 through 286
      removed outlier: 3.782A  pdb=" N   VAL C 286 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 465
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69
      removed outlier: 12.617A  pdb=" N   GLN A  61 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
      removed outlier: 10.907A  pdb=" N   SER A 207 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 205 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   SER A 202 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83
      removed outlier: 6.766A  pdb=" N   CYS A 183 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASP A  81 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU A 181 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   VAL A 182 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   MET A 184 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   ALA A 125 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR A 186 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   VAL A 123 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   LYS A 121 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451
    Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451
      removed outlier: 5.372A  pdb=" N   ILE A 497 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   SER A 500 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A 485 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ASN A 479 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA A 472 " --> pdb=" O   TRP A 520 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   TRP A 520 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A 474 " --> pdb=" O   VAL A 518 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 297
      removed outlier: 4.294A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   PHE A 375 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   ILE A 358 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER A 332 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   PHE A 401 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   GLU A 338 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
      removed outlier: 9.197A  pdb=" N   GLN A 340 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   ALA A 393 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 389 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69
      removed outlier: 12.790A  pdb=" N   GLN B  61 " --> pdb=" O   PRO B 209 " (cutoff:3.500A)
      removed outlier: 11.130A  pdb=" N   SER B 207 " --> pdb=" O   PRO B  63 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLY B  65 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83
      removed outlier: 6.809A  pdb=" N   ILE B  78 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU B 185 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE B  80 " --> pdb=" O   CYS B 183 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LYS B 121 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ALA B 119 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 103
    Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 451
      removed outlier: 4.772A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   LEU B 252 " --> pdb=" O   PHE B 509 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 447 through 451
      removed outlier: 4.772A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   ILE B 497 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   SER B 500 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   GLU B 488 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   GLU B 488 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU B 475 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LYS B 490 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU B 473 " --> pdb=" O   LYS B 490 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA B 472 " --> pdb=" O   TRP B 520 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TRP B 520 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU B 474 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 298
      removed outlier: 4.170A  pdb=" N   ALA B 290 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   PHE B 375 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ILE B 358 " --> pdb=" O   PHE B 375 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER B 332 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   PHE B 401 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   GLU B 338 " --> pdb=" O   PRO B 395 " (cutoff:3.500A)
      removed outlier: 9.109A  pdb=" N   GLN B 340 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   ALA B 393 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 11.866A  pdb=" N   GLU B 342 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 11.519A  pdb=" N   VAL B 391 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.605A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 9.682A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 83
      removed outlier: 6.828A  pdb=" N   ILE C  78 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU C 185 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LYS C 121 " --> pdb=" O   TYR C 186 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 171
    Processing sheet with id=AB7, first strand: chain 'C' and resid 449 through 451
      removed outlier: 3.547A  pdb=" N   GLY C 251 " --> pdb=" O   ARG C 433 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU C 252 " --> pdb=" O   PHE C 509 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 354
      removed outlier: 3.639A  pdb=" N   THR C 353 " --> pdb=" O   ILE C 339 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 339 " --> pdb=" O   THR C 353 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 354
      removed outlier: 3.639A  pdb=" N   THR C 353 " --> pdb=" O   ILE C 339 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 339 " --> pdb=" O   THR C 353 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER C 332 " --> pdb=" O   PHE C 401 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   PHE C 401 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   SER C 397 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLU C 338 " --> pdb=" O   PRO C 395 " (cutoff:3.500A)
      removed outlier: 9.169A  pdb=" N   GLN C 340 " --> pdb=" O   ALA C 393 " (cutoff:3.500A)
      removed outlier: 8.758A  pdb=" N   ALA C 393 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 11.781A  pdb=" N   GLU C 342 " --> pdb=" O   VAL C 391 " (cutoff:3.500A)
      removed outlier: 11.430A  pdb=" N   VAL C 391 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ALA C 290 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 429
      removed outlier: 5.245A  pdb=" N   SER C 500 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLU C 488 " --> pdb=" O   SER C 500 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLU C 488 " --> pdb=" O   LEU C 475 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU C 475 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LYS C 490 " --> pdb=" O   LEU C 473 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU C 473 " --> pdb=" O   LYS C 490 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ALA C 472 " --> pdb=" O   TRP C 520 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TRP C 520 " --> pdb=" O   ALA C 472 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU C 474 " --> pdb=" O   VAL C 518 " (cutoff:3.500A)

    316 hydrogen bonds defined for protein.
    786 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.58

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3828
        1.34 -     1.46: 2085
        1.46 -     1.57: 6133
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 12118
  Sorted by residual:
  bond pdb=" CB  PRO B  23 "
       pdb=" CG  PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.33e+00
  bond pdb=" CG  PRO B  23 "
       pdb=" CD  PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.503  1.545 -0.042 3.40e-02 8.65e+02 1.53e+00
  bond pdb=" CA  ASP B 174 "
       pdb=" CB  ASP B 174 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 7.15e-01
  bond pdb=" CB  ILE A 405 "
       pdb=" CG1 ILE A 405 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 2.00e-02 2.50e+03 7.03e-01
  bond pdb=" C   LEU C 159 "
       pdb=" N   PRO C 160 "
    ideal  model  delta    sigma   weight residual
    1.330  1.340 -0.010 1.23e-02 6.61e+03 6.93e-01
  ... (remaining 12113 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 16370
        2.26 -     4.53: 220
        4.53 -     6.79: 13
        6.79 -     9.06: 6
        9.06 -    11.32: 3
  Bond angle restraints: 16612
  Sorted by residual:
  angle pdb=" C   THR C 363 "
        pdb=" CA  THR C 363 "
        pdb=" CB  THR C 363 "
      ideal   model   delta    sigma   weight residual
     116.54  110.04    6.50 1.15e+00 7.56e-01 3.19e+01
  angle pdb=" C   GLN C 469 "
        pdb=" N   SER C 470 "
        pdb=" CA  SER C 470 "
      ideal   model   delta    sigma   weight residual
     121.90  115.00    6.90 1.26e+00 6.30e-01 3.00e+01
  angle pdb=" CA  PRO B  23 "
        pdb=" N   PRO B  23 "
        pdb=" CD  PRO B  23 "
      ideal   model   delta    sigma   weight residual
     112.00  106.63    5.37 1.40e+00 5.10e-01 1.47e+01
  angle pdb=" CA  THR C 363 "
        pdb=" C   THR C 363 "
        pdb=" N   ASN C 364 "
      ideal   model   delta    sigma   weight residual
     119.52  116.53    2.99 7.90e-01 1.60e+00 1.43e+01
  angle pdb=" N   PHE A 423 "
        pdb=" CA  PHE A 423 "
        pdb=" C   PHE A 423 "
      ideal   model   delta    sigma   weight residual
     110.35  115.58   -5.23 1.40e+00 5.10e-01 1.39e+01
  ... (remaining 16607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 6197
       17.39 -    34.78: 690
       34.78 -    52.17: 222
       52.17 -    69.56: 62
       69.56 -    86.95: 18
  Dihedral angle restraints: 7189
    sinusoidal: 2762
      harmonic: 4427
  Sorted by residual:
  dihedral pdb=" CA  GLY B 195 "
           pdb=" C   GLY B 195 "
           pdb=" N   ASP B 196 "
           pdb=" CA  ASP B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.33   30.67     0      5.00e+00 4.00e-02 3.76e+01
  dihedral pdb=" CA  VAL B  22 "
           pdb=" C   VAL B  22 "
           pdb=" N   PRO B  23 "
           pdb=" CA  PRO B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  GLY A 421 "
           pdb=" C   GLY A 421 "
           pdb=" N   PRO A 422 "
           pdb=" CA  PRO A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -25.80   25.80     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 7186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1393
       0.044 -    0.089: 333
       0.089 -    0.133: 162
       0.133 -    0.178: 3
       0.178 -    0.222: 1
  Chirality restraints: 1892
  Sorted by residual:
  chirality pdb=" CA  PRO B  23 "
            pdb=" N   PRO B  23 "
            pdb=" C   PRO B  23 "
            pdb=" CB  PRO B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CG  LEU B  64 "
            pdb=" CB  LEU B  64 "
            pdb=" CD1 LEU B  64 "
            pdb=" CD2 LEU B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.75e-01
  chirality pdb=" CA  PRO C 129 "
            pdb=" N   PRO C 129 "
            pdb=" C   PRO C 129 "
            pdb=" CB  PRO C 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.06e-01
  ... (remaining 1889 not shown)

  Planarity restraints: 2174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  22 "   -0.093 5.00e-02 4.00e+02   1.40e-01 3.14e+01
        pdb=" N   PRO B  23 "    0.242 5.00e-02 4.00e+02
        pdb=" CA  PRO B  23 "   -0.076 5.00e-02 4.00e+02
        pdb=" CD  PRO B  23 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 128 "   -0.040 5.00e-02 4.00e+02   6.08e-02 5.91e+00
        pdb=" N   PRO C 129 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  62 "    0.038 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO B  63 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B  63 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  63 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2171 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 143
        2.66 -     3.22: 9533
        3.22 -     3.78: 16554
        3.78 -     4.34: 23779
        4.34 -     4.90: 40143
  Nonbonded interactions: 90152
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 383 "
            pdb=" OD1 ASP C 385 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" ND2 ASN C 261 "
            pdb=" O   ILE C 420 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" ND1 HIS C 270 "
            pdb=" OD1 ASP C 272 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" ND2 ASN B 261 "
            pdb=" O   ILE B 420 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" ND2 ASN B  49 "
            pdb=" O   VAL B 216 "
     model   vdw
     2.316 3.120
  ... (remaining 90147 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' and (resid 27 through 530 or resid 601))
  selection = (chain 'B' and (resid 27 through 530 or resid 601))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.460
  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:          0.400
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.560
  Find NCS groups from input model:        0.600
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
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   0.076  12118  Z= 0.123
  Angle     :  0.623  11.321  16612  Z= 0.324
  Chirality :  0.046   0.222   1892
  Planarity :  0.007   0.140   2174
  Dihedral  : 17.272  86.950   4347
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 22.41 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.19), residues: 1523
  helix: -0.25 (0.66), residues: 50
  sheet:  0.06 (0.24), residues: 406
  loop : -1.18 (0.17), residues: 1067

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 169 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.017   0.001   PHE C  80 
 TYR   0.016   0.001   TYR A 217 
 ARG   0.002   0.000   ARG A 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17064 (  305)
  hydrogen bonds       : angle       6.60433 (  786)
  covalent geometry    : bond        0.00286 (12118)
  covalent geometry    : angle       0.62278 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 152
  time to evaluate  : 1.299 
Fit side-chains
  outliers start: 66
  outliers final: 64
  residues processed: 214
  average time/residue: 1.1194
  time to fit residues: 261.7011
Evaluate side-chains
  208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 144
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  257 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  346 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  388 ASP
Chi-restraints excluded: chain C residue  434 THR
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:   30.0000
   chunk 115 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 119 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 138 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 334 GLN
B 367 GLN
B 402 GLN
B 438 GLN
C 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.179381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.114284 restraints weight = 11768.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.67
r_work: 0.3222 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.0496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  12118  Z= 0.160
  Angle     :  0.683  11.708  16612  Z= 0.350
  Chirality :  0.048   0.227   1892
  Planarity :  0.007   0.141   2174
  Dihedral  :  8.922  59.939   1743
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.52 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 19.42 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.20), residues: 1523
  helix: -0.82 (0.64), residues: 52
  sheet:  0.04 (0.24), residues: 430
  loop : -1.14 (0.17), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 520 
 HIS   0.002   0.001   HIS A 270 
 PHE   0.019   0.002   PHE C  80 
 TYR   0.019   0.002   TYR A 217 
 ARG   0.004   0.000   ARG C 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04344 (  305)
  hydrogen bonds       : angle       5.50012 (  786)
  covalent geometry    : bond        0.00388 (12118)
  covalent geometry    : angle       0.68324 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 150
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7027 (mtp85)
REVERT: A  340 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7019 (tp40)
REVERT: B   22 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7708 (t)
REVERT: B  367 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6456 (mt0)
REVERT: C  175 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7925 (tp40)
REVERT: C  289 PHE cc_start: 0.8147 (p90) cc_final: 0.7902 (p90)
REVERT: C  390 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6658 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7566 (pp)
  outliers start: 93
  outliers final: 51
  residues processed: 217
  average time/residue: 1.1194
  time to fit residues: 264.9381
Evaluate side-chains
  206 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 148
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 116 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 148 optimal weight:   10.0000
   chunk 42 optimal weight:   30.0000
   chunk 29 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 136 optimal weight:   20.0000
   chunk 28 optimal weight:   30.0000
   chunk 109 optimal weight:    1.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 367 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.178459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.114673 restraints weight = 11910.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.62
r_work: 0.3192 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.0683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  12118  Z= 0.191
  Angle     :  0.725  12.182  16612  Z= 0.372
  Chirality :  0.050   0.229   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  8.314  59.418   1704
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 20.05 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.19), residues: 1523
  helix: -0.98 (0.64), residues: 52
  sheet:  0.02 (0.24), residues: 412
  loop : -1.20 (0.17), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 169 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.017   0.002   PHE C  80 
 TYR   0.022   0.002   TYR A 217 
 ARG   0.003   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04567 (  305)
  hydrogen bonds       : angle       5.52723 (  786)
  covalent geometry    : bond        0.00471 (12118)
  covalent geometry    : angle       0.72511 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 150
  time to evaluate  : 1.376 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8444 (m)
REVERT: A  224 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6896 (mtt-85)
REVERT: A  238 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7045 (mtp85)
REVERT: A  340 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6959 (tp40)
REVERT: B   22 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7711 (t)
REVERT: B  342 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7099 (tt0)
REVERT: B  367 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6607 (mt0)
REVERT: C  289 PHE cc_start: 0.8173 (p90) cc_final: 0.7952 (p90)
REVERT: C  390 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6713 (ttp-170)
  outliers start: 82
  outliers final: 52
  residues processed: 207
  average time/residue: 1.1198
  time to fit residues: 252.5618
Evaluate side-chains
  206 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 146
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  224 ARG
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 128 optimal weight:   30.0000
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 151 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 137 optimal weight:   30.0000
   chunk 72 optimal weight:    8.9990
   chunk 26 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.178586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.114487 restraints weight = 11809.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.69
r_work: 0.3196 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12118  Z= 0.179
  Angle     :  0.712  12.216  16612  Z= 0.364
  Chirality :  0.049   0.229   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  7.965  58.728   1694
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.71 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 20.44 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.20), residues: 1523
  helix: -1.02 (0.63), residues: 52
  sheet: -0.02 (0.24), residues: 414
  loop : -1.20 (0.17), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 169 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.018   0.002   PHE C  80 
 TYR   0.022   0.002   TYR A 217 
 ARG   0.003   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  305)
  hydrogen bonds       : angle       5.47108 (  786)
  covalent geometry    : bond        0.00441 (12118)
  covalent geometry    : angle       0.71223 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 146
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8555 (t)
REVERT: A  224 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6910 (mtt-85)
REVERT: A  238 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7076 (mtp85)
REVERT: A  340 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7008 (tp40)
REVERT: B   20 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6893 (p0)
REVERT: B   22 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7702 (t)
REVERT: B  166 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8414 (ptt90)
REVERT: B  342 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7114 (tt0)
REVERT: C  289 PHE cc_start: 0.8173 (p90) cc_final: 0.7943 (p90)
REVERT: C  390 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6720 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7589 (pp)
  outliers start: 84
  outliers final: 57
  residues processed: 201
  average time/residue: 1.1786
  time to fit residues: 257.6452
Evaluate side-chains
  215 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 148
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  224 ARG
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 130 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 141 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   chunk 50 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   overall best weight:    6.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 367 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.177464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.111207 restraints weight = 11790.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.47
r_work: 0.3200 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.0850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  12118  Z= 0.223
  Angle     :  0.781  12.884  16612  Z= 0.400
  Chirality :  0.052   0.236   1892
  Planarity :  0.008   0.144   2174
  Dihedral  :  7.957  58.604   1688
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.98 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  8.02 %
    Allowed  : 19.10 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.19), residues: 1523
  helix: -1.14 (0.63), residues: 52
  sheet: -0.02 (0.24), residues: 409
  loop : -1.28 (0.17), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 169 
 HIS   0.005   0.001   HIS C 170 
 PHE   0.017   0.003   PHE B  59 
 TYR   0.026   0.002   TYR C 217 
 ARG   0.005   0.001   ARG C 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04814 (  305)
  hydrogen bonds       : angle       5.56021 (  786)
  covalent geometry    : bond        0.00553 (12118)
  covalent geometry    : angle       0.78127 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 149
  time to evaluate  : 1.368 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8426 (m)
REVERT: A  238 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7005 (mtp85)
REVERT: A  340 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6981 (tt0)
REVERT: B   20 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7018 (p0)
REVERT: B   22 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7694 (t)
REVERT: B   28 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5673 (mm-40)
REVERT: B  166 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8358 (ptt90)
REVERT: B  342 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7126 (tt0)
REVERT: B  367 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6702 (mt0)
REVERT: C  289 PHE cc_start: 0.8200 (p90) cc_final: 0.7956 (p90)
REVERT: C  292 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6104 (mm-30)
REVERT: C  390 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6249 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7581 (pp)
  outliers start: 102
  outliers final: 66
  residues processed: 224
  average time/residue: 1.1092
  time to fit residues: 271.1348
Evaluate side-chains
  226 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 148
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  351 LYS
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 127 optimal weight:    7.9990
   chunk 146 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 82 optimal weight:   30.0000
   chunk 56 optimal weight:    0.9980
   chunk 149 optimal weight:    9.9990
   chunk 39 optimal weight:   30.0000
   chunk 141 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.179279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117196 restraints weight = 11903.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.57
r_work: 0.3234 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.0778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  12118  Z= 0.139
  Angle     :  0.663  11.779  16612  Z= 0.337
  Chirality :  0.047   0.226   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  7.552  58.046   1688
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.78 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 20.99 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.20), residues: 1523
  helix: -0.92 (0.64), residues: 52
  sheet: -0.07 (0.24), residues: 423
  loop : -1.19 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 169 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.018   0.002   PHE C  80 
 TYR   0.017   0.001   TYR A 217 
 ARG   0.002   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  305)
  hydrogen bonds       : angle       5.40466 (  786)
  covalent geometry    : bond        0.00337 (12118)
  covalent geometry    : angle       0.66324 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 151
  time to evaluate  : 1.326 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7119 (mtp85)
REVERT: B   20 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6916 (OUTLIER)
REVERT: B   22 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7685 (t)
REVERT: B  166 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8382 (ptt90)
REVERT: B  342 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7139 (tt0)
REVERT: C  175 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7880 (tp40)
REVERT: C  289 PHE cc_start: 0.8288 (p90) cc_final: 0.8069 (p90)
REVERT: C  390 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6627 (ttp-170)
  outliers start: 78
  outliers final: 54
  residues processed: 205
  average time/residue: 1.1391
  time to fit residues: 255.6931
Evaluate side-chains
  206 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 146
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 115 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 58 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 134 optimal weight:   20.0000
   chunk 28 optimal weight:   40.0000
   chunk 67 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    3.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.179050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.115809 restraints weight = 11960.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.69
r_work: 0.3205 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.0798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12118  Z= 0.151
  Angle     :  0.682  12.000  16612  Z= 0.346
  Chirality :  0.048   0.226   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  7.370  57.241   1684
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 21.07 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.20), residues: 1523
  helix: -0.95 (0.63), residues: 52
  sheet: -0.06 (0.24), residues: 423
  loop : -1.17 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 169 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.017   0.002   PHE C  80 
 TYR   0.021   0.002   TYR A 217 
 ARG   0.003   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  305)
  hydrogen bonds       : angle       5.34364 (  786)
  covalent geometry    : bond        0.00366 (12118)
  covalent geometry    : angle       0.68151 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 146
  time to evaluate  : 1.101 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7078 (mtp85)
REVERT: A  340 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6905 (tp40)
REVERT: B   20 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.6916 (OUTLIER)
REVERT: B   22 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7695 (t)
REVERT: B  166 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8408 (ptt90)
REVERT: B  254 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8266 (p)
REVERT: B  342 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7125 (tt0)
REVERT: B  512 ASP cc_start: 0.7740 (m-30) cc_final: 0.7266 (m-30)
REVERT: C  158 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8436 (mm-40)
REVERT: C  175 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7903 (tp40)
REVERT: C  289 PHE cc_start: 0.8252 (p90) cc_final: 0.8033 (p90)
REVERT: C  390 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6735 (ttp-170)
  outliers start: 74
  outliers final: 55
  residues processed: 198
  average time/residue: 1.1267
  time to fit residues: 243.0091
Evaluate side-chains
  208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 144
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 151 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 132 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 138 optimal weight:   30.0000
   chunk 28 optimal weight:   40.0000
   chunk 112 optimal weight:    0.6980
   chunk 126 optimal weight:    9.9990
   chunk 98 optimal weight:   20.0000
   chunk 128 optimal weight:    6.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.179020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.114448 restraints weight = 11910.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.48
r_work: 0.3227 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.0815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  12118  Z= 0.157
  Angle     :  0.687  12.069  16612  Z= 0.348
  Chirality :  0.048   0.226   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  7.278  57.073   1682
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.71 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 21.31 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.20), residues: 1523
  helix: -0.96 (0.63), residues: 52
  sheet: -0.07 (0.24), residues: 423
  loop : -1.18 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 169 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.017   0.002   PHE C  80 
 TYR   0.022   0.002   TYR A 217 
 ARG   0.003   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  305)
  hydrogen bonds       : angle       5.35326 (  786)
  covalent geometry    : bond        0.00383 (12118)
  covalent geometry    : angle       0.68667 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 143
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7088 (mtp85)
REVERT: A  340 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6920 (tp40)
REVERT: B   20 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6892 (OUTLIER)
REVERT: B   22 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7685 (t)
REVERT: B  166 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8401 (ptt90)
REVERT: B  254 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (p)
REVERT: B  342 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7106 (tt0)
REVERT: B  512 ASP cc_start: 0.7732 (m-30) cc_final: 0.7282 (m-30)
REVERT: C  175 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7872 (tp40)
REVERT: C  289 PHE cc_start: 0.8240 (p90) cc_final: 0.8024 (p90)
REVERT: C  390 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6665 (ttp-170)
  outliers start: 72
  outliers final: 52
  residues processed: 198
  average time/residue: 1.1480
  time to fit residues: 247.1645
Evaluate side-chains
  204 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 144
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 6 optimal weight:    0.0030
   chunk 52 optimal weight:    0.9990
   chunk 114 optimal weight:    9.9990
   chunk 143 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 118 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 33 optimal weight:   30.0000
   chunk 32 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.179227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.113662 restraints weight = 11886.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.52
r_work: 0.3229 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12118  Z= 0.148
  Angle     :  0.674  11.843  16612  Z= 0.342
  Chirality :  0.047   0.225   1892
  Planarity :  0.007   0.142   2174
  Dihedral  :  6.883  56.456   1676
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.52 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.78 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.20), residues: 1523
  helix: -0.92 (0.64), residues: 52
  sheet: -0.04 (0.24), residues: 421
  loop : -1.16 (0.18), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 169 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.017   0.002   PHE C  80 
 TYR   0.020   0.002   TYR A 217 
 ARG   0.003   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  305)
  hydrogen bonds       : angle       5.31035 (  786)
  covalent geometry    : bond        0.00358 (12118)
  covalent geometry    : angle       0.67383 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 146
  time to evaluate  : 1.239 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7067 (mtp85)
REVERT: A  340 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6896 (tp40)
REVERT: B   20 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.6911 (OUTLIER)
REVERT: B   22 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (t)
REVERT: B  166 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8388 (ptt90)
REVERT: B  254 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8259 (p)
REVERT: B  342 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7089 (tt0)
REVERT: B  345 LYS cc_start: 0.5545 (OUTLIER) cc_final: 0.5271 (mttm)
REVERT: B  512 ASP cc_start: 0.7678 (m-30) cc_final: 0.7202 (m-30)
REVERT: C  158 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8189 (mm110)
REVERT: C  175 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7889 (tp40)
REVERT: C  289 PHE cc_start: 0.8202 (p90) cc_final: 0.7986 (p90)
REVERT: C  390 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6693 (ttp-170)
  outliers start: 65
  outliers final: 52
  residues processed: 194
  average time/residue: 1.1842
  time to fit residues: 249.8246
Evaluate side-chains
  206 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 145
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 83 optimal weight:    0.0470
   chunk 127 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   chunk 131 optimal weight:    8.9990
   chunk 11 optimal weight:    0.2980
   chunk 95 optimal weight:   10.0000
   chunk 110 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0050
   overall best weight:    1.4694

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.182123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117966 restraints weight = 11908.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.64
r_work: 0.3257 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.0877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.080  12118  Z= 0.100
  Angle     :  0.582  11.169  16612  Z= 0.294
  Chirality :  0.045   0.217   1892
  Planarity :  0.007   0.139   2174
  Dihedral  :  6.326  54.513   1676
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.99 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.11 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.20), residues: 1523
  helix: -0.57 (0.66), residues: 52
  sheet:  0.06 (0.24), residues: 414
  loop : -1.05 (0.18), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 520 
 HIS   0.003   0.001   HIS C 170 
 PHE   0.020   0.001   PHE C  80 
 TYR   0.011   0.001   TYR A 217 
 ARG   0.006   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03175 (  305)
  hydrogen bonds       : angle       5.10346 (  786)
  covalent geometry    : bond        0.00237 (12118)
  covalent geometry    : angle       0.58191 (16612)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 153
  time to evaluate  : 1.221 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6611 (mtp85)
REVERT: A  340 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6830 (tp40)
REVERT: A  405 ILE cc_start: 0.7907 (pt) cc_final: 0.7706 (pp)
REVERT: B  166 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8485 (ptt90)
REVERT: C  175 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7886 (tp40)
REVERT: C  207 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (t)
REVERT: C  390 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6578 (ttp-170)
  outliers start: 48
  outliers final: 31
  residues processed: 183
  average time/residue: 1.2485
  time to fit residues: 247.8074
Evaluate side-chains
  183 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 129 optimal weight:   40.0000
   chunk 9 optimal weight:    0.3980
   chunk 134 optimal weight:    0.0000
   chunk 23 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 135 optimal weight:   10.0000
   chunk 122 optimal weight:    9.9990
   chunk 84 optimal weight:    4.9990
   chunk 119 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.8790

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
A 479 ASN
B 334 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.181550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.116219 restraints weight = 11916.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.59
r_work: 0.3266 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  12118  Z= 0.107
  Angle     :  0.609  12.196  16612  Z= 0.305
  Chirality :  0.045   0.219   1892
  Planarity :  0.007   0.139   2174
  Dihedral  :  6.045  53.348   1669
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.32 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.82 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -0.99 (0.20), residues: 1523
  helix: -0.50 (0.66), residues: 52
  sheet:  0.04 (0.24), residues: 416
  loop : -1.00 (0.18), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 520 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.018   0.001   PHE C  80 
 TYR   0.014   0.001   TYR A 217 
 ARG   0.005   0.000   ARG C 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 (  305)
  hydrogen bonds       : angle       5.07930 (  786)
  covalent geometry    : bond        0.00254 (12118)
  covalent geometry    : angle       0.60924 (16612)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10965.05 seconds
wall clock time: 189 minutes 2.10 seconds (11342.10 seconds total)