Starting phenix.real_space_refine
on Wed Jul 30 06:09:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uux_42600/07_2025/8uux_42600.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uux_42600/07_2025/8uux_42600.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uux_42600/07_2025/8uux_42600.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uux_42600/07_2025/8uux_42600.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uux_42600/07_2025/8uux_42600.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uux_42600/07_2025/8uux_42600.cif"
  }
  resolution = 2.74
  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    7588      2.51       5
     N    1938      2.21       5
     O    2507      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12084
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 3949
          Classifications: {'peptide': 514}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 468}
    Chain: "B"
      Number of atoms: 3953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 3953
          Classifications: {'peptide': 515}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 468}
    Chain: "C"
      Number of atoms: 3869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 503, 3869
          Classifications: {'peptide': 503}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 458}
    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}
    Chain: "A"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 106
          Classifications: {'water': 106}
          Link IDs: {None: 105}
    Chain: "B"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 119
          Classifications: {'water': 119}
          Link IDs: {None: 118}
    Chain: "C"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 85
          Classifications: {'water': 85}
          Link IDs: {None: 84}
  Time building chain proxies: 8.81, per 1000 atoms: 0.73
  Number of scatterers: 12084
  At special positions: 0
  Unit cell: (118.8, 116.6, 124.3, 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    2507      8.00
     N    1938      7.00
     C    7588      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: 2.61
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2834

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 22 sheets defined
      9.5% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.528A  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: 4.114A  pdb=" N   ASN A  58 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 88
    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: 3.747A  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 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 54 through 58
      removed outlier: 4.114A  pdb=" N   ASN B  58 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 96
    Processing helix  chain 'B' and resid 140 through 144
      removed outlier: 3.752A  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: 3.563A  pdb=" N   TRP B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
      removed outlier: 3.768A  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 372
    Processing helix  chain 'B' and resid 454 through 465
    Processing helix  chain 'C' and resid 37 through 42
      removed outlier: 3.572A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 58
      removed outlier: 3.808A  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 137 through 142
      removed outlier: 4.087A  pdb=" N   THR C 142 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 240
    Processing helix  chain 'C' and resid 282 through 286
      removed outlier: 3.731A  pdb=" N   VAL C 286 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 465
      removed outlier: 3.579A  pdb=" N   VAL C 458 " --> pdb=" O   PRO C 454 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69
      removed outlier: 12.629A  pdb=" N   GLN A  61 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
      removed outlier: 10.826A  pdb=" N   SER A 207 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.816A  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: 7.176A  pdb=" N   ILE A  78 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU A 185 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   PHE A  80 " --> pdb=" O   CYS A 183 " (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 118 through 119
    Processing sheet with id=AA5, first strand: chain 'A' and resid 447 through 451
      removed outlier: 4.795A  pdb=" N   GLU A 447 " --> pdb=" O   MET A 436 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 447 through 451
      removed outlier: 4.795A  pdb=" N   GLU A 447 " --> pdb=" O   MET A 436 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   ILE A 497 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   SER A 500 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU A 485 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASN A 479 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER A 519 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ARG A 476 " --> pdb=" O   VAL A 517 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   VAL A 517 " --> pdb=" O   ARG A 476 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ARG A 478 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   PHE A 515 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 296
      removed outlier: 4.384A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   PHE A 375 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ILE A 358 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   THR A 379 " --> pdb=" O   THR A 354 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   THR A 354 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   SER A 332 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLY A 400 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLN A 334 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ILE A 398 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   GLU A 336 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A 394 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   GLN A 340 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ARG A 392 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   GLU A 342 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      removed outlier: 9.969A  pdb=" N   ARG A 390 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 69
      removed outlier: 12.741A  pdb=" N   GLN B  61 " --> pdb=" O   PRO B 209 " (cutoff:3.500A)
      removed outlier: 10.857A  pdb=" N   SER B 207 " --> pdb=" O   PRO B  63 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   GLY B  65 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83
      removed outlier: 6.781A  pdb=" N   CYS B 183 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASP B  81 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU B 181 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 103
      removed outlier: 6.166A  pdb=" N   TYR B  99 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LEU B 218 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   GLY B 101 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 119
    Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 451
      removed outlier: 4.559A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LEU B 252 " --> pdb=" O   PHE B 509 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 447 through 451
      removed outlier: 4.559A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   ILE B 497 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   SER B 500 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   GLU B 488 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU B 485 " --> pdb=" O   ASN B 479 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASN B 479 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ALA B 472 " --> pdb=" O   TRP B 520 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TRP B 520 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU B 474 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 268 through 269
      removed outlier: 4.496A  pdb=" N   ARG B 268 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 289 through 298
      removed outlier: 4.486A  pdb=" N   ALA B 290 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   PHE B 375 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ILE B 358 " --> pdb=" O   PHE B 375 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   SER B 332 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLY B 400 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLN B 334 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ILE B 398 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   GLU B 336 " --> pdb=" O   ARG B 396 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL B 394 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   GLN B 340 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ARG B 392 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   GLU B 342 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      removed outlier: 10.190A  pdb=" N   ARG B 390 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY B 389 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.643A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 9.667A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 83
      removed outlier: 6.578A  pdb=" N   CYS C 183 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ASP C  81 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   LEU C 181 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LYS C 121 " --> pdb=" O   TYR C 186 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 171
    Processing sheet with id=AC1, first strand: chain 'C' and resid 448 through 451
    Processing sheet with id=AC2, first strand: chain 'C' and resid 268 through 269
      removed outlier: 4.545A  pdb=" N   ARG C 268 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 298
      removed outlier: 6.785A  pdb=" N   PHE C 375 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   ILE C 358 " --> pdb=" O   PHE C 375 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE C 337 " --> pdb=" O   PHE C 355 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   SER C 332 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLY C 400 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLN C 334 " --> pdb=" O   ILE C 398 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE C 398 " --> pdb=" O   GLN C 334 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLU C 336 " --> pdb=" O   ARG C 396 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL C 394 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   GLN C 340 " --> pdb=" O   ARG C 392 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ARG C 392 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ALA C 290 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 427 through 429
      removed outlier: 5.139A  pdb=" N   SER C 500 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   GLU C 488 " --> pdb=" O   SER C 500 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU C 485 " --> pdb=" O   ASN C 479 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ASN C 479 " --> pdb=" O   LEU C 485 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE C 487 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   CYS C 489 " --> pdb=" O   LEU C 475 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ALA C 472 " --> pdb=" O   TRP C 520 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   TRP C 520 " --> pdb=" O   ALA C 472 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU C 474 " --> pdb=" O   VAL C 518 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    828 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: 3.63

  Time building geometry restraints manager: 3.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3835
        1.34 -     1.46: 2450
        1.46 -     1.58: 5740
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 12097
  Sorted by residual:
  bond pdb=" CG  GLN B  19 "
       pdb=" CD  GLN B  19 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.32e+00
  bond pdb=" CB  GLN B  19 "
       pdb=" CG  GLN B  19 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" CA  VAL C 216 "
       pdb=" C   VAL C 216 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.27e-02 6.20e+03 9.45e-01
  bond pdb=" CA  ASP B  20 "
       pdb=" C   ASP B  20 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.80e-02 3.09e+03 9.35e-01
  bond pdb=" N   PRO B  31 "
       pdb=" CA  PRO B  31 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.05e-01
  ... (remaining 12092 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 16156
        1.74 -     3.49: 383
        3.49 -     5.23: 37
        5.23 -     6.98: 6
        6.98 -     8.72: 6
  Bond angle restraints: 16588
  Sorted by residual:
  angle pdb=" C   GLN C 469 "
        pdb=" N   SER C 470 "
        pdb=" CA  SER C 470 "
      ideal   model   delta    sigma   weight residual
     121.90  115.31    6.59 1.26e+00 6.30e-01 2.74e+01
  angle pdb=" C   GLN B 469 "
        pdb=" N   SER B 470 "
        pdb=" CA  SER B 470 "
      ideal   model   delta    sigma   weight residual
     121.90  115.65    6.25 1.26e+00 6.30e-01 2.46e+01
  angle pdb=" C   LEU A 481 "
        pdb=" N   THR A 482 "
        pdb=" CA  THR A 482 "
      ideal   model   delta    sigma   weight residual
     121.54  128.98   -7.44 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   PHE A 461 "
        pdb=" N   ALA A 462 "
        pdb=" CA  ALA A 462 "
      ideal   model   delta    sigma   weight residual
     121.54  128.57   -7.03 1.91e+00 2.74e-01 1.36e+01
  angle pdb=" N   GLY B 195 "
        pdb=" CA  GLY B 195 "
        pdb=" C   GLY B 195 "
      ideal   model   delta    sigma   weight residual
     113.18  121.90   -8.72 2.37e+00 1.78e-01 1.35e+01
  ... (remaining 16583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 6363
       17.64 -    35.28: 623
       35.28 -    52.93: 131
       52.93 -    70.57: 41
       70.57 -    88.21: 15
  Dihedral angle restraints: 7173
    sinusoidal: 2753
      harmonic: 4420
  Sorted by residual:
  dihedral pdb=" CA  THR C 363 "
           pdb=" C   THR C 363 "
           pdb=" N   ASN C 364 "
           pdb=" CA  ASN C 364 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.48   33.52     0      5.00e+00 4.00e-02 4.49e+01
  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  147.37   32.63     0      5.00e+00 4.00e-02 4.26e+01
  dihedral pdb=" CA  ALA C 365 "
           pdb=" C   ALA C 365 "
           pdb=" N   ASP C 366 "
           pdb=" CA  ASP C 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.41   32.59     0      5.00e+00 4.00e-02 4.25e+01
  ... (remaining 7170 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1119
       0.031 -    0.063: 477
       0.063 -    0.094: 151
       0.094 -    0.125: 130
       0.125 -    0.157: 11
  Chirality restraints: 1888
  Sorted by residual:
  chirality pdb=" CA  ASP B 196 "
            pdb=" N   ASP B 196 "
            pdb=" C   ASP B 196 "
            pdb=" CB  ASP B 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CA  VAL C 414 "
            pdb=" N   VAL C 414 "
            pdb=" C   VAL C 414 "
            pdb=" CB  VAL C 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  GLN A  28 "
            pdb=" N   GLN A  28 "
            pdb=" C   GLN A  28 "
            pdb=" CB  GLN A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1885 not shown)

  Planarity restraints: 2172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 128 "   -0.045 5.00e-02 4.00e+02   6.79e-02 7.38e+00
        pdb=" N   PRO C 129 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 219 "   -0.035 5.00e-02 4.00e+02   5.29e-02 4.49e+00
        pdb=" N   PRO C 220 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C 220 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 220 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 193 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 194 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2169 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 344
        2.69 -     3.24: 10251
        3.24 -     3.79: 17529
        3.79 -     4.35: 25488
        4.35 -     4.90: 41767
  Nonbonded interactions: 95379
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 434 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OE1 GLN A 312 "
            pdb=" O   HOH A 702 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   HOH A 709 "
            pdb=" O   HOH A 799 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   HOH A 703 "
            pdb=" O   HOH A 709 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   PRO A 248 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.224 3.040
  ... (remaining 95374 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 29 through 531 or resid 601))
  selection = (chain 'B' and (resid 29 through 531 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:             6.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.120
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.060
  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:10.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
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      :  0.002   0.032  12097  Z= 0.121
  Angle     :  0.629   8.723  16588  Z= 0.342
  Chirality :  0.045   0.157   1888
  Planarity :  0.006   0.068   2172
  Dihedral  : 15.620  88.210   4339
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.70 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.42 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -1.63 (0.19), residues: 1526
  helix: -1.31 (0.57), residues: 56
  sheet: -0.11 (0.25), residues: 396
  loop : -1.55 (0.17), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 169 
 HIS   0.003   0.001   HIS B 170 
 PHE   0.014   0.001   PHE C  80 
 TYR   0.011   0.001   TYR B 227 
 ARG   0.002   0.000   ARG B 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18766 (  321)
  hydrogen bonds       : angle       6.91075 (  828)
  covalent geometry    : bond        0.00243 (12097)
  covalent geometry    : angle       0.62930 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  488 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: B  197 GLU cc_start: 0.6759 (pm20) cc_final: 0.6334 (pp20)
REVERT: C  176 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7409 (mt-10)
REVERT: C  507 LEU cc_start: 0.8222 (tp) cc_final: 0.7974 (tp)
  outliers start: 12
  outliers final: 10
  residues processed: 165
  average time/residue: 1.3582
  time to fit residues: 241.9871
Evaluate side-chains
  154 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 119 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   chunk 88 optimal weight:    5.9990
   chunk 138 optimal weight:    5.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
B 175 GLN
B 402 GLN
C 270 HIS
C 340 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 = 0.3795 r_free = 0.3795 target = 0.170398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.148260 restraints weight = 11295.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 0.79
r_work: 0.3239 rms_B_bonded: 0.89 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work: 0.3029 rms_B_bonded: 3.11 restraints_weight: 0.1250
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.0666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12097  Z= 0.178
  Angle     :  0.725  11.283  16588  Z= 0.376
  Chirality :  0.049   0.175   1888
  Planarity :  0.007   0.069   2172
  Dihedral  :  6.351  57.197   1666
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.23 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 13.00 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.53 (0.20), residues: 1526
  helix: -1.08 (0.59), residues: 51
  sheet: -0.10 (0.25), residues: 405
  loop : -1.47 (0.17), residues: 1070

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 520 
 HIS   0.005   0.001   HIS B 170 
 PHE   0.028   0.002   PHE C 199 
 TYR   0.020   0.002   TYR B 227 
 ARG   0.003   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04710 (  321)
  hydrogen bonds       : angle       5.91081 (  828)
  covalent geometry    : bond        0.00434 (12097)
  covalent geometry    : angle       0.72513 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 151
  time to evaluate  : 1.404 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8641 (m)
REVERT: A  148 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8665 (ttp)
REVERT: A  488 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8031 (mt-10)
REVERT: B   19 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.5239 (mm110)
REVERT: B   21 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7998 (pp)
REVERT: B  197 GLU cc_start: 0.6773 (pm20) cc_final: 0.6363 (pp20)
REVERT: C  155 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8062 (mp0)
REVERT: C  176 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7726 (mt-10)
REVERT: C  407 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7925 (tm-30)
REVERT: C  447 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7584 (tt0)
REVERT: C  469 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7433 (mp10)
  outliers start: 44
  outliers final: 19
  residues processed: 180
  average time/residue: 1.5784
  time to fit residues: 305.8827
Evaluate side-chains
  174 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 2.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  469 GLN
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 80 optimal weight:   20.0000
   chunk 117 optimal weight:   10.0000
   chunk 109 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 78 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 141 optimal weight:    9.9990
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
B 175 GLN
B 261 ASN
B 340 GLN
B 402 GLN
C 340 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 = 0.3793 r_free = 0.3793 target = 0.170275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.147842 restraints weight = 11463.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 0.82
r_work: 0.3244 rms_B_bonded: 0.97 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 1.96 restraints_weight: 0.2500
r_work: 0.3091 rms_B_bonded: 2.97 restraints_weight: 0.1250
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12097  Z= 0.179
  Angle     :  0.728  12.085  16588  Z= 0.376
  Chirality :  0.049   0.174   1888
  Planarity :  0.007   0.070   2172
  Dihedral  :  6.343  55.483   1662
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.36 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 13.55 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.48 (0.20), residues: 1526
  helix: -1.05 (0.62), residues: 51
  sheet: -0.02 (0.25), residues: 405
  loop : -1.47 (0.17), residues: 1070

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 520 
 HIS   0.005   0.001   HIS B 170 
 PHE   0.026   0.002   PHE C 199 
 TYR   0.020   0.002   TYR B 227 
 ARG   0.003   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04493 (  321)
  hydrogen bonds       : angle       5.79215 (  828)
  covalent geometry    : bond        0.00436 (12097)
  covalent geometry    : angle       0.72750 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 150
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8624 (m)
REVERT: A  148 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8662 (ttp)
REVERT: A  340 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7855 (tt0)
REVERT: A  488 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: B   19 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.5113 (mm110)
REVERT: B   21 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8018 (pp)
REVERT: B  197 GLU cc_start: 0.6618 (pm20) cc_final: 0.6159 (pp20)
REVERT: B  514 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8480 (mp)
REVERT: C  155 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8039 (mp0)
REVERT: C  176 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: C  407 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7956 (tm-30)
REVERT: C  447 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7607 (tt0)
REVERT: C  469 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7410 (mp10)
  outliers start: 54
  outliers final: 28
  residues processed: 186
  average time/residue: 1.3933
  time to fit residues: 280.1155
Evaluate side-chains
  184 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  469 GLN
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 148 optimal weight:    6.9990
   chunk 82 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 137 optimal weight:    3.9990
   chunk 142 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 143 optimal weight:   20.0000
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 402 GLN
B 175 GLN
B 261 ASN
B 340 GLN
B 402 GLN
C 340 GLN
C 479 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.170926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.148098 restraints weight = 11375.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 0.83
r_work: 0.3241 rms_B_bonded: 0.96 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 2.05 restraints_weight: 0.2500
r_work: 0.3077 rms_B_bonded: 3.25 restraints_weight: 0.1250
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12097  Z= 0.157
  Angle     :  0.693  10.405  16588  Z= 0.358
  Chirality :  0.048   0.166   1888
  Planarity :  0.007   0.068   2172
  Dihedral  :  6.220  52.421   1662
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.09 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.26 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.37 (0.20), residues: 1526
  helix: -0.88 (0.65), residues: 51
  sheet:  0.03 (0.24), residues: 418
  loop : -1.39 (0.18), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 520 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.023   0.002   PHE C 199 
 TYR   0.019   0.002   TYR B 227 
 ARG   0.003   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  321)
  hydrogen bonds       : angle       5.66264 (  828)
  covalent geometry    : bond        0.00381 (12097)
  covalent geometry    : angle       0.69261 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 148
  time to evaluate  : 1.279 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8626 (m)
REVERT: A  148 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8699 (ttp)
REVERT: A  340 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7899 (tt0)
REVERT: A  356 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7357 (mt-10)
REVERT: B   19 GLN cc_start: 0.5644 (OUTLIER) cc_final: 0.5011 (mm110)
REVERT: B   21 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7997 (pp)
REVERT: B  197 GLU cc_start: 0.6639 (pm20) cc_final: 0.6207 (pp20)
REVERT: B  514 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8490 (mp)
REVERT: C  155 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8043 (mp0)
REVERT: C  176 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: C  407 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7973 (tm-30)
REVERT: C  447 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7618 (tt0)
REVERT: C  453 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8650 (mp)
REVERT: C  469 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7448 (mp10)
  outliers start: 50
  outliers final: 28
  residues processed: 181
  average time/residue: 1.5793
  time to fit residues: 307.4892
Evaluate side-chains
  186 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 146
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  469 GLN
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 125 optimal weight:    8.9990
   chunk 140 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 121 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    4.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 402 GLN
B 175 GLN
B 261 ASN
B 340 GLN
B 402 GLN
C 340 GLN
C 479 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.170915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.147580 restraints weight = 11345.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 0.84
r_work: 0.3238 rms_B_bonded: 0.98 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work: 0.3079 rms_B_bonded: 2.89 restraints_weight: 0.1250
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12097  Z= 0.162
  Angle     :  0.702  11.424  16588  Z= 0.362
  Chirality :  0.048   0.169   1888
  Planarity :  0.007   0.069   2172
  Dihedral  :  6.253  51.537   1662
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.36 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 14.34 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.37 (0.20), residues: 1526
  helix: -0.89 (0.65), residues: 51
  sheet:  0.07 (0.25), residues: 406
  loop : -1.39 (0.17), residues: 1069

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 520 
 HIS   0.005   0.001   HIS B 170 
 PHE   0.024   0.002   PHE C 199 
 TYR   0.019   0.002   TYR B 227 
 ARG   0.003   0.000   ARG C 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  321)
  hydrogen bonds       : angle       5.62865 (  828)
  covalent geometry    : bond        0.00394 (12097)
  covalent geometry    : angle       0.70196 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 148
  time to evaluate  : 1.372 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8616 (m)
REVERT: A  148 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8678 (ttp)
REVERT: A  356 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7364 (mt-10)
REVERT: B   19 GLN cc_start: 0.5626 (OUTLIER) cc_final: 0.4991 (mm110)
REVERT: B   21 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7990 (pp)
REVERT: B  197 GLU cc_start: 0.6626 (pm20) cc_final: 0.6193 (pp20)
REVERT: B  514 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8456 (mp)
REVERT: C  155 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8007 (mp0)
REVERT: C  176 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7984 (mt-10)
REVERT: C  407 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7892 (tm-30)
REVERT: C  447 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7599 (tt0)
REVERT: C  453 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8655 (mp)
REVERT: C  469 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7466 (mp10)
  outliers start: 54
  outliers final: 28
  residues processed: 186
  average time/residue: 1.3670
  time to fit residues: 273.9059
Evaluate side-chains
  185 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 146
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  469 GLN
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 93 optimal weight:   30.0000
   chunk 29 optimal weight:   30.0000
   chunk 106 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 23 optimal weight:    7.9990
   chunk 120 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 148 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 42 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 402 GLN
B 175 GLN
B 261 ASN
B 340 GLN
B 402 GLN
C 340 GLN
C 479 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.171097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.148854 restraints weight = 11541.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 0.85
r_work: 0.3249 rms_B_bonded: 1.07 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work: 0.3108 rms_B_bonded: 2.86 restraints_weight: 0.1250
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.0938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12097  Z= 0.152
  Angle     :  0.684  10.224  16588  Z= 0.352
  Chirality :  0.048   0.165   1888
  Planarity :  0.007   0.068   2172
  Dihedral  :  6.175  49.825   1662
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.03 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 14.58 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.28 (0.20), residues: 1526
  helix: -0.82 (0.66), residues: 51
  sheet:  0.06 (0.24), residues: 436
  loop : -1.32 (0.18), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 520 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.022   0.002   PHE C 199 
 TYR   0.018   0.002   TYR B 227 
 ARG   0.003   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  321)
  hydrogen bonds       : angle       5.57654 (  828)
  covalent geometry    : bond        0.00368 (12097)
  covalent geometry    : angle       0.68366 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 147
  time to evaluate  : 1.480 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8620 (m)
REVERT: A  148 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8676 (ttp)
REVERT: A  356 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7321 (mt-10)
REVERT: B   19 GLN cc_start: 0.5596 (OUTLIER) cc_final: 0.4977 (mm110)
REVERT: B   21 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7971 (pp)
REVERT: B  197 GLU cc_start: 0.6572 (pm20) cc_final: 0.6142 (pp20)
REVERT: B  514 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8462 (mp)
REVERT: C  155 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8011 (mp0)
REVERT: C  176 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7967 (mt-10)
REVERT: C  396 ARG cc_start: 0.7265 (ttt180) cc_final: 0.7034 (ttt180)
REVERT: C  407 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7976 (tm-30)
REVERT: C  447 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7593 (tt0)
REVERT: C  453 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8628 (mp)
REVERT: C  469 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7433 (mp10)
  outliers start: 55
  outliers final: 33
  residues processed: 187
  average time/residue: 1.5888
  time to fit residues: 321.3608
Evaluate side-chains
  191 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 1.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  356 GLU
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  469 GLN
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 110 optimal weight:    5.9990
   chunk 106 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 138 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0870
   chunk 64 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 479 ASN
B 175 GLN
B 261 ASN
B 340 GLN
B 402 GLN
C 340 GLN
C 479 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.174800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.153065 restraints weight = 11544.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 0.80
r_work: 0.3312 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work: 0.3149 rms_B_bonded: 2.87 restraints_weight: 0.1250
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12097  Z= 0.095
  Angle     :  0.580  10.091  16588  Z= 0.299
  Chirality :  0.045   0.218   1888
  Planarity :  0.006   0.064   2172
  Dihedral  :  5.677  47.786   1662
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.50 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.15 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.11 (0.20), residues: 1526
  helix: -0.61 (0.65), residues: 57
  sheet:  0.10 (0.24), residues: 430
  loop : -1.17 (0.18), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 170 
 PHE   0.014   0.001   PHE C  80 
 TYR   0.010   0.001   TYR A 217 
 ARG   0.002   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03121 (  321)
  hydrogen bonds       : angle       5.37526 (  828)
  covalent geometry    : bond        0.00208 (12097)
  covalent geometry    : angle       0.58009 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 1.915 
Fit side-chains
REVERT: A  481 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5922 (mt)
REVERT: B   21 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7777 (pp)
REVERT: B  514 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8407 (mp)
REVERT: C  155 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7940 (mp0)
REVERT: C  176 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7675 (mt-10)
REVERT: C  340 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7575 (tt0)
REVERT: C  396 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6864 (ttt-90)
REVERT: C  407 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7944 (tm-30)
REVERT: C  453 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8512 (mp)
  outliers start: 37
  outliers final: 20
  residues processed: 183
  average time/residue: 1.6591
  time to fit residues: 330.0596
Evaluate side-chains
  174 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  340 GLN
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 85 optimal weight:   30.0000
   chunk 41 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 118 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0030
   chunk 92 optimal weight:   20.0000
   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 115 ASN
A 402 GLN
B 340 GLN
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 = 0.3805 r_free = 0.3805 target = 0.171475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.149226 restraints weight = 11559.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 0.85
r_work: 0.3274 rms_B_bonded: 1.00 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work: 0.3125 rms_B_bonded: 2.94 restraints_weight: 0.1250
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12097  Z= 0.148
  Angle     :  0.662   9.439  16588  Z= 0.340
  Chirality :  0.047   0.172   1888
  Planarity :  0.006   0.065   2172
  Dihedral  :  5.875  46.941   1661
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.90 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.39 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: 1526
  helix: -0.58 (0.67), residues: 51
  sheet:  0.11 (0.24), residues: 419
  loop : -1.18 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.021   0.002   PHE C 199 
 TYR   0.020   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 390 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  321)
  hydrogen bonds       : angle       5.44015 (  828)
  covalent geometry    : bond        0.00359 (12097)
  covalent geometry    : angle       0.66237 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 1.668 
Fit side-chains
REVERT: A  481 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6055 (mt)
REVERT: B   21 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7963 (pp)
REVERT: C  155 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7985 (mp0)
REVERT: C  176 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7814 (mt-10)
REVERT: C  338 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7788 (mp0)
REVERT: C  396 ARG cc_start: 0.7231 (ttt180) cc_final: 0.6788 (ttt-90)
REVERT: C  407 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7991 (tm-30)
REVERT: C  453 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8573 (mp)
  outliers start: 30
  outliers final: 20
  residues processed: 174
  average time/residue: 1.3816
  time to fit residues: 259.5534
Evaluate side-chains
  178 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  459 SER
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 136 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 143 optimal weight:   30.0000
   chunk 4 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0030
   chunk 128 optimal weight:   30.0000
   chunk 114 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   overall best weight:    3.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
B 261 ASN
B 340 GLN
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 = 0.3804 r_free = 0.3804 target = 0.171429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.149324 restraints weight = 11464.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 0.85
r_work: 0.3262 rms_B_bonded: 1.02 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 2.07 restraints_weight: 0.2500
r_work: 0.3101 rms_B_bonded: 3.19 restraints_weight: 0.1250
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12097  Z= 0.147
  Angle     :  0.672   9.761  16588  Z= 0.346
  Chirality :  0.048   0.153   1888
  Planarity :  0.006   0.066   2172
  Dihedral  :  5.990  45.615   1661
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.23 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.47 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.15 (0.20), residues: 1526
  helix: -0.71 (0.66), residues: 51
  sheet:  0.11 (0.24), residues: 419
  loop : -1.20 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.022   0.002   PHE C 199 
 TYR   0.020   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  321)
  hydrogen bonds       : angle       5.49055 (  828)
  covalent geometry    : bond        0.00354 (12097)
  covalent geometry    : angle       0.67209 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 1.281 
Fit side-chains
REVERT: B   21 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8044 (pp)
REVERT: B  514 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8477 (mp)
REVERT: C  155 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7990 (mp0)
REVERT: C  176 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: C  338 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7874 (mp0)
REVERT: C  396 ARG cc_start: 0.7278 (ttt180) cc_final: 0.6824 (ttt-90)
REVERT: C  407 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7926 (tm-30)
REVERT: C  453 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8592 (mp)
REVERT: C  469 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7529 (mp10)
  outliers start: 32
  outliers final: 19
  residues processed: 175
  average time/residue: 1.6544
  time to fit residues: 311.1637
Evaluate side-chains
  174 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 2.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  469 GLN
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 64 optimal weight:    0.0040
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 140 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 88 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 119 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 129 optimal weight:    8.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    3.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
B 175 GLN
B 340 GLN
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 = 0.3806 r_free = 0.3806 target = 0.171552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.149417 restraints weight = 11451.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 0.87
r_work: 0.3252 rms_B_bonded: 1.08 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work: 0.3099 rms_B_bonded: 2.99 restraints_weight: 0.1250
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12097  Z= 0.148
  Angle     :  0.672   9.744  16588  Z= 0.346
  Chirality :  0.048   0.159   1888
  Planarity :  0.006   0.067   2172
  Dihedral  :  5.964  45.715   1661
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.96 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.94 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.15 (0.20), residues: 1526
  helix: -0.69 (0.66), residues: 51
  sheet:  0.09 (0.24), residues: 419
  loop : -1.19 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.022   0.002   PHE C 199 
 TYR   0.019   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  321)
  hydrogen bonds       : angle       5.47494 (  828)
  covalent geometry    : bond        0.00357 (12097)
  covalent geometry    : angle       0.67195 (16588)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 1.414 
Fit side-chains
REVERT: B   21 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8014 (pp)
REVERT: B  514 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8451 (mp)
REVERT: C  155 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7981 (mp0)
REVERT: C  176 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8027 (mt-10)
REVERT: C  338 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (mp0)
REVERT: C  396 ARG cc_start: 0.7276 (ttt180) cc_final: 0.6839 (ttt-90)
REVERT: C  407 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7926 (tm-30)
REVERT: C  453 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8591 (mp)
REVERT: C  469 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7544 (mp10)
  outliers start: 28
  outliers final: 20
  residues processed: 169
  average time/residue: 1.3649
  time to fit residues: 248.8826
Evaluate side-chains
  175 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  107 GLU
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  338 GLU
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  453 LEU
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  469 GLN
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 64 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 9 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
B 175 GLN
B 340 GLN
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 = 0.3823 r_free = 0.3823 target = 0.173203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.151044 restraints weight = 11489.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 0.88
r_work: 0.3260 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 2.26 restraints_weight: 0.2500
r_work: 0.3103 rms_B_bonded: 3.01 restraints_weight: 0.1250
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12097  Z= 0.110
  Angle     :  0.607   8.906  16588  Z= 0.313
  Chirality :  0.046   0.147   1888
  Planarity :  0.006   0.065   2172
  Dihedral  :  5.727  47.067   1661
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.83 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.02 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.08 (0.20), residues: 1526
  helix: -0.67 (0.64), residues: 57
  sheet:  0.09 (0.24), residues: 421
  loop : -1.12 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B 170 
 PHE   0.015   0.002   PHE C 199 
 TYR   0.014   0.001   TYR A 217 
 ARG   0.002   0.000   ARG C 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  321)
  hydrogen bonds       : angle       5.37900 (  828)
  covalent geometry    : bond        0.00255 (12097)
  covalent geometry    : angle       0.60691 (16588)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11119.69 seconds
wall clock time: 196 minutes 39.91 seconds (11799.91 seconds total)