Starting phenix.real_space_refine
on Sat Aug 23 12:34:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uux_42600/08_2025/8uux_42600.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uux_42600/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uux_42600/08_2025/8uux_42600.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uux_42600/08_2025/8uux_42600.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uux_42600/08_2025/8uux_42600.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uux_42600/08_2025/8uux_42600.map"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.17, per 1000 atoms: 0.26
  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: 0.81
  Conformation dependent library (CDL) restraints added in 556.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.32
  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: 1.49

  Time building geometry restraints manager: 1.05 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 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:             14.210
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.100
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.110
-------------------------------------------------------------------------------
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 : 3.55
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 244 
 TYR   0.011   0.001   TYR B 227 
 PHE   0.014   0.001   PHE C  80 
 TRP   0.013   0.001   TRP C 169 
 HIS   0.003   0.001   HIS B 170 

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

*********************** 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  : 0.463 
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: 0.6153
  time to fit residues: 109.2015
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  : 0.359 
-------------------------------------------------------------------------------
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 98 optimal weight:   20.0000
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.174298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.152296 restraints weight = 11528.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 0.86
r_work: 0.3302 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work: 0.3072 rms_B_bonded: 3.80 restraints_weight: 0.1250
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.0618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12097  Z= 0.102
  Angle     :  0.594   8.691  16588  Z= 0.308
  Chirality :  0.045   0.150   1888
  Planarity :  0.006   0.058   2172
  Dihedral  :  5.776  58.176   1666
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.18 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.71 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.20), residues: 1526
  helix: -1.18 (0.56), residues: 63
  sheet:  0.02 (0.25), residues: 413
  loop : -1.34 (0.18), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 437 
 TYR   0.011   0.001   TYR B 227 
 PHE   0.014   0.001   PHE C  80 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (12097)
  covalent geometry    : angle       0.59366 (16588)
  hydrogen bonds       : bond        0.03731 (  321)
  hydrogen bonds       : angle       5.77667 (  828)

*********************** 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
  184 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: A  488 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: B   21 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7712 (pp)
REVERT: B  197 GLU cc_start: 0.6930 (pm20) cc_final: 0.6381 (pp20)
REVERT: C  155 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8071 (mp0)
REVERT: C  407 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7952 (tm-30)
  outliers start: 29
  outliers final: 11
  residues processed: 177
  average time/residue: 0.6262
  time to fit residues: 119.0660
Evaluate side-chains
  165 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain B residue   21 LEU
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  155 GLU
Chi-restraints excluded: chain C residue  354 THR
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  414 VAL
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 17 optimal weight:    0.4980
   chunk 150 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 4 optimal weight:    0.1980
   chunk 101 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 92 optimal weight:    8.9990
   overall best weight:    4.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 402 GLN
B 261 ASN
B 340 GLN
B 402 GLN
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 = 0.3803 r_free = 0.3803 target = 0.171165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.148270 restraints weight = 11491.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 0.87
r_work: 0.3249 rms_B_bonded: 1.06 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 1.93 restraints_weight: 0.2500
r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.1250
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.0773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12097  Z= 0.167
  Angle     :  0.695  10.466  16588  Z= 0.358
  Chirality :  0.048   0.168   1888
  Planarity :  0.006   0.063   2172
  Dihedral  :  6.053  56.686   1661
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.16 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 13.16 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.20), residues: 1526
  helix: -0.77 (0.63), residues: 51
  sheet: -0.02 (0.25), residues: 405
  loop : -1.36 (0.17), residues: 1070

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 180 
 TYR   0.020   0.002   TYR B 227 
 PHE   0.026   0.002   PHE C 199 
 TRP   0.010   0.002   TRP A 520 
 HIS   0.004   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12097)
  covalent geometry    : angle       0.69536 (16588)
  hydrogen bonds       : bond        0.04310 (  321)
  hydrogen bonds       : angle       5.71319 (  828)

*********************** 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
  199 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 152
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8596 (m)
REVERT: A  488 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: B   19 GLN cc_start: 0.5604 (OUTLIER) cc_final: 0.5036 (mm110)
REVERT: B   21 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8009 (pp)
REVERT: B  197 GLU cc_start: 0.6783 (pm20) cc_final: 0.6320 (pp20)
REVERT: B  514 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8475 (mp)
REVERT: C  155 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8005 (mp0)
REVERT: C  176 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7675 (mt-10)
REVERT: C  407 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7953 (tm-30)
REVERT: C  447 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7583 (tt0)
REVERT: C  469 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7395 (mp10)
  outliers start: 47
  outliers final: 18
  residues processed: 184
  average time/residue: 0.7132
  time to fit residues: 140.7249
Evaluate side-chains
  177 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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  176 GLU
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   19 GLN
Chi-restraints excluded: chain B residue   21 LEU
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  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  176 GLU
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  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 41 optimal weight:    9.9990
   chunk 89 optimal weight:   30.0000
   chunk 63 optimal weight:    0.9980
   chunk 34 optimal weight:   30.0000
   chunk 120 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 134 optimal weight:   20.0000
   chunk 151 optimal weight:    9.9990
   chunk 42 optimal weight:   30.0000
   chunk 106 optimal weight:    9.9990
   chunk 81 optimal weight:   50.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 402 GLN
B 261 ASN
B 340 GLN
B 402 GLN
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 = 0.3787 r_free = 0.3787 target = 0.169660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.146814 restraints weight = 11468.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 0.88
r_work: 0.3226 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 1.81 restraints_weight: 0.2500
r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.1250
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.0960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  12097  Z= 0.204
  Angle     :  0.772  14.454  16588  Z= 0.396
  Chirality :  0.051   0.190   1888
  Planarity :  0.007   0.069   2172
  Dihedral  :  6.381  53.648   1661
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.42 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 13.79 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.20), residues: 1526
  helix: -1.01 (0.64), residues: 51
  sheet: -0.02 (0.25), residues: 406
  loop : -1.44 (0.17), residues: 1069

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 152 
 TYR   0.023   0.002   TYR B 227 
 PHE   0.031   0.003   PHE C 199 
 TRP   0.012   0.002   TRP A 520 
 HIS   0.005   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 (12097)
  covalent geometry    : angle       0.77217 (16588)
  hydrogen bonds       : bond        0.04624 (  321)
  hydrogen bonds       : angle       5.72932 (  828)

*********************** 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
  207 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 152
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8625 (m)
REVERT: A  340 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7826 (tt0)
REVERT: A  356 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7163 (mm-30)
REVERT: A  488 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7981 (mt-10)
REVERT: B   19 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5157 (mm110)
REVERT: B   21 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8139 (pp)
REVERT: B  197 GLU cc_start: 0.6597 (pm20) cc_final: 0.6188 (pp20)
REVERT: B  514 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8495 (mp)
REVERT: C  155 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8014 (mp0)
REVERT: C  176 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7960 (mt-10)
REVERT: C  407 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (tm-30)
REVERT: C  447 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7600 (tt0)
REVERT: C  453 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8643 (mp)
REVERT: C  469 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7529 (mp10)
  outliers start: 55
  outliers final: 26
  residues processed: 190
  average time/residue: 0.6846
  time to fit residues: 140.2709
Evaluate side-chains
  186 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
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  149 CYS
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  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  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  176 GLU
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  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 23 optimal weight:   20.0000
   chunk 22 optimal weight:    0.0980
   chunk 125 optimal weight:    7.9990
   chunk 133 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 89 optimal weight:   30.0000
   chunk 16 optimal weight:    7.9990
   chunk 132 optimal weight:    9.9990
   chunk 69 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 122 optimal weight:   20.0000
   overall best weight:    6.2188

-------------------------------------------------------------------------------
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 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 = 0.3780 r_free = 0.3780 target = 0.169069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.146396 restraints weight = 11525.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 0.87
r_work: 0.3228 rms_B_bonded: 1.06 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 2.22 restraints_weight: 0.2500
r_work: 0.3070 rms_B_bonded: 3.00 restraints_weight: 0.1250
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  12097  Z= 0.220
  Angle     :  0.789  14.237  16588  Z= 0.406
  Chirality :  0.051   0.194   1888
  Planarity :  0.007   0.071   2172
  Dihedral  :  6.469  51.128   1661
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.75 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 14.11 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.20), residues: 1526
  helix: -1.15 (0.63), residues: 51
  sheet: -0.00 (0.24), residues: 408
  loop : -1.50 (0.17), residues: 1067

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 180 
 TYR   0.025   0.002   TYR C 217 
 PHE   0.030   0.003   PHE C 199 
 TRP   0.012   0.002   TRP A 520 
 HIS   0.005   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (12097)
  covalent geometry    : angle       0.78920 (16588)
  hydrogen bonds       : bond        0.04727 (  321)
  hydrogen bonds       : angle       5.74681 (  828)

*********************** 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
  207 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 150
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A  100 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8638 (m)
REVERT: A  340 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7804 (tt0)
REVERT: A  356 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7388 (mt-10)
REVERT: A  488 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7995 (mt-10)
REVERT: B   19 GLN cc_start: 0.5764 (OUTLIER) cc_final: 0.5156 (mm110)
REVERT: B   21 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8135 (pp)
REVERT: B  197 GLU cc_start: 0.6686 (pm20) cc_final: 0.6257 (pp20)
REVERT: B  514 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8528 (mp)
REVERT: C  155 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8014 (mp0)
REVERT: C  176 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (mt-10)
REVERT: C  407 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7888 (tm-30)
REVERT: C  447 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7615 (tt0)
REVERT: C  453 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (mp)
REVERT: C  469 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7599 (mp10)
  outliers start: 57
  outliers final: 32
  residues processed: 188
  average time/residue: 0.6987
  time to fit residues: 141.6394
Evaluate side-chains
  196 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 152
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  111 VAL
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  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  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  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  176 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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 146 optimal weight:    6.9990
   chunk 114 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 140 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 100 optimal weight:    6.9990
   overall best weight:    2.2584

-------------------------------------------------------------------------------
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 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 = 0.3810 r_free = 0.3810 target = 0.172022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.150141 restraints weight = 11483.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 0.81
r_work: 0.3284 rms_B_bonded: 0.91 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 2.23 restraints_weight: 0.2500
r_work: 0.3110 rms_B_bonded: 2.89 restraints_weight: 0.1250
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12097  Z= 0.114
  Angle     :  0.631   9.294  16588  Z= 0.327
  Chirality :  0.046   0.158   1888
  Planarity :  0.006   0.066   2172
  Dihedral  :  5.999  49.078   1661
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.83 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.52 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.20), residues: 1526
  helix: -0.75 (0.66), residues: 51
  sheet:  0.13 (0.24), residues: 431
  loop : -1.32 (0.18), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 152 
 TYR   0.015   0.001   TYR A 217 
 PHE   0.015   0.002   PHE C  80 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (12097)
  covalent geometry    : angle       0.63141 (16588)
  hydrogen bonds       : bond        0.03613 (  321)
  hydrogen bonds       : angle       5.52966 (  828)

*********************** 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
  196 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 154
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A  488 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7932 (mt-10)
REVERT: B   21 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7977 (pp)
REVERT: B  197 GLU cc_start: 0.6752 (pm20) cc_final: 0.6280 (pp20)
REVERT: B  514 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8481 (mp)
REVERT: C  155 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: C  176 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7805 (mt-10)
REVERT: C  407 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7923 (tm-30)
REVERT: C  453 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8565 (mp)
REVERT: C  469 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7412 (mp10)
  outliers start: 42
  outliers final: 22
  residues processed: 185
  average time/residue: 0.6928
  time to fit residues: 138.1618
Evaluate side-chains
  178 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  176 GLU
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  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  339 ILE
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  176 GLU
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  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 148 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 105 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 128 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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
A 479 ASN
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 = 0.3809 r_free = 0.3809 target = 0.171825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.149092 restraints weight = 11434.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 0.83
r_work: 0.3260 rms_B_bonded: 1.03 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work: 0.3114 rms_B_bonded: 2.78 restraints_weight: 0.1250
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12097  Z= 0.132
  Angle     :  0.654   9.621  16588  Z= 0.337
  Chirality :  0.047   0.161   1888
  Planarity :  0.006   0.066   2172
  Dihedral  :  5.989  47.913   1661
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.29 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.20), residues: 1526
  helix: -0.70 (0.67), residues: 51
  sheet:  0.09 (0.24), residues: 424
  loop : -1.28 (0.18), residues: 1051

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 152 
 TYR   0.019   0.001   TYR A 217 
 PHE   0.019   0.002   PHE C 199 
 TRP   0.010   0.001   TRP C 169 
 HIS   0.004   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12097)
  covalent geometry    : angle       0.65432 (16588)
  hydrogen bonds       : bond        0.03749 (  321)
  hydrogen bonds       : angle       5.48472 (  828)

*********************** 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
  184 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  488 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7908 (mt-10)
REVERT: B   21 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7943 (pp)
REVERT: B  197 GLU cc_start: 0.6703 (pm20) cc_final: 0.6239 (pp20)
REVERT: B  514 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (mp)
REVERT: C  155 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7977 (mp0)
REVERT: C  176 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7801 (mt-10)
REVERT: C  340 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7528 (tt0)
REVERT: C  407 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7934 (tm-30)
REVERT: C  453 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8558 (mp)
REVERT: C  469 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7451 (mp10)
  outliers start: 37
  outliers final: 25
  residues processed: 173
  average time/residue: 0.7258
  time to fit residues: 135.0979
Evaluate side-chains
  182 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  176 GLU
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  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  339 ILE
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  176 GLU
Chi-restraints excluded: chain C residue  340 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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 112 optimal weight:    0.6980
   chunk 65 optimal weight:    0.2980
   chunk 118 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 131 optimal weight:    0.6980
   chunk 138 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 90 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0980
   overall best weight:    0.9582

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.174602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.152969 restraints weight = 11453.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 0.81
r_work: 0.3305 rms_B_bonded: 0.95 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 2.06 restraints_weight: 0.2500
r_work: 0.3160 rms_B_bonded: 2.76 restraints_weight: 0.1250
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12097  Z= 0.093
  Angle     :  0.579   8.877  16588  Z= 0.299
  Chirality :  0.045   0.149   1888
  Planarity :  0.006   0.063   2172
  Dihedral  :  5.687  47.266   1661
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.44 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.55 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.20), residues: 1526
  helix: -0.59 (0.65), residues: 57
  sheet:  0.10 (0.24), residues: 430
  loop : -1.14 (0.18), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 244 
 TYR   0.012   0.001   TYR A 217 
 PHE   0.013   0.001   PHE C  80 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (12097)
  covalent geometry    : angle       0.57880 (16588)
  hydrogen bonds       : bond        0.03177 (  321)
  hydrogen bonds       : angle       5.35494 (  828)

*********************** 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
  185 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A  481 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5976 (mt)
REVERT: B   21 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7785 (pp)
REVERT: B  514 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8432 (mp)
REVERT: C  155 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7900 (mp0)
REVERT: C  176 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7650 (mt-10)
REVERT: C  407 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7959 (tm-30)
REVERT: C  447 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7600 (tt0)
REVERT: C  453 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8516 (mp)
  outliers start: 31
  outliers final: 20
  residues processed: 180
  average time/residue: 0.6968
  time to fit residues: 135.0633
Evaluate side-chains
  177 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
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  339 ILE
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  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  447 GLU
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 43 optimal weight:    9.9990
   chunk 142 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 27 optimal weight:   30.0000
   chunk 20 optimal weight:    0.0170
   chunk 65 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 135 optimal weight:    0.2980
   overall best weight:    1.6220

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.174069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.150927 restraints weight = 11473.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 0.89
r_work: 0.3295 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 2.18 restraints_weight: 0.2500
r_work: 0.3149 rms_B_bonded: 3.00 restraints_weight: 0.1250
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12097  Z= 0.101
  Angle     :  0.591   9.002  16588  Z= 0.303
  Chirality :  0.045   0.153   1888
  Planarity :  0.006   0.061   2172
  Dihedral  :  5.644  48.117   1661
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.64 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.23 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.20), residues: 1526
  helix: -0.53 (0.65), residues: 57
  sheet:  0.17 (0.24), residues: 422
  loop : -1.11 (0.19), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 322 
 TYR   0.013   0.001   TYR A 217 
 PHE   0.013   0.002   PHE C 199 
 TRP   0.009   0.001   TRP C 169 
 HIS   0.004   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (12097)
  covalent geometry    : angle       0.59076 (16588)
  hydrogen bonds       : bond        0.03238 (  321)
  hydrogen bonds       : angle       5.27018 (  828)

*********************** 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
  184 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.470 
Fit side-chains
REVERT: B   21 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7813 (pp)
REVERT: C  155 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7949 (mp0)
REVERT: C  176 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: C  407 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7995 (tm-30)
REVERT: C  447 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7615 (tt0)
REVERT: C  453 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8524 (mp)
  outliers start: 32
  outliers final: 21
  residues processed: 178
  average time/residue: 0.6959
  time to fit residues: 133.7264
Evaluate side-chains
  176 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
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  276 LEU
Chi-restraints excluded: chain B residue  339 ILE
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  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  499 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 133 optimal weight:   10.0000
   chunk 142 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 129 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   overall best weight:    3.1588

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.172354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.148091 restraints weight = 11479.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 0.84
r_work: 0.3251 rms_B_bonded: 1.16 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 2.25 restraints_weight: 0.2500
r_work: 0.3088 rms_B_bonded: 3.10 restraints_weight: 0.1250
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12097  Z= 0.135
  Angle     :  0.646   9.331  16588  Z= 0.332
  Chirality :  0.047   0.159   1888
  Planarity :  0.006   0.062   2172
  Dihedral  :  5.857  47.548   1661
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.29 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.39 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.20), residues: 1526
  helix: -0.50 (0.67), residues: 51
  sheet:  0.17 (0.24), residues: 422
  loop : -1.11 (0.18), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 322 
 TYR   0.018   0.001   TYR A 217 
 PHE   0.020   0.002   PHE C 199 
 TRP   0.009   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (12097)
  covalent geometry    : angle       0.64648 (16588)
  hydrogen bonds       : bond        0.03680 (  321)
  hydrogen bonds       : angle       5.36686 (  828)

********************** 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
  179 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.563 
Fit side-chains
REVERT: B   21 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7964 (pp)
REVERT: B  514 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8455 (mp)
REVERT: C  155 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7951 (mp0)
REVERT: C  176 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7899 (mt-10)
REVERT: C  407 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7871 (tm-30)
REVERT: C  447 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7588 (tt0)
REVERT: C  453 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8563 (mp)
  outliers start: 29
  outliers final: 21
  residues processed: 172
  average time/residue: 0.6787
  time to fit residues: 125.7392
Evaluate side-chains
  179 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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  276 LEU
Chi-restraints excluded: chain B residue  339 ILE
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  176 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  447 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 147 optimal weight:    9.9990
   chunk 133 optimal weight:   20.0000
   chunk 23 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 146 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0870
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.8962

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.173862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.151826 restraints weight = 11499.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 0.90
r_work: 0.3292 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 1.96 restraints_weight: 0.2500
r_work: 0.3156 rms_B_bonded: 2.95 restraints_weight: 0.1250
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  12097  Z= 0.105
  Angle     :  0.596   9.029  16588  Z= 0.307
  Chirality :  0.045   0.147   1888
  Planarity :  0.006   0.061   2172
  Dihedral  :  5.692  48.942   1661
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.77 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.23 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.21), residues: 1526
  helix: -0.62 (0.64), residues: 57
  sheet:  0.18 (0.24), residues: 437
  loop : -1.07 (0.19), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 152 
 TYR   0.014   0.001   TYR A 217 
 PHE   0.014   0.002   PHE C 199 
 TRP   0.010   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (12097)
  covalent geometry    : angle       0.59605 (16588)
  hydrogen bonds       : bond        0.03316 (  321)
  hydrogen bonds       : angle       5.31189 (  828)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5209.02 seconds
wall clock time: 89 minutes 18.29 seconds (5358.29 seconds total)