Starting phenix.real_space_refine
on Tue Jul 29 16:53:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6s6l_10103/07_2025/6s6l_10103.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6s6l_10103/07_2025/6s6l_10103.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6s6l_10103/07_2025/6s6l_10103.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6s6l_10103/07_2025/6s6l_10103.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6s6l_10103/07_2025/6s6l_10103.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6s6l_10103/07_2025/6s6l_10103.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    7476      2.51       5
     N    1905      2.21       5
     O    2158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11587
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3838
          Classifications: {'peptide': 500}
          Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 455}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 3886
          Classifications: {'peptide': 508}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 43, 'TRANS': 461}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 502, 3863
          Classifications: {'peptide': 502}
          Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 457}
  Time building chain proxies: 9.19, per 1000 atoms: 0.79
  Number of scatterers: 11587
  At special positions: 0
  Unit cell: (97.98, 110.76, 116.085, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    2158      8.00
     N    1905      7.00
     C    7476      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2792

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 19 sheets defined
      10.2% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 54 through 58
      removed outlier: 4.128A  pdb=" N   ASN A  58 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 88
      removed outlier: 3.584A  pdb=" N   LEU A  88 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 85 through 88'
    Processing helix  chain 'A' and resid 89 through 96
    Processing helix  chain 'A' and resid 139 through 144
      removed outlier: 3.798A  pdb=" N   THR A 142 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE A 144 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 240
      removed outlier: 3.870A  pdb=" N   CYS A 240 " --> pdb=" O   PRO A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.634A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 465
      removed outlier: 3.692A  pdb=" N   VAL A 458 " --> pdb=" O   PRO A 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 42
      removed outlier: 4.066A  pdb=" N   ALA B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 3.910A  pdb=" N   ASN B  58 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 88
      removed outlier: 3.839A  pdb=" N   LEU B  88 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 85 through 88'
    Processing helix  chain 'B' and resid 89 through 96
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 137 through 142
      removed outlier: 4.575A  pdb=" N   THR B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 240
      removed outlier: 3.846A  pdb=" N   CYS B 240 " --> pdb=" O   PRO B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.736A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 465
    Processing helix  chain 'C' and resid 37 through 42
      removed outlier: 3.593A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 58
      removed outlier: 3.764A  pdb=" N   ASN C  58 " --> pdb=" O   ILE C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 88
      removed outlier: 3.865A  pdb=" N   LEU C  88 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
      No H-bonds generated for '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: 4.049A  pdb=" N   THR C 142 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 465
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50
      removed outlier: 3.692A  pdb=" N   SER A 202 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   ASN A 105 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   ASP A 212 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL A 103 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   ASN A 214 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   GLY A 101 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL A 216 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   TYR A  99 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69
      removed outlier: 12.275A  pdb=" N   GLN A  61 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
      removed outlier: 11.359A  pdb=" N   SER A 207 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A 202 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   ASN A 105 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   ASP A 212 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL A 103 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   ASN A 214 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   GLY A 101 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL A 216 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   TYR A  99 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83
      removed outlier: 6.835A  pdb=" N   ILE A  78 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   LEU A 185 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A  80 " --> pdb=" O   CYS A 183 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451
      removed outlier: 3.515A  pdb=" N   LEU A 507 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451
      removed outlier: 5.169A  pdb=" N   ILE A 497 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   SER A 500 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   LEU A 485 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ASN A 479 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   SER A 519 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ARG A 476 " --> pdb=" O   VAL A 517 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL A 517 " --> pdb=" O   ARG A 476 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ARG A 478 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   PHE A 515 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269
      removed outlier: 4.324A  pdb=" N   ARG A 268 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 298
      removed outlier: 4.724A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 17.065A  pdb=" N   ARG A 373 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 12.507A  pdb=" N   GLY A 360 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   PHE A 375 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   ILE A 358 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLY A 333 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER A 332 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLY A 400 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLN A 334 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE A 398 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   GLU A 336 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL A 394 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   GLN A 340 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ARG A 392 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   GLU A 342 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      removed outlier: 9.939A  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: 4.218A  pdb=" N   CYS B  62 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU B 205 " --> pdb=" O   CYS B  62 " (cutoff:3.500A)
      removed outlier: 9.834A  pdb=" N   LEU B  64 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
      removed outlier: 9.952A  pdb=" N   GLY B 203 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 9.786A  pdb=" N   GLU B  66 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 11.273A  pdb=" N   VAL B 201 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83
      removed outlier: 6.672A  pdb=" N   CYS B 183 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ASP B  81 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B 181 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   LYS B 121 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   ALA B 119 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171
    Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 253
      removed outlier: 3.992A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 298
      removed outlier: 6.837A  pdb=" N   PHE B 375 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   ILE B 358 " --> pdb=" O   PHE B 375 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLN B 334 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   GLY B 400 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   GLU B 336 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILE B 398 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   GLU B 338 " --> pdb=" O   ARG B 396 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ARG B 396 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   GLN B 340 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 9.997A  pdb=" N   VAL B 394 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 11.177A  pdb=" N   GLU B 342 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 12.228A  pdb=" N   ARG B 392 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 427 through 429
      removed outlier: 4.005A  pdb=" N   TYR B 496 " --> pdb=" O   TYR B 492 " (cutoff:3.500A)
      removed outlier: 5.249A  pdb=" N   SER B 500 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   GLU B 488 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR B 477 " --> pdb=" O   PHE B 487 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ALA B 472 " --> pdb=" O   TRP B 520 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   TRP B 520 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LEU B 474 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.482A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 11.390A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASN C 105 " --> pdb=" O   ALA C 210 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP C 212 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   VAL C 103 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   ASN C 214 " --> pdb=" O   GLY C 101 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   GLY C 101 " --> pdb=" O   ASN C 214 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.482A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 11.390A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASN C 105 " --> pdb=" O   ALA C 210 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP C 212 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   VAL C 103 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   ASN C 214 " --> pdb=" O   GLY C 101 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   GLY C 101 " --> pdb=" O   ASN C 214 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 83
      removed outlier: 6.567A  pdb=" N   CYS C 183 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ASP C  81 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   LEU C 181 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LYS C 121 " --> pdb=" O   TYR C 186 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 447 through 451
      removed outlier: 4.139A  pdb=" N   GLU C 447 " --> pdb=" O   MET C 436 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   LEU C 252 " --> pdb=" O   PHE C 509 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 447 through 451
      removed outlier: 4.139A  pdb=" N   GLU C 447 " --> pdb=" O   MET C 436 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   ILE C 497 " --> pdb=" O   LEU C 430 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   TYR C 496 " --> pdb=" O   TYR C 492 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   SER C 500 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   GLU C 488 " --> pdb=" O   SER C 500 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU C 485 " --> pdb=" O   ASN C 479 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ASN C 479 " --> pdb=" O   LEU C 485 " (cutoff:3.500A)
      removed outlier: 6.938A  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: 6.776A  pdb=" N   LEU C 474 " --> pdb=" O   VAL C 518 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 298
      removed outlier: 4.392A  pdb=" N   ALA C 290 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   PHE C 375 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   ILE C 358 " --> pdb=" O   PHE C 375 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   SER C 332 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLY C 400 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLN C 334 " --> pdb=" O   ILE C 398 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ILE C 398 " --> pdb=" O   GLN C 334 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLU C 336 " --> pdb=" O   ARG C 396 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   GLN C 340 " --> pdb=" O   ARG C 392 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ARG C 392 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   GLU C 342 " --> pdb=" O   ARG C 390 " (cutoff:3.500A)
      removed outlier: 9.234A  pdb=" N   ARG C 390 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    939 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.65

  Time building geometry restraints manager: 3.13 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1943
        1.31 -     1.44: 3204
        1.44 -     1.57: 6688
        1.57 -     1.70: 0
        1.70 -     1.83: 72
  Bond restraints: 11907
  Sorted by residual:
  bond pdb=" CB  VAL B  60 "
       pdb=" CG2 VAL B  60 "
    ideal  model  delta    sigma   weight residual
    1.521  1.367  0.154 3.30e-02 9.18e+02 2.19e+01
  bond pdb=" CA  CYS A 183 "
       pdb=" CB  CYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.534  1.439  0.096 2.47e-02 1.64e+03 1.50e+01
  bond pdb=" C   ASN B 192 "
       pdb=" N   SER B 193 "
    ideal  model  delta    sigma   weight residual
    1.335  1.233  0.101 3.04e-02 1.08e+03 1.11e+01
  bond pdb=" CB  THR C 219 "
       pdb=" CG2 THR C 219 "
    ideal  model  delta    sigma   weight residual
    1.521  1.418  0.103 3.30e-02 9.18e+02 9.78e+00
  bond pdb=" CB  VAL B 103 "
       pdb=" CG1 VAL B 103 "
    ideal  model  delta    sigma   weight residual
    1.521  1.421  0.100 3.30e-02 9.18e+02 9.24e+00
  ... (remaining 11902 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.83: 16081
        3.83 -     7.65: 224
        7.65 -    11.48: 16
       11.48 -    15.31: 4
       15.31 -    19.14: 2
  Bond angle restraints: 16327
  Sorted by residual:
  angle pdb=" CA  LEU B 112 "
        pdb=" CB  LEU B 112 "
        pdb=" CG  LEU B 112 "
      ideal   model   delta    sigma   weight residual
     116.30  135.44  -19.14 3.50e+00 8.16e-02 2.99e+01
  angle pdb=" C   TYR A 186 "
        pdb=" N   THR A 187 "
        pdb=" CA  THR A 187 "
      ideal   model   delta    sigma   weight residual
     121.59  139.71  -18.12 3.54e+00 7.98e-02 2.62e+01
  angle pdb=" N   PRO B 132 "
        pdb=" CA  PRO B 132 "
        pdb=" C   PRO B 132 "
      ideal   model   delta    sigma   weight residual
     112.47  122.46   -9.99 2.06e+00 2.36e-01 2.35e+01
  angle pdb=" CA  VAL B  22 "
        pdb=" C   VAL B  22 "
        pdb=" N   PRO B  23 "
      ideal   model   delta    sigma   weight residual
     117.00  121.16   -4.16 9.50e-01 1.11e+00 1.91e+01
  angle pdb=" C   VAL B 216 "
        pdb=" N   TYR B 217 "
        pdb=" CA  TYR B 217 "
      ideal   model   delta    sigma   weight residual
     121.86  115.08    6.78 1.58e+00 4.01e-01 1.84e+01
  ... (remaining 16322 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.00: 6617
       14.00 -    28.00: 360
       28.00 -    42.01: 63
       42.01 -    56.01: 9
       56.01 -    70.01: 3
  Dihedral angle restraints: 7052
    sinusoidal: 2701
      harmonic: 4351
  Sorted by residual:
  dihedral pdb=" CA  PRO B 194 "
           pdb=" C   PRO B 194 "
           pdb=" N   GLY B 195 "
           pdb=" CA  GLY B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.61  -26.39     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  VAL C 103 "
           pdb=" C   VAL C 103 "
           pdb=" N   GLY C 104 "
           pdb=" CA  GLY C 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.89   26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  LEU A  64 "
           pdb=" C   LEU A  64 "
           pdb=" N   GLY A  65 "
           pdb=" CA  GLY A  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.75  -25.25     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 7049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1533
       0.089 -    0.178: 289
       0.178 -    0.267: 34
       0.267 -    0.356: 5
       0.356 -    0.445: 1
  Chirality restraints: 1862
  Sorted by residual:
  chirality pdb=" CB  ILE C 226 "
            pdb=" CA  ILE C 226 "
            pdb=" CG1 ILE C 226 "
            pdb=" CG2 ILE C 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CA  PRO B 132 "
            pdb=" N   PRO B 132 "
            pdb=" C   PRO B 132 "
            pdb=" CB  PRO B 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CG  LEU A 206 "
            pdb=" CB  LEU A 206 "
            pdb=" CD1 LEU A 206 "
            pdb=" CD2 LEU A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1859 not shown)

  Planarity restraints: 2135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B  61 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.97e+00
        pdb=" CD  GLN B  61 "    0.049 2.00e-02 2.50e+03
        pdb=" OE1 GLN B  61 "   -0.018 2.00e-02 2.50e+03
        pdb=" NE2 GLN B  61 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 219 "   -0.014 2.00e-02 2.50e+03   2.71e-02 7.35e+00
        pdb=" C   THR B 219 "    0.047 2.00e-02 2.50e+03
        pdb=" O   THR B 219 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PRO B 220 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  52 "   -0.044 5.00e-02 4.00e+02   6.62e-02 7.01e+00
        pdb=" N   PRO B  53 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B  53 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  53 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 2132 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2813
        2.79 -     3.32: 9528
        3.32 -     3.85: 20007
        3.85 -     4.37: 23381
        4.37 -     4.90: 40613
  Nonbonded interactions: 96342
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  52 "
            pdb=" OH  TYR B  99 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OH  TYR B  91 "
            pdb=" O   CYS C 143 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG1 THR A 241 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG  SER A 282 "
            pdb=" OG1 THR B 241 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR B 363 "
            pdb=" OE1 GLU B 407 "
     model   vdw
     2.317 3.040
  ... (remaining 96337 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 30 through 221 or resid 229 through 531))
  selection = (chain 'B' and (resid 30 through 191 or resid 199 through 531))
  selection = (chain 'C' and (resid 30 through 191 or resid 199 through 221 or resid 229 throu \ 
gh 531))
}

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:             8.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     30.820
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6370
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      :  0.014   0.154  11907  Z= 0.552
  Angle     :  1.122  19.136  16327  Z= 0.582
  Chirality :  0.069   0.445   1862
  Planarity :  0.010   0.066   2135
  Dihedral  :  9.314  70.011   4260
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.52 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.18), residues: 1498
  helix: -2.94 (0.38), residues: 58
  sheet: -1.44 (0.23), residues: 427
  loop : -2.14 (0.17), residues: 1013

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP A 102 
 HIS   0.015   0.004   HIS B  94 
 PHE   0.032   0.005   PHE A  80 
 TYR   0.030   0.004   TYR A 186 
 ARG   0.019   0.002   ARG C 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15919 (  325)
  hydrogen bonds       : angle       8.40072 (  939)
  covalent geometry    : bond        0.01372 (11907)
  covalent geometry    : angle       1.12183 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   98 MET cc_start: 0.8881 (ptt) cc_final: 0.8163 (ptp)
  outliers start: 2
  outliers final: 2
  residues processed: 126
  average time/residue: 0.3426
  time to fit residues: 57.2648
Evaluate side-chains
  94 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  103 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:   40.0000
   chunk 113 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 38 optimal weight:   50.0000
   chunk 76 optimal weight:   50.0000
   chunk 60 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 45 optimal weight:   30.0000
   chunk 71 optimal weight:    8.9990
   chunk 87 optimal weight:   50.0000
   chunk 136 optimal weight:    6.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
A 105 ASN
A 170 HIS
A 214 ASN
A 334 GLN
A 340 GLN
B 105 ASN
B 170 HIS
B 265 GLN
B 334 GLN
C 105 ASN
C 170 HIS
** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.217366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.203792 restraints weight = 15004.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 0.71
r_work: 0.4214 rms_B_bonded: 1.38 restraints_weight: 0.5000
r_work: 0.4183 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11907  Z= 0.167
  Angle     :  0.643  11.454  16327  Z= 0.323
  Chirality :  0.047   0.182   1862
  Planarity :  0.007   0.066   2135
  Dihedral  :  5.848  57.030   1628
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  4.72 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.19), residues: 1498
  helix: -1.33 (0.54), residues: 62
  sheet: -1.06 (0.24), residues: 415
  loop : -1.57 (0.18), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 264 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.022   0.002   PHE C  80 
 TYR   0.018   0.002   TYR A 496 
 ARG   0.008   0.001   ARG B 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  325)
  hydrogen bonds       : angle       6.92323 (  939)
  covalent geometry    : bond        0.00391 (11907)
  covalent geometry    : angle       0.64340 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  436 MET cc_start: 0.3545 (mtm) cc_final: 0.2897 (mtm)
REVERT: C   98 MET cc_start: 0.8884 (ptt) cc_final: 0.8289 (ptp)
REVERT: C  469 GLN cc_start: 0.6864 (mt0) cc_final: 0.6643 (mm-40)
  outliers start: 4
  outliers final: 1
  residues processed: 106
  average time/residue: 0.3201
  time to fit residues: 45.9280
Evaluate side-chains
  89 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 100 optimal weight:    0.4980
   chunk 139 optimal weight:   10.0000
   chunk 119 optimal weight:    5.9990
   chunk 94 optimal weight:   50.0000
   chunk 4 optimal weight:    0.6980
   chunk 142 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
B 334 GLN
B 340 GLN
C  50 GLN
C 173 GLN
C 340 GLN
C 493 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.217983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.204453 restraints weight = 15181.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 0.76
r_work: 0.4223 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.4190 rms_B_bonded: 1.97 restraints_weight: 0.2500
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11907  Z= 0.109
  Angle     :  0.565  10.649  16327  Z= 0.280
  Chirality :  0.045   0.150   1862
  Planarity :  0.006   0.053   2135
  Dihedral  :  5.226  54.577   1626
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.68 %
    Favored  : 93.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.20), residues: 1498
  helix: -0.58 (0.58), residues: 62
  sheet: -0.90 (0.24), residues: 400
  loop : -1.23 (0.18), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 264 
 HIS   0.002   0.001   HIS A 270 
 PHE   0.015   0.001   PHE C  80 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.011   0.000   ARG A 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03318 (  325)
  hydrogen bonds       : angle       6.41897 (  939)
  covalent geometry    : bond        0.00249 (11907)
  covalent geometry    : angle       0.56533 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  436 MET cc_start: 0.3675 (mtm) cc_final: 0.3089 (mtm)
  outliers start: 10
  outliers final: 2
  residues processed: 97
  average time/residue: 0.3279
  time to fit residues: 43.0189
Evaluate side-chains
  85 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain C residue  206 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 125 optimal weight:   40.0000
   chunk 40 optimal weight:   50.0000
   chunk 142 optimal weight:   30.0000
   chunk 2 optimal weight:    6.9990
   chunk 63 optimal weight:    8.9990
   chunk 113 optimal weight:    8.9990
   chunk 41 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 24 optimal weight:   30.0000
   chunk 73 optimal weight:   50.0000
   chunk 110 optimal weight:    0.9980
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN
B 109 GLN
** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.215183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.201217 restraints weight = 14979.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.4309 rms_B_bonded: 0.72
r_work: 0.4193 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.4164 rms_B_bonded: 1.76 restraints_weight: 0.2500
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  11907  Z= 0.277
  Angle     :  0.687  11.470  16327  Z= 0.338
  Chirality :  0.050   0.245   1862
  Planarity :  0.006   0.056   2135
  Dihedral  :  5.543  56.807   1626
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.21 %
    Favored  : 91.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.20), residues: 1498
  helix: -0.72 (0.56), residues: 63
  sheet: -0.79 (0.25), residues: 399
  loop : -1.12 (0.18), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 264 
 HIS   0.006   0.002   HIS B  94 
 PHE   0.019   0.002   PHE B 375 
 TYR   0.025   0.002   TYR B 477 
 ARG   0.006   0.001   ARG A 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  325)
  hydrogen bonds       : angle       6.51647 (  939)
  covalent geometry    : bond        0.00679 (11907)
  covalent geometry    : angle       0.68718 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 5
  residues processed: 96
  average time/residue: 0.3290
  time to fit residues: 42.7473
Evaluate side-chains
  86 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  206 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 53 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:   30.0000
   chunk 91 optimal weight:   50.0000
   chunk 110 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 28 optimal weight:   40.0000
   chunk 124 optimal weight:   20.0000
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
C 493 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.217191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.202719 restraints weight = 15026.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 0.82
r_work: 0.4188 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.4154 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11907  Z= 0.116
  Angle     :  0.562  10.969  16327  Z= 0.277
  Chirality :  0.045   0.264   1862
  Planarity :  0.005   0.053   2135
  Dihedral  :  5.105  55.870   1626
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.69 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.20), residues: 1498
  helix: -0.37 (0.58), residues: 63
  sheet: -0.58 (0.25), residues: 380
  loop : -0.99 (0.18), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP B 264 
 HIS   0.002   0.001   HIS B 242 
 PHE   0.019   0.001   PHE B 375 
 TYR   0.017   0.001   TYR B 477 
 ARG   0.005   0.000   ARG B 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03166 (  325)
  hydrogen bonds       : angle       6.27070 (  939)
  covalent geometry    : bond        0.00268 (11907)
  covalent geometry    : angle       0.56226 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  179 MET cc_start: 0.8296 (ttm) cc_final: 0.8032 (tpp)
  outliers start: 13
  outliers final: 8
  residues processed: 96
  average time/residue: 0.3212
  time to fit residues: 41.7466
Evaluate side-chains
  93 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  413 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 81 optimal weight:   50.0000
   chunk 62 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 68 optimal weight:    0.5980
   chunk 35 optimal weight:   40.0000
   chunk 21 optimal weight:   50.0000
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
C 493 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.216141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.203045 restraints weight = 15197.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4328 rms_B_bonded: 0.72
r_work: 0.4206 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.4169 rms_B_bonded: 1.94 restraints_weight: 0.2500
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11907  Z= 0.165
  Angle     :  0.594  10.998  16327  Z= 0.292
  Chirality :  0.046   0.281   1862
  Planarity :  0.006   0.053   2135
  Dihedral  :  5.131  56.694   1626
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.25 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.21), residues: 1498
  helix: -0.29 (0.57), residues: 63
  sheet: -0.55 (0.25), residues: 382
  loop : -0.89 (0.19), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP B 264 
 HIS   0.003   0.001   HIS B 146 
 PHE   0.018   0.002   PHE B 375 
 TYR   0.016   0.001   TYR B 477 
 ARG   0.003   0.000   ARG B 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03236 (  325)
  hydrogen bonds       : angle       6.24339 (  939)
  covalent geometry    : bond        0.00397 (11907)
  covalent geometry    : angle       0.59402 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6160 (mp10)
REVERT: B  179 MET cc_start: 0.8327 (ttm) cc_final: 0.8039 (tpp)
  outliers start: 16
  outliers final: 13
  residues processed: 96
  average time/residue: 0.3078
  time to fit residues: 40.8423
Evaluate side-chains
  95 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  214 ASN
Chi-restraints excluded: chain C residue  488 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:   30.0000
   chunk 110 optimal weight:    0.0980
   chunk 61 optimal weight:    0.7980
   chunk 97 optimal weight:   30.0000
   chunk 6 optimal weight:    0.9990
   chunk 78 optimal weight:   30.0000
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    2.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.216537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.202962 restraints weight = 15295.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.4328 rms_B_bonded: 0.76
r_work: 0.4204 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.4170 rms_B_bonded: 2.05 restraints_weight: 0.2500
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11907  Z= 0.140
  Angle     :  0.569  11.059  16327  Z= 0.280
  Chirality :  0.045   0.323   1862
  Planarity :  0.005   0.050   2135
  Dihedral  :  5.007  56.493   1626
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.73 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.21), residues: 1498
  helix: -0.07 (0.58), residues: 63
  sheet: -0.61 (0.25), residues: 394
  loop : -0.81 (0.19), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP B 264 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.018   0.002   PHE B 375 
 TYR   0.018   0.001   TYR C 501 
 ARG   0.004   0.000   ARG B 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03118 (  325)
  hydrogen bonds       : angle       6.14125 (  939)
  covalent geometry    : bond        0.00334 (11907)
  covalent geometry    : angle       0.56864 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.297 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6201 (mp10)
REVERT: B  179 MET cc_start: 0.8347 (ttm) cc_final: 0.8049 (tpp)
  outliers start: 18
  outliers final: 11
  residues processed: 99
  average time/residue: 0.3209
  time to fit residues: 43.6893
Evaluate side-chains
  95 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  488 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 145 optimal weight:    9.9990
   chunk 128 optimal weight:   50.0000
   chunk 32 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:   50.0000
   chunk 147 optimal weight:   40.0000
   chunk 125 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 173 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.216091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.202422 restraints weight = 15136.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.4321 rms_B_bonded: 0.78
r_work: 0.4193 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.4157 rms_B_bonded: 2.11 restraints_weight: 0.2500
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11907  Z= 0.159
  Angle     :  0.582  11.073  16327  Z= 0.287
  Chirality :  0.046   0.352   1862
  Planarity :  0.005   0.050   2135
  Dihedral  :  5.021  56.873   1626
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.05 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.21), residues: 1498
  helix:  0.01 (0.59), residues: 63
  sheet: -0.55 (0.25), residues: 389
  loop : -0.78 (0.19), residues: 1046

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.002   TRP B 264 
 HIS   0.003   0.001   HIS B 146 
 PHE   0.015   0.002   PHE C 117 
 TYR   0.017   0.001   TYR C 501 
 ARG   0.003   0.000   ARG C 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03143 (  325)
  hydrogen bonds       : angle       6.10384 (  939)
  covalent geometry    : bond        0.00383 (11907)
  covalent geometry    : angle       0.58208 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6210 (mp10)
REVERT: B  179 MET cc_start: 0.8362 (ttm) cc_final: 0.8058 (tpp)
REVERT: C  173 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7162 (mm110)
REVERT: C  184 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8054 (ptp)
  outliers start: 19
  outliers final: 12
  residues processed: 98
  average time/residue: 0.3190
  time to fit residues: 42.3738
Evaluate side-chains
  100 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  173 GLN
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  214 ASN
Chi-restraints excluded: chain C residue  488 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 71 optimal weight:   20.0000
   chunk 124 optimal weight:   20.0000
   chunk 49 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 110 optimal weight:    0.7980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
C  33 GLN
C 173 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.217331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.202683 restraints weight = 15177.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.4321 rms_B_bonded: 0.80
r_work: 0.4194 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.4162 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11907  Z= 0.103
  Angle     :  0.544  10.960  16327  Z= 0.269
  Chirality :  0.044   0.259   1862
  Planarity :  0.005   0.051   2135
  Dihedral  :  4.838  55.905   1626
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.13 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.21), residues: 1498
  helix:  0.17 (0.61), residues: 63
  sheet: -0.51 (0.25), residues: 387
  loop : -0.73 (0.19), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP B 264 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.012   0.001   PHE B  80 
 TYR   0.015   0.001   TYR C 501 
 ARG   0.006   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03085 (  325)
  hydrogen bonds       : angle       6.05443 (  939)
  covalent geometry    : bond        0.00236 (11907)
  covalent geometry    : angle       0.54434 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6179 (mp10)
REVERT: B  179 MET cc_start: 0.8337 (ttm) cc_final: 0.8050 (tpp)
REVERT: C  184 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (ptp)
  outliers start: 17
  outliers final: 10
  residues processed: 95
  average time/residue: 0.3150
  time to fit residues: 40.5563
Evaluate side-chains
  98 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  117 PHE
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  214 ASN
Chi-restraints excluded: chain C residue  488 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 95 optimal weight:   30.0000
   chunk 97 optimal weight:    0.6980
   chunk 118 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 129 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 109 GLN
C  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.216254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.202527 restraints weight = 15060.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4321 rms_B_bonded: 0.76
r_work: 0.4198 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.4160 rms_B_bonded: 2.13 restraints_weight: 0.2500
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6539
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11907  Z= 0.155
  Angle     :  0.578  10.904  16327  Z= 0.285
  Chirality :  0.046   0.309   1862
  Planarity :  0.005   0.050   2135
  Dihedral  :  4.943  56.750   1626
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.69 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.21), residues: 1498
  helix:  0.14 (0.60), residues: 63
  sheet: -0.50 (0.25), residues: 389
  loop : -0.71 (0.19), residues: 1046

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 264 
 HIS   0.003   0.001   HIS B 146 
 PHE   0.014   0.002   PHE C 117 
 TYR   0.024   0.001   TYR A 328 
 ARG   0.006   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  325)
  hydrogen bonds       : angle       6.08837 (  939)
  covalent geometry    : bond        0.00373 (11907)
  covalent geometry    : angle       0.57833 (16327)

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

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

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2996 Ramachandran restraints generated.
    1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6212 (mp10)
REVERT: B  179 MET cc_start: 0.8377 (ttm) cc_final: 0.8063 (tpp)
REVERT: C  184 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8060 (ptp)
  outliers start: 12
  outliers final: 9
  residues processed: 92
  average time/residue: 0.3115
  time to fit residues: 38.7462
Evaluate side-chains
  95 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain C residue  214 ASN
Chi-restraints excluded: chain C residue  488 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 35 optimal weight:   30.0000
   chunk 139 optimal weight:   40.0000
   chunk 24 optimal weight:   50.0000
   chunk 114 optimal weight:    0.0270
   chunk 137 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 126 optimal weight:    8.9990
   overall best weight:    5.0046

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

Flipped N/Q/H residues before XYZ refinement:
B 334 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.215595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.201693 restraints weight = 15110.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.4311 rms_B_bonded: 0.80
r_work: 0.4182 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.4143 rms_B_bonded: 2.16 restraints_weight: 0.2500
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11907  Z= 0.202
  Angle     :  0.623  11.192  16327  Z= 0.306
  Chirality :  0.047   0.338   1862
  Planarity :  0.005   0.047   2135
  Dihedral  :  5.114  57.079   1626
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.61 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.51 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.21), residues: 1498
  helix:  0.03 (0.60), residues: 63
  sheet: -0.46 (0.26), residues: 390
  loop : -0.71 (0.19), residues: 1045

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B 264 
 HIS   0.003   0.001   HIS B  94 
 PHE   0.016   0.002   PHE A 117 
 TYR   0.016   0.002   TYR A 328 
 ARG   0.008   0.000   ARG C 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03402 (  325)
  hydrogen bonds       : angle       6.20157 (  939)
  covalent geometry    : bond        0.00491 (11907)
  covalent geometry    : angle       0.62311 (16327)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7633.86 seconds
wall clock time: 134 minutes 31.89 seconds (8071.89 seconds total)