Starting phenix.real_space_refine
on Wed May 14 12:21:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eaq_47840/05_2025/9eaq_47840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eaq_47840/05_2025/9eaq_47840.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eaq_47840/05_2025/9eaq_47840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eaq_47840/05_2025/9eaq_47840.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eaq_47840/05_2025/9eaq_47840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eaq_47840/05_2025/9eaq_47840.cif"
  }
  resolution = 2.7
  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=   0.005 sd=   0.189
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    7604      2.51       5
     N    1942      2.21       5
     O    2205      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11799
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      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: "B"
      Number of atoms: 3963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 3963
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 470}
    Chain: "C"
      Number of atoms: 3883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3883
          Classifications: {'peptide': 504}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459}
  Time building chain proxies: 9.69, per 1000 atoms: 0.82
  Number of scatterers: 11799
  At special positions: 0
  Unit cell: (118.8, 117.7, 123.2, 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    2205      8.00
     N    1942      7.00
     C    7604      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: 2.71
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2842

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 19 sheets defined
      9.8% alpha, 35.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.550A  pdb=" N   ALA A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 58
      removed outlier: 3.995A  pdb=" N   ASN A  58 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 88
      removed outlier: 3.537A  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 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: 3.792A  pdb=" N   PHE A 144 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 240
      removed outlier: 3.520A  pdb=" N   CYS A 240 " --> pdb=" O   PRO A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 372
    Processing helix  chain 'B' and resid 41 through 45
    Processing helix  chain 'B' and resid 52 through 58
      removed outlier: 4.076A  pdb=" N   ASN B  58 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 88
      removed outlier: 3.525A  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 140 through 144
      removed outlier: 3.560A  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: 3.693A  pdb=" N   TRP B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
      removed outlier: 3.798A  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 454 through 465
    Processing helix  chain 'C' and resid 37 through 42
      removed outlier: 3.612A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 52 through 58
      removed outlier: 3.632A  pdb=" N   GLN C  57 " --> pdb=" O   TRP C  54 " (cutoff:3.500A)
      removed outlier: 3.777A  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: 4.014A  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: 3.519A  pdb=" N   TRP C 285 " --> pdb=" O   SER C 282 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL C 286 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 282 through 286'
    Processing helix  chain 'C' and resid 454 through 465
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69
      removed outlier: 12.550A  pdb=" N   GLN A  61 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
      removed outlier: 10.790A  pdb=" N   SER A 207 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A 202 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   ASN A 105 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP A 212 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   VAL A 103 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ASN A 214 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLY A 101 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69
      removed outlier: 12.550A  pdb=" N   GLN A  61 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
      removed outlier: 10.790A  pdb=" N   SER A 207 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A 202 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   ASN A 105 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP A 212 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   VAL A 103 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ASN A 214 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLY A 101 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83
      removed outlier: 6.829A  pdb=" N   CYS A 183 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASP A  81 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   LEU A 181 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LYS A 121 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   ALA A 119 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451
      removed outlier: 4.412A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 509 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451
      removed outlier: 5.212A  pdb=" N   ILE A 497 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR A 496 " --> pdb=" O   TYR A 492 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   SER A 500 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ALA A 472 " --> pdb=" O   TRP A 520 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   TRP A 520 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU A 474 " --> pdb=" O   VAL A 518 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296
      removed outlier: 4.144A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   GLU A 303 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 7.029A  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: 6.338A  pdb=" N   SER A 332 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY A 400 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   GLN A 334 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ILE A 398 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   GLU A 336 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL A 394 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLN A 340 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   ARG A 392 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY A 389 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69
      removed outlier: 12.826A  pdb=" N   GLN B  61 " --> pdb=" O   PRO B 209 " (cutoff:3.500A)
      removed outlier: 11.183A  pdb=" N   SER B 207 " --> pdb=" O   PRO B  63 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   GLY B  65 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83
      removed outlier: 6.937A  pdb=" N   ILE B  78 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LEU B 185 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE B  80 " --> pdb=" O   CYS B 183 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS B 121 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ALA B 119 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 103
      removed outlier: 6.335A  pdb=" N   TYR B  99 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU B 218 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   GLY B 101 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 448 through 451
      removed outlier: 4.241A  pdb=" N   LEU B 252 " --> pdb=" O   PHE B 509 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 448 through 451
      removed outlier: 5.339A  pdb=" N   ILE B 497 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   SER B 500 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   GLU B 488 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   GLU B 488 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU B 475 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LYS B 490 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LEU B 473 " --> pdb=" O   LYS B 490 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ALA B 472 " --> pdb=" O   TRP B 520 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   TRP B 520 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU B 474 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 358
      removed outlier: 4.538A  pdb=" N   GLN B 334 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   GLY B 400 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   GLU B 336 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   ILE B 398 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   GLU B 338 " --> pdb=" O   ARG B 396 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   ARG B 396 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   GLN B 340 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 10.587A  pdb=" N   VAL B 394 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 11.821A  pdb=" N   GLU B 342 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 13.258A  pdb=" N   ARG B 392 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ALA B 290 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.692A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 9.641A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ASN C 105 " --> pdb=" O   ALA C 210 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ASP C 212 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   VAL C 103 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ASN C 214 " --> pdb=" O   GLY C 101 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLY C 101 " --> pdb=" O   ASN C 214 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.692A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 9.641A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ASN C 105 " --> pdb=" O   ALA C 210 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ASP C 212 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   VAL C 103 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ASN C 214 " --> pdb=" O   GLY C 101 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLY C 101 " --> pdb=" O   ASN C 214 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 83
      removed outlier: 6.725A  pdb=" N   ILE C  78 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU C 185 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   LYS C 121 " --> pdb=" O   TYR C 186 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 449 through 451
      removed outlier: 3.510A  pdb=" N   GLY C 251 " --> pdb=" O   ARG C 433 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU C 252 " --> pdb=" O   PHE C 509 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 351 through 358
      removed outlier: 3.819A  pdb=" N   THR C 353 " --> pdb=" O   ILE C 339 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE C 339 " --> pdb=" O   THR C 353 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   GLN C 334 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   GLY C 400 " --> pdb=" O   GLN C 334 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLU C 336 " --> pdb=" O   ILE C 398 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ILE C 398 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 8.800A  pdb=" N   GLU C 338 " --> pdb=" O   ARG C 396 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ARG C 396 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 9.625A  pdb=" N   GLN C 340 " --> pdb=" O   VAL C 394 " (cutoff:3.500A)
      removed outlier: 10.712A  pdb=" N   VAL C 394 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ALA C 290 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 427 through 429
      removed outlier: 3.768A  pdb=" N   ALA C 472 " --> pdb=" O   VAL C 521 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 485 through 487
      removed outlier: 7.161A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    852 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: 3.77

  Time building geometry restraints manager: 3.21 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: 3845
        1.34 -     1.46: 2510
        1.46 -     1.58: 5698
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 12125
  Sorted by residual:
  bond pdb=" CB  PRO B  23 "
       pdb=" CG  PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.492  1.566 -0.074 5.00e-02 4.00e+02 2.20e+00
  bond pdb=" CA  ASP B 174 "
       pdb=" CB  ASP B 174 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.021 1.69e-02 3.50e+03 1.59e+00
  bond pdb=" CG  PRO B  23 "
       pdb=" CD  PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.503  1.546 -0.043 3.40e-02 8.65e+02 1.57e+00
  bond pdb=" CB  ASP B 174 "
       pdb=" CG  ASP B 174 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.13e+00
  bond pdb=" C   VAL B  22 "
       pdb=" N   PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.12e+00
  ... (remaining 12120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 16580
        3.27 -     6.53: 42
        6.53 -     9.80: 2
        9.80 -    13.06: 1
       13.06 -    16.33: 1
  Bond angle restraints: 16626
  Sorted by residual:
  angle pdb=" CA  LEU B  64 "
        pdb=" CB  LEU B  64 "
        pdb=" CG  LEU B  64 "
      ideal   model   delta    sigma   weight residual
     116.30  132.63  -16.33 3.50e+00 8.16e-02 2.18e+01
  angle pdb=" CA  PRO B  23 "
        pdb=" N   PRO B  23 "
        pdb=" CD  PRO B  23 "
      ideal   model   delta    sigma   weight residual
     112.00  106.50    5.50 1.40e+00 5.10e-01 1.54e+01
  angle pdb=" CA  LEU B 112 "
        pdb=" CB  LEU B 112 "
        pdb=" CG  LEU B 112 "
      ideal   model   delta    sigma   weight residual
     116.30  127.60  -11.30 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" C   GLN B 173 "
        pdb=" N   ASP B 174 "
        pdb=" CA  ASP B 174 "
      ideal   model   delta    sigma   weight residual
     121.54  126.48   -4.94 1.91e+00 2.74e-01 6.70e+00
  angle pdb=" N   PRO B  23 "
        pdb=" CA  PRO B  23 "
        pdb=" C   PRO B  23 "
      ideal   model   delta    sigma   weight residual
     112.47  117.60   -5.13 2.06e+00 2.36e-01 6.20e+00
  ... (remaining 16621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 6143
       17.29 -    34.58: 746
       34.58 -    51.87: 212
       51.87 -    69.16: 72
       69.16 -    86.45: 20
  Dihedral angle restraints: 7193
    sinusoidal: 2762
      harmonic: 4431
  Sorted by residual:
  dihedral pdb=" CA  GLY B 195 "
           pdb=" C   GLY B 195 "
           pdb=" N   ASP B 196 "
           pdb=" CA  ASP B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.96   33.04     0      5.00e+00 4.00e-02 4.37e+01
  dihedral pdb=" CA  VAL B  22 "
           pdb=" C   VAL B  22 "
           pdb=" N   PRO B  23 "
           pdb=" CA  PRO B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.04  -24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  GLY A 421 "
           pdb=" C   GLY A 421 "
           pdb=" N   PRO A 422 "
           pdb=" CA  PRO A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -24.55   24.55     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 7190 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1445
       0.044 -    0.088: 287
       0.088 -    0.133: 158
       0.133 -    0.177: 1
       0.177 -    0.221: 1
  Chirality restraints: 1892
  Sorted by residual:
  chirality pdb=" CA  PRO B  23 "
            pdb=" N   PRO B  23 "
            pdb=" C   PRO B  23 "
            pdb=" CB  PRO B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CG  LEU B  64 "
            pdb=" CB  LEU B  64 "
            pdb=" CD1 LEU B  64 "
            pdb=" CD2 LEU B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  ILE A 157 "
            pdb=" N   ILE A 157 "
            pdb=" C   ILE A 157 "
            pdb=" CB  ILE A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1889 not shown)

  Planarity restraints: 2178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  22 "   -0.091 5.00e-02 4.00e+02   1.37e-01 3.01e+01
        pdb=" N   PRO B  23 "    0.237 5.00e-02 4.00e+02
        pdb=" CA  PRO B  23 "   -0.074 5.00e-02 4.00e+02
        pdb=" CD  PRO B  23 "   -0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 196 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.69e+00
        pdb=" CG  ASP B 196 "   -0.041 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 196 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 196 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 128 "   -0.037 5.00e-02 4.00e+02   5.67e-02 5.15e+00
        pdb=" N   PRO C 129 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 2175 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3017
        2.80 -     3.33: 9250
        3.33 -     3.85: 18218
        3.85 -     4.38: 21308
        4.38 -     4.90: 37830
  Nonbonded interactions: 89623
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 224 "
            pdb=" O   SER A 463 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OH  TYR A 501 "
            pdb=" O   GLY A 505 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASP C 150 "
            pdb=" OG1 THR C 153 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   ASP A 150 "
            pdb=" OG1 THR A 153 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" NH1 ARG C 244 "
            pdb=" OD1 ASP C 330 "
     model   vdw
     2.384 3.120
  ... (remaining 89618 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 27 through 530)
  selection = (chain 'B' and resid 27 through 530)
  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:             16.160
  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:          0.480
  Check model and map are aligned:         0.110
  Set scattering table:                    0.110
  Process input model:                     31.350
  Find NCS groups from input model:        0.670
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:17.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
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   0.074  12125  Z= 0.103
  Angle     :  0.572  16.328  16626  Z= 0.289
  Chirality :  0.044   0.221   1892
  Planarity :  0.006   0.137   2178
  Dihedral  : 17.465  86.445   4351
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.84 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 24.29 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.20), residues: 1529
  helix: -0.06 (0.70), residues: 51
  sheet:  0.30 (0.23), residues: 458
  loop : -1.00 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 270 
 PHE   0.020   0.001   PHE C  80 
 TYR   0.012   0.001   TYR C 496 
 ARG   0.002   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16964 (  304)
  hydrogen bonds       : angle       7.85689 (  852)
  covalent geometry    : bond        0.00233 (12125)
  covalent geometry    : angle       0.57190 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 108
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A  437 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.5385 (ttt-90)
REVERT: B  310 ILE cc_start: 0.5471 (OUTLIER) cc_final: 0.5182 (pp)
REVERT: C  523 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7527 (ttm170)
  outliers start: 52
  outliers final: 45
  residues processed: 159
  average time/residue: 1.1049
  time to fit residues: 192.1471
Evaluate side-chains
  150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  166 ARG
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  451 CYS
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  149 CYS
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  299 SER
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  388 ASP
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 77 optimal weight:   30.0000
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 88 optimal weight:    0.4980
   chunk 138 optimal weight:   10.0000
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 270 HIS
A 469 GLN
A 493 ASN
B 340 GLN
B 438 GLN
C 261 ASN
C 263 GLN
C 265 GLN
C 270 HIS
C 493 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.223392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.130196 restraints weight = 10765.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 11.46
r_work: 0.2783 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.0621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12125  Z= 0.132
  Angle     :  0.619  13.476  16626  Z= 0.313
  Chirality :  0.045   0.226   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  7.651  69.419   1723
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.30 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 22.80 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.20), residues: 1529
  helix: -0.56 (0.64), residues: 52
  sheet:  0.31 (0.23), residues: 436
  loop : -1.01 (0.18), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 270 
 PHE   0.021   0.001   PHE C  80 
 TYR   0.016   0.001   TYR A 217 
 ARG   0.002   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  304)
  hydrogen bonds       : angle       6.06386 (  852)
  covalent geometry    : bond        0.00322 (12125)
  covalent geometry    : angle       0.61900 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 104
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A  437 ARG cc_start: 0.5866 (mtm-85) cc_final: 0.3237 (ttt-90)
REVERT: A  501 TYR cc_start: 0.6636 (t80) cc_final: 0.6381 (t80)
REVERT: B  175 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7561 (mp10)
REVERT: B  516 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6090 (mp0)
REVERT: C  476 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5878 (ttp-170)
REVERT: C  523 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7079 (ttm170)
  outliers start: 58
  outliers final: 30
  residues processed: 151
  average time/residue: 1.1683
  time to fit residues: 192.5208
Evaluate side-chains
  133 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  476 ARG
Chi-restraints excluded: chain C residue  480 THR
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 116 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 148 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   chunk 29 optimal weight:   40.0000
   chunk 72 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 136 optimal weight:   40.0000
   chunk 28 optimal weight:   30.0000
   chunk 109 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   overall best weight:    5.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
B 438 GLN
** C 263 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.221349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.151141 restraints weight = 10730.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 4.79
r_work: 0.2768 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  12125  Z= 0.206
  Angle     :  0.712  14.371  16626  Z= 0.362
  Chirality :  0.049   0.240   1892
  Planarity :  0.007   0.139   2178
  Dihedral  :  7.058  58.722   1684
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.69 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 21.93 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.20), residues: 1529
  helix: -1.31 (0.61), residues: 52
  sheet:  0.24 (0.24), residues: 438
  loop : -1.11 (0.18), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A  94 
 PHE   0.019   0.002   PHE C  80 
 TYR   0.023   0.002   TYR A 217 
 ARG   0.005   0.000   ARG B 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04330 (  304)
  hydrogen bonds       : angle       6.00972 (  852)
  covalent geometry    : bond        0.00518 (12125)
  covalent geometry    : angle       0.71180 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 97
  time to evaluate  : 1.448 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8283 (m)
REVERT: A  349 LYS cc_start: 0.4342 (OUTLIER) cc_final: 0.2854 (pttp)
REVERT: A  501 TYR cc_start: 0.6913 (t80) cc_final: 0.6667 (t80)
REVERT: B  175 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7546 (mp10)
REVERT: B  371 GLN cc_start: 0.4127 (OUTLIER) cc_final: 0.3818 (pm20)
REVERT: B  516 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6356 (mp0)
REVERT: C  238 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6263 (ptp90)
REVERT: C  523 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7164 (ttm170)
  outliers start: 67
  outliers final: 39
  residues processed: 153
  average time/residue: 1.1302
  time to fit residues: 189.1242
Evaluate side-chains
  140 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 95
  time to evaluate  : 2.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  371 GLN
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  238 ARG
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  394 VAL
Chi-restraints excluded: chain C residue  404 THR
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  480 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 151 optimal weight:   20.0000
   chunk 59 optimal weight:    0.8980
   chunk 137 optimal weight:   50.0000
   chunk 72 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 84 optimal weight:    0.2980
   chunk 104 optimal weight:    0.8980
   chunk 7 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 438 GLN
C 270 HIS
C 464 ASN
C 493 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.224842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.152941 restraints weight = 10795.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 5.30
r_work: 0.2814 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.0833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.079  12125  Z= 0.095
  Angle     :  0.565  14.494  16626  Z= 0.284
  Chirality :  0.044   0.222   1892
  Planarity :  0.006   0.137   2178
  Dihedral  :  6.201  57.560   1678
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.84 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.51 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.20), residues: 1529
  helix: -0.76 (0.62), residues: 52
  sheet:  0.20 (0.23), residues: 443
  loop : -0.97 (0.18), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.001   0.001   HIS A  94 
 PHE   0.023   0.001   PHE C  80 
 TYR   0.010   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03076 (  304)
  hydrogen bonds       : angle       5.61975 (  852)
  covalent geometry    : bond        0.00226 (12125)
  covalent geometry    : angle       0.56499 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 108
  time to evaluate  : 1.316 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4261 (OUTLIER) cc_final: 0.2907 (pttp)
REVERT: A  501 TYR cc_start: 0.6881 (t80) cc_final: 0.6604 (t80)
REVERT: B  175 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7328 (mp10)
REVERT: B  371 GLN cc_start: 0.4218 (OUTLIER) cc_final: 0.3991 (pm20)
REVERT: C  317 TYR cc_start: 0.7361 (t80) cc_final: 0.7039 (t80)
REVERT: C  336 GLU cc_start: 0.5984 (mp0) cc_final: 0.5698 (mp0)
REVERT: C  397 SER cc_start: 0.7407 (OUTLIER) cc_final: 0.7071 (t)
REVERT: C  412 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6489 (pp)
REVERT: C  523 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7143 (ttm170)
  outliers start: 48
  outliers final: 25
  residues processed: 151
  average time/residue: 1.1443
  time to fit residues: 188.5883
Evaluate side-chains
  136 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  350 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  371 GLN
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  397 SER
Chi-restraints excluded: chain C residue  412 LEU
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  480 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 141 optimal weight:    3.9990
   chunk 81 optimal weight:    0.1980
   chunk 42 optimal weight:   40.0000
   chunk 50 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:   40.0000
   chunk 74 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   overall best weight:    3.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
B 438 GLN
C 270 HIS
C 493 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.222617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.130854 restraints weight = 10666.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 10.07
r_work: 0.2769 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
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      :  0.003   0.080  12125  Z= 0.139
  Angle     :  0.624  14.921  16626  Z= 0.314
  Chirality :  0.046   0.233   1892
  Planarity :  0.006   0.137   2178
  Dihedral  :  6.242  57.899   1674
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.30 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.06 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.20), residues: 1529
  helix: -0.87 (0.63), residues: 52
  sheet:  0.26 (0.24), residues: 438
  loop : -1.00 (0.18), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.018   0.002   PHE C  80 
 TYR   0.016   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (  304)
  hydrogen bonds       : angle       5.64063 (  852)
  covalent geometry    : bond        0.00343 (12125)
  covalent geometry    : angle       0.62355 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 109
  time to evaluate  : 1.198 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4313 (OUTLIER) cc_final: 0.2913 (pttm)
REVERT: A  437 ARG cc_start: 0.5745 (mtm-85) cc_final: 0.5093 (ptt90)
REVERT: A  501 TYR cc_start: 0.6805 (t80) cc_final: 0.6507 (t80)
REVERT: B   21 LEU cc_start: 0.8146 (mt) cc_final: 0.7448 (mt)
REVERT: B  175 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7327 (mp10)
REVERT: B  371 GLN cc_start: 0.3969 (OUTLIER) cc_final: 0.3709 (pm20)
REVERT: B  512 ASP cc_start: 0.7880 (m-30) cc_final: 0.7208 (m-30)
REVERT: C  412 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6384 (pp)
  outliers start: 46
  outliers final: 32
  residues processed: 148
  average time/residue: 1.1528
  time to fit residues: 185.8586
Evaluate side-chains
  140 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  371 GLN
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  412 LEU
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  480 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 149 optimal weight:   30.0000
   chunk 39 optimal weight:   40.0000
   chunk 141 optimal weight:    0.3980
   chunk 106 optimal weight:    9.9990
   chunk 31 optimal weight:   50.0000
   chunk 42 optimal weight:    0.0070
   chunk 50 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 84 optimal weight:   30.0000
   chunk 150 optimal weight:    5.9990
   overall best weight:    4.0804

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
B 438 GLN
C 270 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.222107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.139272 restraints weight = 10799.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 6.77
r_work: 0.2761 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  12125  Z= 0.163
  Angle     :  0.660  15.761  16626  Z= 0.333
  Chirality :  0.047   0.239   1892
  Planarity :  0.007   0.139   2178
  Dihedral  :  6.349  58.288   1672
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.56 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 23.35 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.20), residues: 1529
  helix: -1.08 (0.63), residues: 52
  sheet:  0.29 (0.24), residues: 436
  loop : -1.05 (0.18), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A  94 
 PHE   0.018   0.002   PHE C  80 
 TYR   0.022   0.002   TYR A 217 
 ARG   0.008   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  304)
  hydrogen bonds       : angle       5.65949 (  852)
  covalent geometry    : bond        0.00404 (12125)
  covalent geometry    : angle       0.65991 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 102
  time to evaluate  : 1.349 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4074 (OUTLIER) cc_final: 0.2693 (pttm)
REVERT: A  501 TYR cc_start: 0.6858 (t80) cc_final: 0.6537 (t80)
REVERT: B   21 LEU cc_start: 0.8139 (mt) cc_final: 0.7243 (mt)
REVERT: B  175 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7286 (mp10)
REVERT: B  228 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6242 (ttt180)
REVERT: B  371 GLN cc_start: 0.4205 (OUTLIER) cc_final: 0.3874 (pm20)
REVERT: B  516 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6108 (mp0)
REVERT: C  238 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6139 (ptp90)
REVERT: C  412 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6465 (pp)
REVERT: C  523 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.7201 (ttm170)
  outliers start: 57
  outliers final: 36
  residues processed: 150
  average time/residue: 1.1490
  time to fit residues: 189.1742
Evaluate side-chains
  142 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 99
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ARG
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  371 GLN
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  238 ARG
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  412 LEU
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  480 THR
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    0.0020
   chunk 54 optimal weight:    0.6980
   chunk 134 optimal weight:   40.0000
   chunk 28 optimal weight:    9.9990
   chunk 67 optimal weight:    0.2980
   chunk 77 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 29 optimal weight:   40.0000
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 214 ASN
A 493 ASN
B 438 GLN
C 270 HIS
C 493 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.225024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.157773 restraints weight = 10925.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 4.72
r_work: 0.2849 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.076  12125  Z= 0.093
  Angle     :  0.560  15.570  16626  Z= 0.280
  Chirality :  0.044   0.225   1892
  Planarity :  0.006   0.137   2178
  Dihedral  :  5.804  58.871   1672
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.84 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 25.31 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.20), residues: 1529
  helix: -0.50 (0.64), residues: 52
  sheet:  0.28 (0.24), residues: 441
  loop : -0.90 (0.19), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.001   0.000   HIS C 170 
 PHE   0.023   0.001   PHE C  80 
 TYR   0.014   0.001   TYR A 496 
 ARG   0.005   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02849 (  304)
  hydrogen bonds       : angle       5.35366 (  852)
  covalent geometry    : bond        0.00224 (12125)
  covalent geometry    : angle       0.56043 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 114
  time to evaluate  : 1.360 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4153 (OUTLIER) cc_final: 0.2951 (pttm)
REVERT: A  437 ARG cc_start: 0.5994 (mtm-85) cc_final: 0.5369 (ptt90)
REVERT: A  501 TYR cc_start: 0.7025 (t80) cc_final: 0.6686 (t80)
REVERT: B   21 LEU cc_start: 0.7982 (mt) cc_final: 0.7415 (mt)
REVERT: B  175 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7224 (mp10)
REVERT: B  371 GLN cc_start: 0.4238 (OUTLIER) cc_final: 0.3912 (pm20)
REVERT: C  317 TYR cc_start: 0.7485 (t80) cc_final: 0.7193 (t80)
REVERT: C  523 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7215 (ttm170)
  outliers start: 36
  outliers final: 23
  residues processed: 143
  average time/residue: 1.2588
  time to fit residues: 195.6781
Evaluate side-chains
  137 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  371 GLN
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  480 THR
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 112 optimal weight:    4.9990
   chunk 126 optimal weight:    8.9990
   chunk 98 optimal weight:   20.0000
   chunk 128 optimal weight:   50.0000
   chunk 47 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0670
   chunk 40 optimal weight:   20.0000
   chunk 38 optimal weight:   30.0000
   overall best weight:    4.7524

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
B 438 GLN
C 270 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.221821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.152554 restraints weight = 10811.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 5.00
r_work: 0.2752 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  12125  Z= 0.182
  Angle     :  0.683  15.826  16626  Z= 0.345
  Chirality :  0.048   0.241   1892
  Planarity :  0.007   0.139   2178
  Dihedral  :  6.116  56.660   1669
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.30 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 24.14 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.20), residues: 1529
  helix: -1.01 (0.62), residues: 52
  sheet:  0.28 (0.24), residues: 436
  loop : -1.01 (0.18), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 102 
 HIS   0.004   0.001   HIS A  94 
 PHE   0.016   0.002   PHE C  80 
 TYR   0.023   0.002   TYR A 217 
 ARG   0.005   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  304)
  hydrogen bonds       : angle       5.60429 (  852)
  covalent geometry    : bond        0.00455 (12125)
  covalent geometry    : angle       0.68339 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 103
  time to evaluate  : 1.521 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8495 (mt)
REVERT: A  349 LYS cc_start: 0.4226 (OUTLIER) cc_final: 0.2854 (pttm)
REVERT: A  437 ARG cc_start: 0.5851 (mtm-85) cc_final: 0.5220 (ptt90)
REVERT: A  501 TYR cc_start: 0.6930 (t80) cc_final: 0.6623 (t80)
REVERT: B   21 LEU cc_start: 0.8221 (mt) cc_final: 0.7421 (mt)
REVERT: B  175 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7216 (mp10)
REVERT: B  516 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6326 (mp0)
REVERT: C  523 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7235 (ttm170)
  outliers start: 47
  outliers final: 28
  residues processed: 141
  average time/residue: 1.1939
  time to fit residues: 183.3363
Evaluate side-chains
  134 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 89 optimal weight:   30.0000
   chunk 142 optimal weight:   20.0000
   chunk 132 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9990
   chunk 135 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 151 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN
B 438 GLN
C 270 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.223872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.156815 restraints weight = 10780.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 4.66
r_work: 0.2814 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12125  Z= 0.106
  Angle     :  0.589  16.332  16626  Z= 0.295
  Chirality :  0.045   0.232   1892
  Planarity :  0.006   0.137   2178
  Dihedral  :  5.748  56.988   1669
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.10 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.00 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.20), residues: 1529
  helix: -0.77 (0.63), residues: 52
  sheet:  0.30 (0.24), residues: 437
  loop : -0.97 (0.19), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.023   0.001   PHE C  80 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.005   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03104 (  304)
  hydrogen bonds       : angle       5.42239 (  852)
  covalent geometry    : bond        0.00258 (12125)
  covalent geometry    : angle       0.58921 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 1.179 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4129 (OUTLIER) cc_final: 0.2899 (pttm)
REVERT: A  437 ARG cc_start: 0.5953 (mtm-85) cc_final: 0.5314 (ptt90)
REVERT: A  501 TYR cc_start: 0.7057 (t80) cc_final: 0.6709 (t80)
REVERT: B   21 LEU cc_start: 0.8075 (mt) cc_final: 0.7382 (mt)
REVERT: B  142 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8437 (m)
REVERT: B  175 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7202 (mp10)
REVERT: C  523 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7225 (ttm170)
  outliers start: 35
  outliers final: 24
  residues processed: 138
  average time/residue: 1.2531
  time to fit residues: 187.3813
Evaluate side-chains
  135 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 125 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 96 optimal weight:    8.9990
   chunk 98 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 124 optimal weight:    5.9990
   chunk 123 optimal weight:    0.9980
   chunk 29 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 438 GLN
C 270 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.222931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.153995 restraints weight = 10724.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 4.83
r_work: 0.2803 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  12125  Z= 0.134
  Angle     :  0.624  15.674  16626  Z= 0.313
  Chirality :  0.046   0.236   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  5.860  56.875   1669
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.43 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.00 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.20), residues: 1529
  helix: -0.85 (0.63), residues: 52
  sheet:  0.31 (0.24), residues: 435
  loop : -0.99 (0.19), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.018   0.001   PHE C  80 
 TYR   0.018   0.001   TYR A 496 
 ARG   0.005   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03411 (  304)
  hydrogen bonds       : angle       5.45044 (  852)
  covalent geometry    : bond        0.00329 (12125)
  covalent geometry    : angle       0.62439 (16626)

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

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

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3058 Ramachandran restraints generated.
    1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 1.317 
Fit side-chains
REVERT: A  311 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6944 (mm-30)
REVERT: A  349 LYS cc_start: 0.3864 (OUTLIER) cc_final: 0.2716 (pttm)
REVERT: A  437 ARG cc_start: 0.5924 (mtm-85) cc_final: 0.5277 (ptt90)
REVERT: A  501 TYR cc_start: 0.6987 (t80) cc_final: 0.6643 (t80)
REVERT: B   21 LEU cc_start: 0.8149 (mt) cc_final: 0.7431 (mt)
REVERT: B  142 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8416 (m)
REVERT: B  175 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7261 (mp10)
REVERT: C  523 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7232 (ttm170)
  outliers start: 35
  outliers final: 26
  residues processed: 139
  average time/residue: 1.2549
  time to fit residues: 189.1694
Evaluate side-chains
  138 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  530 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 115 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:   40.0000
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 118 optimal weight:    0.0030
   chunk 126 optimal weight:   30.0000
   chunk 11 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 137 optimal weight:    0.0870
   overall best weight:    1.7972

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

Flipped N/Q/H residues before XYZ refinement:
B 438 GLN
C 270 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.224085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.160400 restraints weight = 10716.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 4.34
r_work: 0.2811 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12125  Z= 0.106
  Angle     :  0.589  16.635  16626  Z= 0.294
  Chirality :  0.045   0.228   1892
  Planarity :  0.006   0.137   2178
  Dihedral  :  5.656  57.113   1669
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.17 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 24.92 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.20), residues: 1529
  helix: -0.67 (0.63), residues: 52
  sheet:  0.31 (0.24), residues: 437
  loop : -0.94 (0.19), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS C 170 
 PHE   0.022   0.001   PHE C  80 
 TYR   0.017   0.001   TYR A 496 
 ARG   0.005   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03078 (  304)
  hydrogen bonds       : angle       5.34553 (  852)
  covalent geometry    : bond        0.00258 (12125)
  covalent geometry    : angle       0.58925 (16626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9599.50 seconds
wall clock time: 166 minutes 27.53 seconds (9987.53 seconds total)