Starting phenix.real_space_refine
on Tue Jun 10 15:25:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eaq_47840/06_2025/9eaq_47840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eaq_47840/06_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_47840/06_2025/9eaq_47840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eaq_47840/06_2025/9eaq_47840.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eaq_47840/06_2025/9eaq_47840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eaq_47840/06_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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.17, per 1000 atoms: 0.86
  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: 2.87
  Conformation dependent library (CDL) restraints added in 1.8 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: 1.51
  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: 4.69

  Time building geometry restraints manager: 3.40 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:             167.830
  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:             0.030
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     34.190
  Find NCS groups from input model:        0.640
  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:15.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  218.650
-------------------------------------------------------------------------------
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  : 1.279 
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: 1.0928
  time to fit residues: 190.3497
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  : 1.254 
-------------------------------------------------------------------------------
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 = 10765.642|
|-----------------------------------------------------------------------------|
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: 4.67 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
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       6.06385 (  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  : 1.802 
Fit side-chains
REVERT: A  437 ARG cc_start: 0.5890 (mtm-85) cc_final: 0.3249 (ttt-90)
REVERT: A  501 TYR cc_start: 0.6653 (t80) cc_final: 0.6402 (t80)
REVERT: B  175 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7561 (mp10)
REVERT: B  516 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6113 (mp0)
REVERT: C  476 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.5898 (ttp-170)
REVERT: C  523 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7081 (ttm170)
  outliers start: 58
  outliers final: 30
  residues processed: 151
  average time/residue: 1.4011
  time to fit residues: 230.3567
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  : 1.542 
-------------------------------------------------------------------------------
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:   40.0000
   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:    9.9990
   chunk 109 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.4307 r_free = 0.4307 target = 0.220977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.150541 restraints weight = 10729.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 4.81
r_work: 0.2768 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12125  Z= 0.220
  Angle     :  0.731  14.486  16626  Z= 0.372
  Chirality :  0.050   0.240   1892
  Planarity :  0.007   0.141   2178
  Dihedral  :  7.152  59.448   1684
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.95 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 21.86 %
    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: -1.05 (0.20), residues: 1529
  helix: -1.44 (0.60), residues: 52
  sheet:  0.26 (0.24), residues: 437
  loop : -1.14 (0.18), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 102 
 HIS   0.006   0.001   HIS A  94 
 PHE   0.019   0.002   PHE C  80 
 TYR   0.024   0.002   TYR A 217 
 ARG   0.004   0.000   ARG B 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04472 (  304)
  hydrogen bonds       : angle       6.04276 (  852)
  covalent geometry    : bond        0.00549 (12125)
  covalent geometry    : angle       0.73123 (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
  163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 95
  time to evaluate  : 2.176 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8233 (m)
REVERT: A  349 LYS cc_start: 0.4327 (OUTLIER) cc_final: 0.2841 (pttp)
REVERT: A  501 TYR cc_start: 0.6881 (t80) cc_final: 0.6637 (t80)
REVERT: B  175 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7536 (mp10)
REVERT: B  371 GLN cc_start: 0.4101 (OUTLIER) cc_final: 0.3805 (pm20)
REVERT: B  516 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6202 (mp0)
REVERT: C  238 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6240 (ptp90)
REVERT: C  384 LEU cc_start: 0.2894 (OUTLIER) cc_final: 0.2661 (tt)
REVERT: C  523 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7196 (ttm170)
  outliers start: 68
  outliers final: 38
  residues processed: 151
  average time/residue: 1.6416
  time to fit residues: 272.6727
Evaluate side-chains
  138 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 93
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
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  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  384 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:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 151 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 137 optimal weight:   50.0000
   chunk 72 optimal weight:    0.1980
   chunk 26 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 84 optimal weight:    5.9990
   chunk 104 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.224283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.148222 restraints weight = 10777.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 5.81
r_work: 0.2810 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.0867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.081  12125  Z= 0.100
  Angle     :  0.574  14.649  16626  Z= 0.289
  Chirality :  0.044   0.220   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  6.182  58.982   1676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.97 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 23.74 %
    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: -0.91 (0.20), residues: 1529
  helix: -0.85 (0.62), residues: 52
  sheet:  0.20 (0.23), residues: 443
  loop : -1.00 (0.18), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A  94 
 PHE   0.023   0.001   PHE C  80 
 TYR   0.011   0.001   TYR A 217 
 ARG   0.002   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 (  304)
  hydrogen bonds       : angle       5.64350 (  852)
  covalent geometry    : bond        0.00237 (12125)
  covalent geometry    : angle       0.57432 (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
  152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 108
  time to evaluate  : 1.977 
Fit side-chains
REVERT: A  106 MET cc_start: 0.9074 (mtp) cc_final: 0.8833 (mtm)
REVERT: A  349 LYS cc_start: 0.4242 (OUTLIER) cc_final: 0.2863 (pttm)
REVERT: A  501 TYR cc_start: 0.6892 (t80) cc_final: 0.6624 (t80)
REVERT: B  175 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7327 (mp10)
REVERT: B  371 GLN cc_start: 0.4228 (OUTLIER) cc_final: 0.4001 (pm20)
REVERT: C  397 SER cc_start: 0.7374 (OUTLIER) cc_final: 0.7091 (t)
REVERT: C  412 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6460 (pp)
REVERT: C  523 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7144 (ttm170)
  outliers start: 44
  outliers final: 23
  residues processed: 147
  average time/residue: 1.1853
  time to fit residues: 190.8593
Evaluate side-chains
  133 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
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  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 B residue  449 ILE
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  397 SER
Chi-restraints excluded: chain C residue  412 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:    9.9990
   chunk 141 optimal weight:    0.0050
   chunk 81 optimal weight:    0.6980
   chunk 42 optimal weight:   50.0000
   chunk 50 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 9 optimal weight:    0.3980
   chunk 85 optimal weight:   40.0000
   chunk 74 optimal weight:    2.9990
   chunk 135 optimal weight:    8.9990
   overall best weight:    2.6198

-------------------------------------------------------------------------------
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 = 0.4326 r_free = 0.4326 target = 0.223145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.151228 restraints weight = 10682.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 5.06
r_work: 0.2797 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12125  Z= 0.123
  Angle     :  0.607  15.157  16626  Z= 0.305
  Chirality :  0.045   0.226   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  6.097  59.334   1672
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.04 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.51 %
    Favored  : 72.48 %
  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: -0.82 (0.63), residues: 52
  sheet:  0.23 (0.24), residues: 441
  loop : -0.98 (0.18), residues: 1036

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   0.019   0.001   PHE C  80 
 TYR   0.015   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03362 (  304)
  hydrogen bonds       : angle       5.56362 (  852)
  covalent geometry    : bond        0.00303 (12125)
  covalent geometry    : angle       0.60668 (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
  162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 111
  time to evaluate  : 1.121 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4237 (OUTLIER) cc_final: 0.2883 (pttm)
REVERT: A  437 ARG cc_start: 0.5903 (mtm-85) cc_final: 0.5270 (ptt90)
REVERT: A  501 TYR cc_start: 0.6894 (t80) cc_final: 0.6604 (t80)
REVERT: B  175 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7303 (mp10)
REVERT: B  371 GLN cc_start: 0.4142 (OUTLIER) cc_final: 0.3845 (pm20)
REVERT: B  512 ASP cc_start: 0.7974 (m-30) cc_final: 0.7259 (m-30)
REVERT: C  397 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.7202 (t)
REVERT: C  412 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6484 (pp)
REVERT: C  523 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7162 (ttm170)
  outliers start: 51
  outliers final: 33
  residues processed: 155
  average time/residue: 1.1207
  time to fit residues: 190.2974
Evaluate side-chains
  143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 105
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
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  449 ILE
Chi-restraints excluded: chain B residue  529 SER
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  397 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 149 optimal weight:   30.0000
   chunk 39 optimal weight:   40.0000
   chunk 141 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   chunk 31 optimal weight:   50.0000
   chunk 42 optimal weight:    8.9990
   chunk 50 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 84 optimal weight:   30.0000
   chunk 150 optimal weight:   20.0000
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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 = 0.4305 r_free = 0.4305 target = 0.220647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.142556 restraints weight = 10774.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 5.96
r_work: 0.2724 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  12125  Z= 0.237
  Angle     :  0.750  15.378  16626  Z= 0.381
  Chirality :  0.051   0.247   1892
  Planarity :  0.007   0.141   2178
  Dihedral  :  6.682  58.375   1672
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.21 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.72 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.20), residues: 1529
  helix: -1.54 (0.61), residues: 52
  sheet:  0.26 (0.24), residues: 435
  loop : -1.15 (0.18), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 102 
 HIS   0.006   0.001   HIS A  94 
 PHE   0.018   0.002   PHE C  59 
 TYR   0.025   0.002   TYR A 217 
 ARG   0.004   0.001   ARG A 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04405 (  304)
  hydrogen bonds       : angle       5.85187 (  852)
  covalent geometry    : bond        0.00597 (12125)
  covalent geometry    : angle       0.74957 (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
  162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 100
  time to evaluate  : 1.258 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8497 (mt)
REVERT: A  100 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8488 (t)
REVERT: A  349 LYS cc_start: 0.4152 (OUTLIER) cc_final: 0.2703 (pttm)
REVERT: A  501 TYR cc_start: 0.6890 (t80) cc_final: 0.6600 (t80)
REVERT: B  175 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7458 (mp10)
REVERT: B  512 ASP cc_start: 0.7995 (m-30) cc_final: 0.7280 (m-30)
REVERT: B  516 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6093 (mp0)
REVERT: C  238 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6157 (ptp90)
REVERT: C  397 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.7223 (t)
REVERT: C  412 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6371 (pp)
REVERT: C  523 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.7200 (ttm170)
  outliers start: 62
  outliers final: 38
  residues processed: 151
  average time/residue: 1.4170
  time to fit residues: 236.6200
Evaluate side-chains
  144 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 98
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
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  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  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  353 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  449 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   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  397 SER
Chi-restraints excluded: chain C residue  412 LEU
Chi-restraints excluded: chain C residue  420 ILE
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:    0.0170
   chunk 54 optimal weight:    1.9990
   chunk 134 optimal weight:   40.0000
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 77 optimal weight:   30.0000
   chunk 74 optimal weight:   30.0000
   chunk 7 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 29 optimal weight:   30.0000
   overall best weight:    1.8024

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.223287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.154867 restraints weight = 10891.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 4.76
r_work: 0.2816 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  12125  Z= 0.108
  Angle     :  0.595  15.857  16626  Z= 0.299
  Chirality :  0.045   0.226   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  6.083  56.313   1672
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.17 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 23.58 %
    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: -0.92 (0.20), residues: 1529
  helix: -0.93 (0.62), residues: 52
  sheet:  0.26 (0.24), residues: 437
  loop : -1.02 (0.18), 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   0.013   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03176 (  304)
  hydrogen bonds       : angle       5.51526 (  852)
  covalent geometry    : bond        0.00260 (12125)
  covalent geometry    : angle       0.59502 (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
  160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 108
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  106 MET cc_start: 0.9095 (mtp) cc_final: 0.8848 (mtm)
REVERT: A  349 LYS cc_start: 0.4072 (OUTLIER) cc_final: 0.2685 (pttm)
REVERT: A  501 TYR cc_start: 0.7009 (t80) cc_final: 0.6660 (t80)
REVERT: B   21 LEU cc_start: 0.8005 (mt) cc_final: 0.7541 (mt)
REVERT: B  142 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8440 (m)
REVERT: B  175 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7296 (mp10)
REVERT: B  371 GLN cc_start: 0.4292 (OUTLIER) cc_final: 0.3992 (pm20)
REVERT: B  512 ASP cc_start: 0.8248 (m-30) cc_final: 0.8032 (m-30)
REVERT: B  516 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6216 (mp0)
REVERT: C  397 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.7306 (t)
REVERT: C  523 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7204 (ttm170)
  outliers start: 52
  outliers final: 33
  residues processed: 150
  average time/residue: 1.2671
  time to fit residues: 207.3471
Evaluate side-chains
  145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
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  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  106 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  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 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   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  397 SER
Chi-restraints excluded: chain C residue  424 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:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 126 optimal weight:    5.9990
   chunk 98 optimal weight:   20.0000
   chunk 128 optimal weight:   50.0000
   chunk 47 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    0.1980
   chunk 40 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    2.6186

-------------------------------------------------------------------------------
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 = 0.4325 r_free = 0.4325 target = 0.222879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.153754 restraints weight = 10836.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 4.81
r_work: 0.2807 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  12125  Z= 0.124
  Angle     :  0.615  15.632  16626  Z= 0.309
  Chirality :  0.045   0.233   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  6.104  56.469   1672
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.43 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.82 %
    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: -0.82 (0.63), residues: 52
  sheet:  0.26 (0.24), residues: 439
  loop : -1.00 (0.18), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A  94 
 PHE   0.019   0.001   PHE C  80 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.002   0.000   ARG B 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  304)
  hydrogen bonds       : angle       5.48590 (  852)
  covalent geometry    : bond        0.00305 (12125)
  covalent geometry    : angle       0.61527 (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
  157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 108
  time to evaluate  : 1.354 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.3988 (OUTLIER) cc_final: 0.2603 (pttm)
REVERT: A  437 ARG cc_start: 0.5911 (mtm-85) cc_final: 0.5281 (ptt90)
REVERT: A  501 TYR cc_start: 0.7003 (t80) cc_final: 0.6648 (t80)
REVERT: B   21 LEU cc_start: 0.8089 (mt) cc_final: 0.7533 (mt)
REVERT: B  142 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8416 (m)
REVERT: B  175 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7208 (mp10)
REVERT: B  371 GLN cc_start: 0.4401 (OUTLIER) cc_final: 0.4090 (pm20)
REVERT: B  516 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6262 (mp0)
REVERT: C  397 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7282 (t)
REVERT: C  523 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.7198 (ttm170)
  outliers start: 49
  outliers final: 34
  residues processed: 149
  average time/residue: 1.5240
  time to fit residues: 248.5152
Evaluate side-chains
  147 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 1.587 
-------------------------------------------------------------------------------
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  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  142 THR
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 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  397 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 32 optimal weight:   30.0000
   chunk 7 optimal weight:    0.6980
   chunk 89 optimal weight:   30.0000
   chunk 142 optimal weight:    8.9990
   chunk 132 optimal weight:   20.0000
   chunk 81 optimal weight:    0.0040
   chunk 135 optimal weight:   30.0000
   chunk 30 optimal weight:    0.0030
   chunk 151 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.5406

-------------------------------------------------------------------------------
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 = 0.4327 r_free = 0.4327 target = 0.223130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.154978 restraints weight = 10752.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 4.74
r_work: 0.2804 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1113

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= 0.122
  Angle     :  0.614  16.321  16626  Z= 0.307
  Chirality :  0.045   0.232   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  6.029  56.584   1672
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.17 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.29 %
    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: -0.87 (0.20), residues: 1529
  helix: -0.79 (0.63), residues: 52
  sheet:  0.26 (0.24), residues: 439
  loop : -0.98 (0.19), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS A  94 
 PHE   0.019   0.001   PHE C  80 
 TYR   0.017   0.001   TYR A 496 
 ARG   0.009   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  304)
  hydrogen bonds       : angle       5.46542 (  852)
  covalent geometry    : bond        0.00298 (12125)
  covalent geometry    : angle       0.61427 (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
  154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 109
  time to evaluate  : 2.483 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.2843 (pttm)
REVERT: A  437 ARG cc_start: 0.5947 (mtm-85) cc_final: 0.5309 (ptt90)
REVERT: A  501 TYR cc_start: 0.6978 (t80) cc_final: 0.6614 (t80)
REVERT: B   21 LEU cc_start: 0.8055 (mt) cc_final: 0.7449 (mt)
REVERT: B  142 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8416 (m)
REVERT: B  175 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7198 (mp10)
REVERT: B  238 ARG cc_start: 0.6650 (ptm160) cc_final: 0.6296 (ptp-170)
REVERT: B  371 GLN cc_start: 0.4446 (OUTLIER) cc_final: 0.4127 (pm20)
REVERT: B  516 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6243 (mp0)
REVERT: C  397 SER cc_start: 0.7610 (OUTLIER) cc_final: 0.7283 (t)
  outliers start: 45
  outliers final: 33
  residues processed: 144
  average time/residue: 1.5429
  time to fit residues: 242.3737
Evaluate side-chains
  146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
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  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  142 THR
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 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  397 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 145 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 98 optimal weight:    9.9990
   chunk 72 optimal weight:   20.0000
   chunk 124 optimal weight:    3.9990
   chunk 123 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 = 0.4330 r_free = 0.4330 target = 0.223446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.157367 restraints weight = 10712.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 4.54
r_work: 0.2823 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1125

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= 0.117
  Angle     :  0.605  15.982  16626  Z= 0.303
  Chirality :  0.045   0.229   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  5.914  56.634   1671
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.49 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.45 %
    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: -0.84 (0.20), residues: 1529
  helix: -0.72 (0.63), residues: 52
  sheet:  0.27 (0.24), residues: 439
  loop : -0.96 (0.19), residues: 1038

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   0.020   0.001   PHE C  80 
 TYR   0.017   0.001   TYR A 496 
 ARG   0.008   0.000   ARG C 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  304)
  hydrogen bonds       : angle       5.41384 (  852)
  covalent geometry    : bond        0.00285 (12125)
  covalent geometry    : angle       0.60482 (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
  153 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 110
  time to evaluate  : 1.664 
Fit side-chains
REVERT: A  349 LYS cc_start: 0.3951 (OUTLIER) cc_final: 0.2748 (pttm)
REVERT: A  437 ARG cc_start: 0.5875 (mtm-85) cc_final: 0.5240 (ptt90)
REVERT: A  501 TYR cc_start: 0.7062 (t80) cc_final: 0.6695 (t80)
REVERT: B   21 LEU cc_start: 0.8052 (mt) cc_final: 0.7470 (mt)
REVERT: B  142 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8415 (m)
REVERT: B  238 ARG cc_start: 0.6716 (ptm160) cc_final: 0.6322 (ptp-170)
REVERT: B  371 GLN cc_start: 0.4485 (OUTLIER) cc_final: 0.4151 (pm20)
REVERT: B  516 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6234 (mp0)
REVERT: C  397 SER cc_start: 0.7460 (OUTLIER) cc_final: 0.7182 (t)
  outliers start: 43
  outliers final: 33
  residues processed: 145
  average time/residue: 1.5342
  time to fit residues: 242.9520
Evaluate side-chains
  145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 107
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
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  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  142 THR
Chi-restraints excluded: chain B residue  148 MET
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 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  397 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 36 optimal weight:   30.0000
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 118 optimal weight:    2.9990
   chunk 126 optimal weight:   30.0000
   chunk 11 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 137 optimal weight:    0.0020
   overall best weight:    2.3996

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.223303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.156812 restraints weight = 10698.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 4.58
r_work: 0.2802 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1161

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= 0.118
  Angle     :  0.609  16.594  16626  Z= 0.304
  Chirality :  0.045   0.230   1892
  Planarity :  0.006   0.138   2178
  Dihedral  :  5.889  56.581   1671
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.04 %
    Favored  : 94.83 %
  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: -0.84 (0.20), residues: 1529
  helix: -0.76 (0.63), residues: 52
  sheet:  0.28 (0.24), residues: 441
  loop : -0.96 (0.19), residues: 1036

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   0.019   0.001   PHE C  80 
 TYR   0.019   0.001   TYR A 496 
 ARG   0.004   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03250 (  304)
  hydrogen bonds       : angle       5.41203 (  852)
  covalent geometry    : bond        0.00290 (12125)
  covalent geometry    : angle       0.60937 (16626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10347.06 seconds
wall clock time: 184 minutes 29.23 seconds (11069.23 seconds total)