Starting phenix.real_space_refine
on Wed May 14 16:54:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eap_47839/05_2025/9eap_47839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eap_47839/05_2025/9eap_47839.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/9eap_47839/05_2025/9eap_47839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eap_47839/05_2025/9eap_47839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eap_47839/05_2025/9eap_47839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eap_47839/05_2025/9eap_47839.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=   0.004 sd=   0.160
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    7673      2.51       5
     N    1944      2.21       5
     O    2218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11883
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 3949
          Classifications: {'peptide': 514}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 467}
    Chain: "B"
      Number of atoms: 3963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 3963
          Classifications: {'peptide': 516}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 469}
    Chain: "C"
      Number of atoms: 3875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3875
          Classifications: {'peptide': 504}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 458}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'CHO': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'CHO': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'CHO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.82, per 1000 atoms: 0.83
  Number of scatterers: 11883
  At special positions: 0
  Unit cell: (124.3, 115.5, 122.1, 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    2218      8.00
     N    1944      7.00
     C    7673      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: 2.77
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2840

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 23 sheets defined
      8.1% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 4.132A  pdb=" N   ALA A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 85 through 88
      removed outlier: 3.776A  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 140 through 144
      removed outlier: 3.672A  pdb=" N   PHE A 144 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 240
    Processing helix  chain 'B' and resid 37 through 42
      removed outlier: 4.532A  pdb=" N   ALA B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'B' and resid 85 through 88
      removed outlier: 3.719A  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 137 through 142
      removed outlier: 3.529A  pdb=" N   ILE B 141 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   THR B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 137 through 142'
    Processing helix  chain 'B' and resid 236 through 240
    Processing helix  chain 'B' and resid 368 through 372
    Processing helix  chain 'B' and resid 454 through 465
    Processing helix  chain 'C' and resid 37 through 42
      removed outlier: 4.177A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 56
    Processing helix  chain 'C' and resid 85 through 88
      removed outlier: 3.686A  pdb=" N   LEU C  88 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 85 through 88'
    Processing helix  chain 'C' and resid 89 through 96
    Processing helix  chain 'C' and resid 140 through 144
      removed outlier: 3.771A  pdb=" N   PHE C 144 " --> pdb=" O   ILE C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 240
    Processing helix  chain 'C' and resid 454 through 465
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83
      removed outlier: 7.116A  pdb=" N   ILE A  78 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU A 185 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A  80 " --> pdb=" O   CYS A 183 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   CYS A 183 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ALA A 125 " --> pdb=" O   CYS A 183 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LEU A 185 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL A 123 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS A 121 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   LEU A 189 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ALA A 119 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171
      removed outlier: 3.643A  pdb=" N   HIS A 170 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP A 102 " --> pdb=" O   HIS A 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451
    Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296
      removed outlier: 4.231A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   PHE A 375 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   ILE A 358 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   SER A 332 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   PHE A 401 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   GLU A 338 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLN A 340 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   ALA A 393 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 11.495A  pdb=" N   GLU A 342 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 11.172A  pdb=" N   VAL A 391 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 429
      removed outlier: 7.090A  pdb=" N   TYR A 477 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 429
      removed outlier: 3.757A  pdb=" N   SER A 519 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   ARG A 476 " --> pdb=" O   VAL A 517 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   VAL A 517 " --> pdb=" O   ARG A 476 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ARG A 478 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   PHE A 515 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 69
      removed outlier: 12.584A  pdb=" N   GLN B  61 " --> pdb=" O   PRO B 209 " (cutoff:3.500A)
      removed outlier: 11.144A  pdb=" N   SER B 207 " --> pdb=" O   PRO B  63 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   GLY B  65 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 78 through 83
      removed outlier: 6.740A  pdb=" N   ILE B  78 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LEU B 185 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   LEU B 181 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL B 127 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   CYS B 183 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   ALA B 125 " --> pdb=" O   CYS B 183 " (cutoff:3.500A)
      removed outlier: 5.880A  pdb=" N   LEU B 185 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL B 123 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS B 121 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU B 189 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ALA B 119 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 99 through 103
      removed outlier: 6.627A  pdb=" N   TYR B  99 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU B 218 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   GLY B 101 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASN B 214 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 449 through 451
      removed outlier: 4.215A  pdb=" N   LEU B 252 " --> pdb=" O   PHE B 509 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 449 through 451
      removed outlier: 5.701A  pdb=" N   ILE B 497 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR B 496 " --> pdb=" O   TYR B 492 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   SER B 500 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   GLU B 488 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ALA B 472 " --> pdb=" O   TRP B 520 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   TRP B 520 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU B 474 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG B 476 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG B 478 " --> pdb=" O   ILE B 514 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 289 through 298
      removed outlier: 4.002A  pdb=" N   ALA B 290 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   PHE B 375 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   ILE B 358 " --> pdb=" O   PHE B 375 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER B 377 " --> pdb=" O   GLU B 356 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU B 356 " --> pdb=" O   SER B 377 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   SER B 332 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   GLY B 400 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   GLN B 334 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ILE B 398 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLU B 336 " --> pdb=" O   ARG B 396 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 394 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   GLN B 340 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ARG B 392 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   GLU B 342 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      removed outlier: 9.746A  pdb=" N   ARG B 390 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.449A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 9.658A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 83
      removed outlier: 6.763A  pdb=" N   ILE C  78 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU C 185 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   LEU C 181 " --> pdb=" O   VAL C 127 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL C 127 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   CYS C 183 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   ALA C 125 " --> pdb=" O   CYS C 183 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   LEU C 185 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   VAL C 123 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171
      removed outlier: 3.744A  pdb=" N   HIS C 170 " --> pdb=" O   TRP C 102 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TRP C 102 " --> pdb=" O   HIS C 170 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 449 through 451
      removed outlier: 4.346A  pdb=" N   LEU C 252 " --> pdb=" O   PHE C 509 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 290 through 297
      removed outlier: 4.161A  pdb=" N   ALA C 290 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 358
      removed outlier: 7.252A  pdb=" N   SER C 332 " --> pdb=" O   PHE C 401 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   PHE C 401 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   SER C 397 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   GLU C 338 " --> pdb=" O   PRO C 395 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 341 through 342
    Processing sheet with id=AC4, first strand: chain 'C' and resid 428 through 429
      removed outlier: 4.077A  pdb=" N   TYR C 496 " --> pdb=" O   TYR C 492 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE C 487 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 428 through 429
      removed outlier: 4.077A  pdb=" N   TYR C 496 " --> pdb=" O   TYR C 492 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ALA C 472 " --> pdb=" O   TRP C 520 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   TRP C 520 " --> pdb=" O   ALA C 472 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU C 474 " --> pdb=" O   VAL C 518 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG C 478 " --> pdb=" O   ILE C 514 " (cutoff:3.500A)

    291 hydrogen bonds defined for protein.
    705 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.63

  Time building geometry restraints manager: 3.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3853
        1.34 -     1.46: 1981
        1.46 -     1.57: 6311
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 12217
  Sorted by residual:
  bond pdb=" CA  ASP B 196 "
       pdb=" CB  ASP B 196 "
    ideal  model  delta    sigma   weight residual
    1.530  1.553 -0.023 1.69e-02 3.50e+03 1.82e+00
  bond pdb=" CB  GLN A 469 "
       pdb=" CG  GLN A 469 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.80e+00
  bond pdb=" CA  GLN A 469 "
       pdb=" CB  GLN A 469 "
    ideal  model  delta    sigma   weight residual
    1.530  1.552 -0.021 1.69e-02 3.50e+03 1.60e+00
  bond pdb=" CB  ASP B 196 "
       pdb=" CG  ASP B 196 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.30e+00
  bond pdb=" CA  ASP B 174 "
       pdb=" CB  ASP B 174 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.69e-02 3.50e+03 1.16e+00
  ... (remaining 12212 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 16354
        2.08 -     4.17: 354
        4.17 -     6.25: 49
        6.25 -     8.34: 10
        8.34 -    10.42: 3
  Bond angle restraints: 16770
  Sorted by residual:
  angle pdb=" CA  GLN A 469 "
        pdb=" CB  GLN A 469 "
        pdb=" CG  GLN A 469 "
      ideal   model   delta    sigma   weight residual
     114.10  123.31   -9.21 2.00e+00 2.50e-01 2.12e+01
  angle pdb=" C   GLU C 447 "
        pdb=" N   ALA C 448 "
        pdb=" CA  ALA C 448 "
      ideal   model   delta    sigma   weight residual
     121.70  128.24   -6.54 1.80e+00 3.09e-01 1.32e+01
  angle pdb=" CB  LYS A 351 "
        pdb=" CG  LYS A 351 "
        pdb=" CD  LYS A 351 "
      ideal   model   delta    sigma   weight residual
     111.30  119.11   -7.81 2.30e+00 1.89e-01 1.15e+01
  angle pdb=" CA  ASP B 196 "
        pdb=" CB  ASP B 196 "
        pdb=" CG  ASP B 196 "
      ideal   model   delta    sigma   weight residual
     112.60  115.96   -3.36 1.00e+00 1.00e+00 1.13e+01
  angle pdb=" C   ASP B 366 "
        pdb=" N   GLN B 367 "
        pdb=" CA  GLN B 367 "
      ideal   model   delta    sigma   weight residual
     121.70  127.74   -6.04 1.80e+00 3.09e-01 1.13e+01
  ... (remaining 16765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.36: 6595
       22.36 -    44.73: 638
       44.73 -    67.09: 134
       67.09 -    89.46: 22
       89.46 -   111.82: 11
  Dihedral angle restraints: 7400
    sinusoidal: 2973
      harmonic: 4427
  Sorted by residual:
  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 -138.81  -41.19     0      5.00e+00 4.00e-02 6.79e+01
  dihedral pdb=" CA  PRO B 361 "
           pdb=" C   PRO B 361 "
           pdb=" N   THR B 362 "
           pdb=" CA  THR B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -139.67  -40.33     0      5.00e+00 4.00e-02 6.51e+01
  dihedral pdb=" CA  GLY B 195 "
           pdb=" C   GLY B 195 "
           pdb=" N   ASP B 196 "
           pdb=" CA  ASP B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.50   34.50     0      5.00e+00 4.00e-02 4.76e+01
  ... (remaining 7397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1100
       0.030 -    0.061: 506
       0.061 -    0.091: 175
       0.091 -    0.121: 125
       0.121 -    0.152: 15
  Chirality restraints: 1921
  Sorted by residual:
  chirality pdb=" CG  LEU C 258 "
            pdb=" CB  LEU C 258 "
            pdb=" CD1 LEU C 258 "
            pdb=" CD2 LEU C 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  VAL A 378 "
            pdb=" N   VAL A 378 "
            pdb=" C   VAL A 378 "
            pdb=" CB  VAL A 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CB  ILE C 358 "
            pdb=" CA  ILE C 358 "
            pdb=" CG1 ILE C 358 "
            pdb=" CG2 ILE C 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.87e-01
  ... (remaining 1918 not shown)

  Planarity restraints: 2182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  22 "   -0.047 5.00e-02 4.00e+02   7.24e-02 8.38e+00
        pdb=" N   PRO B  23 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B  23 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  23 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 196 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.84e+00
        pdb=" C   ASP B 196 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ASP B 196 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU B 197 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 469 "    0.012 2.00e-02 2.50e+03   2.42e-02 5.83e+00
        pdb=" C   GLN A 469 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLN A 469 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER A 470 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2179 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 408
        2.70 -     3.25: 10797
        3.25 -     3.80: 17057
        3.80 -     4.35: 20428
        4.35 -     4.90: 36790
  Nonbonded interactions: 85480
  Sorted by model distance:
  nonbonded pdb=" O   ALA B  25 "
            pdb=" N   GLU B  27 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" O   SER C  96 "
            pdb=" OG  SER C  96 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG1 THR C 482 "
            pdb=" OE1 GLN C 484 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   GLU B 456 "
            pdb=" OE1 GLU B 456 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   PRO B  63 "
            pdb=" OG  SER B 519 "
     model   vdw
     2.252 3.040
  ... (remaining 85475 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 90 or (resid 91 and (name N or name CA or name  \ 
C or name O )) or resid 92 through 530 or resid 601))
  selection = (chain 'B' and (resid 27 through 90 or (resid 91 and (name N or name CA or name  \ 
C or name O )) or resid 92 through 530 or resid 601))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.210
  Find NCS groups from input model:        0.600
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5275
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      :  0.004   0.040  12217  Z= 0.180
  Angle     :  0.729  10.424  16770  Z= 0.374
  Chirality :  0.045   0.152   1921
  Planarity :  0.005   0.072   2182
  Dihedral  : 18.584 111.820   4560
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.85 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 33.52 %
    Favored  : 62.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.21), residues: 1528
  helix: -0.63 (0.71), residues: 56
  sheet: -0.23 (0.26), residues: 421
  loop : -1.39 (0.19), residues: 1051

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 146 
 PHE   0.030   0.001   PHE C 401 
 TYR   0.021   0.001   TYR B 435 
 ARG   0.008   0.000   ARG A 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16397 (  272)
  hydrogen bonds       : angle       6.99735 (  705)
  covalent geometry    : bond        0.00408 (12217)
  covalent geometry    : angle       0.72920 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 227
  time to evaluate  : 1.296 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6068 (pm20) cc_final: 0.5307 (mm-30)
REVERT: A   88 LEU cc_start: 0.5290 (mt) cc_final: 0.5042 (mt)
REVERT: A  105 ASN cc_start: 0.6381 (OUTLIER) cc_final: 0.6040 (m110)
REVERT: A  117 PHE cc_start: 0.6189 (m-10) cc_final: 0.5929 (m-80)
REVERT: A  149 CYS cc_start: 0.6261 (t) cc_final: 0.6035 (m)
REVERT: A  181 LEU cc_start: 0.5060 (tt) cc_final: 0.4824 (tp)
REVERT: A  214 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.5929 (p0)
REVERT: A  222 ILE cc_start: 0.5822 (pt) cc_final: 0.5457 (mp)
REVERT: A  328 TYR cc_start: 0.5934 (t80) cc_final: 0.5352 (t80)
REVERT: A  402 GLN cc_start: 0.4486 (mp10) cc_final: 0.4259 (mp10)
REVERT: A  519 SER cc_start: 0.7063 (m) cc_final: 0.6752 (p)
REVERT: A  523 ARG cc_start: 0.5996 (tpp80) cc_final: 0.5165 (ttp-110)
REVERT: B   48 ILE cc_start: 0.5677 (pt) cc_final: 0.5344 (mt)
REVERT: B   58 ASN cc_start: 0.5713 (p0) cc_final: 0.5458 (p0)
REVERT: B  106 MET cc_start: 0.6243 (mtm) cc_final: 0.5984 (tpp)
REVERT: B  235 ILE cc_start: 0.7009 (pt) cc_final: 0.6785 (pp)
REVERT: B  329 PRO cc_start: 0.6170 (Cg_exo) cc_final: 0.5913 (Cg_endo)
REVERT: B  394 VAL cc_start: 0.4784 (OUTLIER) cc_final: 0.4391 (t)
REVERT: B  436 MET cc_start: 0.1932 (mpp) cc_final: -0.0170 (mtt)
REVERT: B  464 ASN cc_start: 0.5411 (OUTLIER) cc_final: 0.4155 (m-40)
REVERT: B  493 ASN cc_start: 0.6261 (p0) cc_final: 0.5912 (p0)
REVERT: B  512 ASP cc_start: 0.7010 (m-30) cc_final: 0.6654 (t0)
REVERT: B  514 ILE cc_start: 0.7417 (pt) cc_final: 0.7007 (pp)
REVERT: C   33 GLN cc_start: 0.6378 (mt0) cc_final: 0.6006 (mt0)
REVERT: C   49 ASN cc_start: 0.7127 (m110) cc_final: 0.6803 (m110)
REVERT: C   61 GLN cc_start: 0.5935 (tt0) cc_final: 0.5582 (tp40)
REVERT: C   74 THR cc_start: 0.7040 (p) cc_final: 0.6788 (t)
REVERT: C  137 THR cc_start: 0.6173 (p) cc_final: 0.5920 (p)
REVERT: C  174 ASP cc_start: 0.6610 (m-30) cc_final: 0.6222 (p0)
REVERT: C  222 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6257 (pt)
REVERT: C  432 PHE cc_start: 0.5072 (m-80) cc_final: 0.4564 (m-80)
REVERT: C  436 MET cc_start: 0.5735 (mmm) cc_final: 0.5245 (mmt)
REVERT: C  471 GLU cc_start: 0.7449 (tp30) cc_final: 0.6926 (tp30)
REVERT: C  516 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6390 (mt-10)
  outliers start: 54
  outliers final: 15
  residues processed: 267
  average time/residue: 0.8659
  time to fit residues: 257.3994
Evaluate side-chains
  153 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  105 ASN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain B residue  192 ASN
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  464 ASN
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  196 ASP
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  222 ILE
Chi-restraints excluded: chain C residue  313 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  514 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:   30.0000
   chunk 115 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:   40.0000
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 119 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 88 optimal weight:   20.0000
   chunk 138 optimal weight:    0.9980
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  49 ASN
A  58 ASN
A  89 ASN
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 ASN
B 105 ASN
B 192 ASN
B 270 HIS
C  50 GLN
C 105 ASN
C 265 GLN
C 312 GLN
C 455 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.229608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.201064 restraints weight = 11899.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.4149 rms_B_bonded: 1.18
r_work: 0.3839 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work: 0.3730 rms_B_bonded: 3.29 restraints_weight: 0.1250
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12217  Z= 0.185
  Angle     :  0.775   9.398  16770  Z= 0.394
  Chirality :  0.050   0.220   1921
  Planarity :  0.006   0.058   2182
  Dihedral  :  8.028  96.852   1897
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.22 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 27.14 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.21), residues: 1528
  helix: -0.72 (0.63), residues: 58
  sheet: -0.25 (0.25), residues: 434
  loop : -1.47 (0.18), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 102 
 HIS   0.010   0.002   HIS C 146 
 PHE   0.037   0.002   PHE C 199 
 TYR   0.022   0.002   TYR B 317 
 ARG   0.006   0.001   ARG C 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  272)
  hydrogen bonds       : angle       6.15504 (  705)
  covalent geometry    : bond        0.00423 (12217)
  covalent geometry    : angle       0.77479 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 133
  time to evaluate  : 1.433 
Fit side-chains
REVERT: A  214 ASN cc_start: 0.8325 (p0) cc_final: 0.8023 (p0)
REVERT: A  335 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5157 (mp)
REVERT: B  357 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4948 (ptm)
REVERT: B  359 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3724 (tm)
REVERT: C   33 GLN cc_start: 0.8492 (mt0) cc_final: 0.8098 (mt0)
REVERT: C  155 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7347 (mp0)
REVERT: C  197 GLU cc_start: 0.3532 (OUTLIER) cc_final: 0.3229 (tt0)
REVERT: C  464 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8267 (m-40)
  outliers start: 69
  outliers final: 20
  residues processed: 189
  average time/residue: 1.1254
  time to fit residues: 232.8335
Evaluate side-chains
  134 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  430 LEU
Chi-restraints excluded: chain C residue  464 ASN
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:    0.3980
   chunk 23 optimal weight:   20.0000
   chunk 81 optimal weight:   30.0000
   chunk 144 optimal weight:    6.9990
   chunk 151 optimal weight:    7.9990
   chunk 110 optimal weight:   10.0000
   chunk 58 optimal weight:    0.5980
   chunk 95 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    3.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 236 GLN
B 261 ASN
B 270 HIS
B 469 GLN
C  50 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.222874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.152900 restraints weight = 11848.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 7.54
r_work: 0.3028 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12217  Z= 0.172
  Angle     :  0.707   8.548  16770  Z= 0.358
  Chirality :  0.048   0.201   1921
  Planarity :  0.006   0.059   2182
  Dihedral  :  6.855  58.738   1874
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.41 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 25.57 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.20), residues: 1528
  helix: -0.38 (0.64), residues: 53
  sheet: -0.21 (0.25), residues: 425
  loop : -1.41 (0.18), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 169 
 HIS   0.007   0.002   HIS C 146 
 PHE   0.025   0.002   PHE C 199 
 TYR   0.022   0.002   TYR B 227 
 ARG   0.005   0.001   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04639 (  272)
  hydrogen bonds       : angle       5.83376 (  705)
  covalent geometry    : bond        0.00415 (12217)
  covalent geometry    : angle       0.70714 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 128
  time to evaluate  : 1.207 
Fit side-chains
REVERT: A  148 MET cc_start: 0.9003 (ttm) cc_final: 0.8470 (tpp)
REVERT: A  456 GLU cc_start: 0.6878 (mp0) cc_final: 0.6498 (mp0)
REVERT: A  471 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7519 (mm-30)
REVERT: A  478 ARG cc_start: 0.6859 (ptp-170) cc_final: 0.6350 (mtp85)
REVERT: B   40 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8879 (mt)
REVERT: B  112 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7234 (mt)
REVERT: B  238 ARG cc_start: 0.7006 (ptp-110) cc_final: 0.6662 (ptp-110)
REVERT: B  258 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6547 (mp)
REVERT: B  328 TYR cc_start: 0.7094 (t80) cc_final: 0.6826 (t80)
REVERT: B  359 LEU cc_start: 0.2968 (OUTLIER) cc_final: 0.2559 (tm)
REVERT: C  155 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7805 (mp0)
REVERT: C  174 ASP cc_start: 0.8310 (m-30) cc_final: 0.7838 (t0)
REVERT: C  197 GLU cc_start: 0.3203 (OUTLIER) cc_final: 0.2429 (tt0)
REVERT: C  228 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7671 (ttm170)
REVERT: C  238 ARG cc_start: 0.8113 (ptp90) cc_final: 0.6404 (tmt90)
REVERT: C  264 TRP cc_start: 0.8006 (m-10) cc_final: 0.7734 (m-10)
REVERT: C  275 LEU cc_start: 0.8153 (mp) cc_final: 0.7877 (mt)
REVERT: C  336 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.5121 (mp0)
REVERT: C  407 GLU cc_start: 0.6505 (mp0) cc_final: 0.5971 (tt0)
  outliers start: 75
  outliers final: 34
  residues processed: 187
  average time/residue: 1.0965
  time to fit residues: 224.2947
Evaluate side-chains
  156 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 113
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  428 VAL
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  313 ASP
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 78 optimal weight:   30.0000
   chunk 134 optimal weight:   40.0000
   chunk 99 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 28 optimal weight:   30.0000
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 GLN
B 192 ASN
** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 GLN
C 263 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.219090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.146592 restraints weight = 11662.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 7.89
r_work: 0.2935 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.6238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  12217  Z= 0.241
  Angle     :  0.806  10.832  16770  Z= 0.413
  Chirality :  0.053   0.225   1921
  Planarity :  0.007   0.061   2182
  Dihedral  :  7.297  58.319   1872
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.22 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 22.97 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.20), residues: 1528
  helix: -1.22 (0.61), residues: 53
  sheet: -0.26 (0.25), residues: 413
  loop : -1.54 (0.17), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 169 
 HIS   0.008   0.002   HIS C 146 
 PHE   0.021   0.003   PHE C 199 
 TYR   0.024   0.002   TYR B 227 
 ARG   0.006   0.001   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04762 (  272)
  hydrogen bonds       : angle       6.01568 (  705)
  covalent geometry    : bond        0.00597 (12217)
  covalent geometry    : angle       0.80633 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 120
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8597 (tpp)
REVERT: A  154 LEU cc_start: 0.8881 (mp) cc_final: 0.8502 (mt)
REVERT: A  471 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7605 (mm-30)
REVERT: A  478 ARG cc_start: 0.7179 (ptp-170) cc_final: 0.6660 (mtp85)
REVERT: A  526 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7687 (tm-30)
REVERT: B   72 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8373 (mpp80)
REVERT: B  112 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7251 (mt)
REVERT: B  242 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7144 (t70)
REVERT: B  359 LEU cc_start: 0.3108 (OUTLIER) cc_final: 0.2627 (tm)
REVERT: C  155 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7779 (mp0)
REVERT: C  174 ASP cc_start: 0.8243 (m-30) cc_final: 0.7772 (t0)
REVERT: C  196 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6616 (p0)
REVERT: C  197 GLU cc_start: 0.3384 (OUTLIER) cc_final: 0.2123 (tt0)
REVERT: C  228 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7798 (ttm170)
REVERT: C  238 ARG cc_start: 0.7888 (ptp90) cc_final: 0.6365 (tmt90)
REVERT: C  312 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6982 (mt0)
REVERT: C  336 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.5071 (mp0)
REVERT: C  384 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.5035 (mm)
REVERT: C  407 GLU cc_start: 0.6846 (mp0) cc_final: 0.6232 (tt0)
REVERT: C  410 ASP cc_start: 0.5850 (m-30) cc_final: 0.5370 (m-30)
  outliers start: 84
  outliers final: 34
  residues processed: 185
  average time/residue: 1.1186
  time to fit residues: 225.7217
Evaluate side-chains
  156 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 108
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  526 GLN
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   72 ARG
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain C residue  196 ASP
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  312 GLN
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  384 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0370
   chunk 32 optimal weight:   40.0000
   chunk 122 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:   30.0000
   chunk 113 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    1.9664

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.221208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.150699 restraints weight = 11750.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 7.57
r_work: 0.3009 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.6294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12217  Z= 0.114
  Angle     :  0.628   7.954  16770  Z= 0.320
  Chirality :  0.046   0.154   1921
  Planarity :  0.006   0.054   2182
  Dihedral  :  6.737  58.035   1872
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.89 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 25.33 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.20), residues: 1528
  helix: -0.82 (0.62), residues: 53
  sheet: -0.22 (0.25), residues: 419
  loop : -1.39 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 169 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.016   0.001   PHE C  80 
 TYR   0.013   0.001   TYR A 217 
 ARG   0.003   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  272)
  hydrogen bonds       : angle       5.61551 (  705)
  covalent geometry    : bond        0.00266 (12217)
  covalent geometry    : angle       0.62808 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 117
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A  148 MET cc_start: 0.8938 (ttm) cc_final: 0.8396 (tpp)
REVERT: A  154 LEU cc_start: 0.8833 (mp) cc_final: 0.8441 (mt)
REVERT: A  471 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7605 (mm-30)
REVERT: A  478 ARG cc_start: 0.7194 (ptp-170) cc_final: 0.6908 (ptm160)
REVERT: A  497 ILE cc_start: 0.7208 (mm) cc_final: 0.6924 (mt)
REVERT: A  516 GLU cc_start: 0.8051 (tt0) cc_final: 0.7414 (mt-10)
REVERT: B  359 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2577 (tm)
REVERT: C   82 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8088 (pp)
REVERT: C  155 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7973 (mp0)
REVERT: C  174 ASP cc_start: 0.8204 (m-30) cc_final: 0.7744 (t0)
REVERT: C  197 GLU cc_start: 0.3325 (OUTLIER) cc_final: 0.2514 (tt0)
REVERT: C  229 MET cc_start: 0.8698 (tpp) cc_final: 0.8461 (tpp)
REVERT: C  238 ARG cc_start: 0.7828 (ptp90) cc_final: 0.6264 (tmt90)
REVERT: C  336 GLU cc_start: 0.5410 (OUTLIER) cc_final: 0.4969 (mp0)
REVERT: C  407 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6186 (tt0)
REVERT: C  410 ASP cc_start: 0.5760 (m-30) cc_final: 0.5176 (m-30)
REVERT: C  436 MET cc_start: 0.6359 (mmt) cc_final: 0.5674 (mmt)
  outliers start: 51
  outliers final: 22
  residues processed: 155
  average time/residue: 1.1964
  time to fit residues: 201.4894
Evaluate side-chains
  139 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  471 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 79 optimal weight:   50.0000
   chunk 140 optimal weight:    0.9980
   chunk 47 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 37 optimal weight:   50.0000
   chunk 147 optimal weight:   10.0000
   chunk 142 optimal weight:   30.0000
   chunk 24 optimal weight:    0.5980
   chunk 35 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   overall best weight:    5.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.217943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.144736 restraints weight = 11774.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 8.13
r_work: 0.2933 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.6633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  12217  Z= 0.229
  Angle     :  0.773  10.224  16770  Z= 0.395
  Chirality :  0.051   0.231   1921
  Planarity :  0.007   0.058   2182
  Dihedral  :  7.091  56.651   1871
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.87 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 24.47 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.20), residues: 1528
  helix: -1.30 (0.61), residues: 53
  sheet: -0.16 (0.25), residues: 403
  loop : -1.55 (0.17), residues: 1072

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 169 
 HIS   0.006   0.002   HIS C 146 
 PHE   0.017   0.003   PHE C 199 
 TYR   0.024   0.002   TYR B 227 
 ARG   0.007   0.001   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  272)
  hydrogen bonds       : angle       5.79177 (  705)
  covalent geometry    : bond        0.00576 (12217)
  covalent geometry    : angle       0.77290 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 115
  time to evaluate  : 1.294 
Fit side-chains
REVERT: A   66 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7513 (mp0)
REVERT: A  148 MET cc_start: 0.9080 (ttm) cc_final: 0.8567 (tpp)
REVERT: A  154 LEU cc_start: 0.8854 (mp) cc_final: 0.8489 (mt)
REVERT: A  471 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7600 (mm-30)
REVERT: A  478 ARG cc_start: 0.7343 (ptp-170) cc_final: 0.7134 (ptm160)
REVERT: A  516 GLU cc_start: 0.8033 (tt0) cc_final: 0.7443 (mt-10)
REVERT: B  359 LEU cc_start: 0.3011 (OUTLIER) cc_final: 0.2609 (tm)
REVERT: B  437 ARG cc_start: 0.2228 (OUTLIER) cc_final: 0.1647 (pmt170)
REVERT: C  174 ASP cc_start: 0.8161 (m-30) cc_final: 0.7722 (t0)
REVERT: C  196 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6640 (p0)
REVERT: C  197 GLU cc_start: 0.3251 (OUTLIER) cc_final: 0.2203 (tt0)
REVERT: C  228 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7776 (ttm170)
REVERT: C  238 ARG cc_start: 0.7880 (ptp90) cc_final: 0.6365 (tmt90)
REVERT: C  336 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5140 (mp0)
REVERT: C  374 VAL cc_start: 0.5894 (OUTLIER) cc_final: 0.5656 (p)
REVERT: C  407 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6541 (tt0)
REVERT: C  410 ASP cc_start: 0.5954 (m-30) cc_final: 0.5620 (m-30)
REVERT: C  436 MET cc_start: 0.6658 (mmt) cc_final: 0.6214 (mmt)
REVERT: C  509 PHE cc_start: 0.6857 (m-80) cc_final: 0.6348 (m-80)
  outliers start: 63
  outliers final: 33
  residues processed: 163
  average time/residue: 1.2081
  time to fit residues: 217.1666
Evaluate side-chains
  149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 106
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  437 ARG
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  196 ASP
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  514 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 131 optimal weight:    7.9990
   chunk 111 optimal weight:    0.6980
   chunk 110 optimal weight:    7.9990
   chunk 105 optimal weight:    5.9990
   chunk 127 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 116 optimal weight:    0.7980
   chunk 128 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 35 optimal weight:   20.0000
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 GLN
B 263 GLN

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 = 0.219605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.147717 restraints weight = 11769.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 7.92
r_work: 0.2954 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.6724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12217  Z= 0.136
  Angle     :  0.658  10.378  16770  Z= 0.335
  Chirality :  0.047   0.186   1921
  Planarity :  0.006   0.053   2182
  Dihedral  :  6.824  57.208   1871
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.28 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.89 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.20), residues: 1528
  helix: -1.08 (0.61), residues: 53
  sheet: -0.15 (0.25), residues: 410
  loop : -1.42 (0.18), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 169 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.016   0.002   PHE C  80 
 TYR   0.018   0.001   TYR A 217 
 ARG   0.008   0.000   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  272)
  hydrogen bonds       : angle       5.60851 (  705)
  covalent geometry    : bond        0.00325 (12217)
  covalent geometry    : angle       0.65804 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 117
  time to evaluate  : 1.278 
Fit side-chains
REVERT: A  148 MET cc_start: 0.9025 (ttm) cc_final: 0.8494 (tpp)
REVERT: A  154 LEU cc_start: 0.8839 (mp) cc_final: 0.8458 (mt)
REVERT: A  471 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7535 (mm-30)
REVERT: A  478 ARG cc_start: 0.7257 (ptp-170) cc_final: 0.7000 (ptm160)
REVERT: A  516 GLU cc_start: 0.7941 (tt0) cc_final: 0.7366 (mt-10)
REVERT: B   72 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8357 (mpp80)
REVERT: B  359 LEU cc_start: 0.2873 (OUTLIER) cc_final: 0.2525 (tm)
REVERT: C  174 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7757 (t0)
REVERT: C  197 GLU cc_start: 0.2751 (OUTLIER) cc_final: 0.2014 (tt0)
REVERT: C  228 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7658 (ttm170)
REVERT: C  238 ARG cc_start: 0.7833 (ptp90) cc_final: 0.6319 (tmt90)
REVERT: C  322 ARG cc_start: 0.6516 (ttp-110) cc_final: 0.6283 (ttm110)
REVERT: C  336 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.5073 (mp0)
REVERT: C  407 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6289 (tt0)
REVERT: C  410 ASP cc_start: 0.5850 (m-30) cc_final: 0.5222 (m-30)
REVERT: C  436 MET cc_start: 0.6762 (mmt) cc_final: 0.6253 (mmt)
REVERT: C  482 THR cc_start: 0.7058 (p) cc_final: 0.6832 (t)
REVERT: C  509 PHE cc_start: 0.6765 (m-80) cc_final: 0.6255 (m-80)
  outliers start: 47
  outliers final: 25
  residues processed: 151
  average time/residue: 1.2166
  time to fit residues: 199.6026
Evaluate side-chains
  144 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   72 ARG
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  471 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 133 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 104 optimal weight:    0.9980
   chunk 137 optimal weight:   20.0000
   chunk 146 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 116 optimal weight:   10.0000
   chunk 129 optimal weight:   20.0000
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.218314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.145169 restraints weight = 11717.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 8.38
r_work: 0.2926 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.6985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12217  Z= 0.175
  Angle     :  0.711  12.209  16770  Z= 0.363
  Chirality :  0.048   0.220   1921
  Planarity :  0.006   0.056   2182
  Dihedral  :  6.948  59.480   1871
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.54 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 25.33 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.20), residues: 1528
  helix: -1.28 (0.60), residues: 53
  sheet: -0.13 (0.25), residues: 412
  loop : -1.47 (0.17), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 169 
 HIS   0.005   0.001   HIS C 242 
 PHE   0.014   0.002   PHE C 487 
 TYR   0.020   0.002   TYR B 217 
 ARG   0.005   0.001   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04102 (  272)
  hydrogen bonds       : angle       5.67970 (  705)
  covalent geometry    : bond        0.00429 (12217)
  covalent geometry    : angle       0.71138 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 111
  time to evaluate  : 1.178 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7673 (mm-30) cc_final: 0.6988 (tm-30)
REVERT: A  148 MET cc_start: 0.9055 (ttm) cc_final: 0.8527 (tpp)
REVERT: A  154 LEU cc_start: 0.8832 (mp) cc_final: 0.8455 (mt)
REVERT: A  471 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7582 (mm-30)
REVERT: A  478 ARG cc_start: 0.7331 (ptp-170) cc_final: 0.7044 (ptm160)
REVERT: A  516 GLU cc_start: 0.7885 (tt0) cc_final: 0.7445 (mt-10)
REVERT: B   72 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8341 (mpp80)
REVERT: B  359 LEU cc_start: 0.2871 (OUTLIER) cc_final: 0.2510 (tm)
REVERT: C  155 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7704 (mp0)
REVERT: C  174 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7741 (t0)
REVERT: C  197 GLU cc_start: 0.2892 (OUTLIER) cc_final: 0.1944 (tt0)
REVERT: C  228 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7749 (ttm170)
REVERT: C  238 ARG cc_start: 0.7796 (ptp90) cc_final: 0.6365 (tmt90)
REVERT: C  322 ARG cc_start: 0.6648 (ttp-110) cc_final: 0.6438 (ttm110)
REVERT: C  336 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.5082 (mp0)
REVERT: C  407 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6621 (tt0)
REVERT: C  410 ASP cc_start: 0.5745 (m-30) cc_final: 0.5471 (m-30)
REVERT: C  436 MET cc_start: 0.6866 (mmt) cc_final: 0.6385 (mmt)
REVERT: C  509 PHE cc_start: 0.6935 (m-80) cc_final: 0.6442 (m-80)
  outliers start: 50
  outliers final: 31
  residues processed: 147
  average time/residue: 1.1441
  time to fit residues: 183.5746
Evaluate side-chains
  148 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   72 ARG
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 133 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 89 optimal weight:    7.9990
   chunk 145 optimal weight:   10.0000
   chunk 48 optimal weight:    8.9990
   chunk 117 optimal weight:    2.9990
   chunk 84 optimal weight:   40.0000
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.218504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.146408 restraints weight = 11678.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 7.89
r_work: 0.2939 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.7145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12217  Z= 0.169
  Angle     :  0.691  11.373  16770  Z= 0.353
  Chirality :  0.048   0.197   1921
  Planarity :  0.006   0.054   2182
  Dihedral  :  6.921  59.626   1871
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.02 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 25.96 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.20), residues: 1528
  helix: -1.23 (0.61), residues: 53
  sheet: -0.12 (0.24), residues: 418
  loop : -1.46 (0.18), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 169 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.015   0.002   PHE C  80 
 TYR   0.020   0.002   TYR A 217 
 ARG   0.005   0.001   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  272)
  hydrogen bonds       : angle       5.66643 (  705)
  covalent geometry    : bond        0.00414 (12217)
  covalent geometry    : angle       0.69097 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 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: 46
    poor density    : 107
  time to evaluate  : 1.263 
Fit side-chains
REVERT: A  148 MET cc_start: 0.9046 (ttm) cc_final: 0.8515 (tpp)
REVERT: A  154 LEU cc_start: 0.8825 (mp) cc_final: 0.8471 (mt)
REVERT: A  471 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7599 (mm-30)
REVERT: A  478 ARG cc_start: 0.7330 (ptp-170) cc_final: 0.7033 (ptm160)
REVERT: A  516 GLU cc_start: 0.7877 (tt0) cc_final: 0.7501 (mt-10)
REVERT: B   72 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8353 (mpp80)
REVERT: B  359 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2513 (tm)
REVERT: C  155 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7712 (mp0)
REVERT: C  174 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7766 (t0)
REVERT: C  197 GLU cc_start: 0.2682 (OUTLIER) cc_final: 0.1893 (tt0)
REVERT: C  228 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7643 (ttm170)
REVERT: C  238 ARG cc_start: 0.7800 (ptp90) cc_final: 0.6380 (tmt90)
REVERT: C  336 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4872 (mp0)
REVERT: C  407 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6408 (tt0)
REVERT: C  410 ASP cc_start: 0.5739 (m-30) cc_final: 0.5034 (m-30)
REVERT: C  436 MET cc_start: 0.6901 (mmt) cc_final: 0.6459 (mmt)
REVERT: C  509 PHE cc_start: 0.6995 (m-80) cc_final: 0.6479 (m-80)
  outliers start: 46
  outliers final: 31
  residues processed: 142
  average time/residue: 1.1235
  time to fit residues: 174.3686
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  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   72 ARG
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  471 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 124 optimal weight:   20.0000
   chunk 144 optimal weight:   20.0000
   chunk 89 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 139 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 28 optimal weight:   40.0000
   chunk 122 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B 340 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.221301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.167110 restraints weight = 11722.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 4.36
r_work: 0.3044 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.7162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12217  Z= 0.104
  Angle     :  0.607  11.556  16770  Z= 0.308
  Chirality :  0.045   0.152   1921
  Planarity :  0.006   0.051   2182
  Dihedral  :  6.608  59.108   1871
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.15 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 26.67 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.20), residues: 1528
  helix: -0.75 (0.63), residues: 53
  sheet: -0.01 (0.25), residues: 419
  loop : -1.30 (0.18), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 169 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.016   0.001   PHE C  80 
 TYR   0.013   0.001   TYR A 217 
 ARG   0.005   0.000   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  272)
  hydrogen bonds       : angle       5.44356 (  705)
  covalent geometry    : bond        0.00239 (12217)
  covalent geometry    : angle       0.60745 (16770)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 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: 37
    poor density    : 115
  time to evaluate  : 1.299 
Fit side-chains
REVERT: A  148 MET cc_start: 0.8879 (ttm) cc_final: 0.8338 (tpp)
REVERT: A  154 LEU cc_start: 0.8803 (mp) cc_final: 0.8442 (mt)
REVERT: A  434 THR cc_start: 0.7365 (m) cc_final: 0.6909 (m)
REVERT: A  478 ARG cc_start: 0.7307 (ptp-170) cc_final: 0.7009 (ptm160)
REVERT: A  488 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6255 (mt-10)
REVERT: A  516 GLU cc_start: 0.7797 (tt0) cc_final: 0.7503 (mt-10)
REVERT: B  141 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9098 (tt)
REVERT: B  359 LEU cc_start: 0.3034 (OUTLIER) cc_final: 0.2646 (tm)
REVERT: C  155 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7746 (mp0)
REVERT: C  174 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7753 (t0)
REVERT: C  197 GLU cc_start: 0.3566 (tt0) cc_final: 0.3012 (tt0)
REVERT: C  228 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7624 (ttm170)
REVERT: C  238 ARG cc_start: 0.7794 (ptp90) cc_final: 0.6405 (tmt90)
REVERT: C  322 ARG cc_start: 0.6799 (ttp-110) cc_final: 0.6582 (ttm110)
REVERT: C  336 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.4874 (mp0)
REVERT: C  407 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6413 (tt0)
REVERT: C  410 ASP cc_start: 0.5716 (m-30) cc_final: 0.5070 (m-30)
REVERT: C  436 MET cc_start: 0.6875 (mmt) cc_final: 0.6435 (mmt)
REVERT: C  482 THR cc_start: 0.7189 (p) cc_final: 0.6966 (t)
REVERT: C  509 PHE cc_start: 0.6933 (m-80) cc_final: 0.6412 (m-80)
  outliers start: 37
  outliers final: 28
  residues processed: 142
  average time/residue: 1.2272
  time to fit residues: 190.7723
Evaluate side-chains
  144 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  521 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  228 ARG
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain C residue  288 CYS
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  341 THR
Chi-restraints excluded: chain C residue  407 GLU
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 115 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 150 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 141 optimal weight:    5.9990
   overall best weight:    2.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.219877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.148834 restraints weight = 11659.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 7.82
r_work: 0.2967 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.7223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12217  Z= 0.123
  Angle     :  0.635  11.502  16770  Z= 0.323
  Chirality :  0.046   0.175   1921
  Planarity :  0.006   0.052   2182
  Dihedral  :  6.606  58.800   1871
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.96 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 26.28 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.75 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.20), residues: 1528
  helix: -0.74 (0.63), residues: 53
  sheet: -0.03 (0.25), residues: 423
  loop : -1.26 (0.18), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 169 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.014   0.002   PHE C  80 
 TYR   0.015   0.001   TYR B 217 
 ARG   0.009   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  272)
  hydrogen bonds       : angle       5.47012 (  705)
  covalent geometry    : bond        0.00292 (12217)
  covalent geometry    : angle       0.63497 (16770)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8881.23 seconds
wall clock time: 154 minutes 19.66 seconds (9259.66 seconds total)