Starting phenix.real_space_refine
on Sun Nov 17 01:39:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/11_2024/7xyc_33519.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/11_2024/7xyc_33519.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/11_2024/7xyc_33519.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/11_2024/7xyc_33519.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/11_2024/7xyc_33519.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyc_33519/11_2024/7xyc_33519.cif"
  }
  resolution = 3.8
  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=   0.000 sd=   0.005
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      54      5.16       5
     C    7944      2.51       5
     N    2148      2.21       5
     O    2475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 12621
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 4207
          Classifications: {'peptide': 562}
          Link IDs: {'PTRANS': 16, 'TRANS': 545}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 8.29, per 1000 atoms: 0.66
  Number of scatterers: 12621
  At special positions: 0
  Unit cell: (91.26, 90.09, 136.89, 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      54     16.00
     O    2475      8.00
     N    2148      7.00
     C    7944      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: 2.91
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 27 sheets defined
      6.2% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 28
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.857A  pdb=" N   SER A 114 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.574A  pdb=" N   ASP A 390 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'B' and resid 21 through 28
    Processing helix  chain 'B' and resid 89 through 91
      No H-bonds generated for 'chain 'B' and resid 89 through 91'
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.857A  pdb=" N   SER B 114 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.574A  pdb=" N   ASP B 390 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
    Processing helix  chain 'C' and resid 21 through 28
    Processing helix  chain 'C' and resid 89 through 91
      No H-bonds generated for 'chain 'C' and resid 89 through 91'
    Processing helix  chain 'C' and resid 101 through 114
      removed outlier: 3.857A  pdb=" N   SER C 114 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 390
      removed outlier: 3.574A  pdb=" N   ASP C 390 " --> pdb=" O   GLN C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 426
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19
      removed outlier: 6.352A  pdb=" N   TRP A  17 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU A  53 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87
      removed outlier: 6.755A  pdb=" N   ILE A  86 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136
      removed outlier: 7.116A  pdb=" N   GLY A 198 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU A 199 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE A 230 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 151
    Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184
      removed outlier: 6.133A  pdb=" N   LEU A 183 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR A 216 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR A 242 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE A 218 " --> pdb=" O   TYR A 242 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   ILE A 239 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   TYR A 272 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   PHE A 241 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   PHE A 291 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR A 316 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET A 293 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   LEU A 318 " --> pdb=" O   MET A 293 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE A 295 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   VAL A 313 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ASN A 345 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL A 315 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL A 347 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA A 317 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE A 344 " --> pdb=" O   ASN A 373 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   SER A 375 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL A 346 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE A 372 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   SER A 406 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A 374 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 222 through 224
      removed outlier: 6.866A  pdb=" N   PHE A 223 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A 246 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 286
      removed outlier: 5.994A  pdb=" N   ILE A 284 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE A 305 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE A 334 " --> pdb=" O   HIS A 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 445
      removed outlier: 3.754A  pdb=" N   VAL A 476 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR A 559 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY A 522 " --> pdb=" O   TYR A 513 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 456
      removed outlier: 3.727A  pdb=" N   LEU A 456 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A 567 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE A 570 " --> pdb=" O   SER A 494 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER A 494 " --> pdb=" O   ILE A 570 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19
      removed outlier: 6.352A  pdb=" N   TRP B  17 " --> pdb=" O   PHE B  39 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU B  53 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 87
      removed outlier: 6.755A  pdb=" N   ILE B  86 " --> pdb=" O   PHE B 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 136
      removed outlier: 7.116A  pdb=" N   GLY B 198 " --> pdb=" O   TYR B 160 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   ARG B 231 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU B 199 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE B 230 " --> pdb=" O   TYR B 257 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 151
    Processing sheet with id=AB5, first strand: chain 'B' and resid 183 through 184
      removed outlier: 6.133A  pdb=" N   LEU B 183 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR B 216 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR B 242 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE B 218 " --> pdb=" O   TYR B 242 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE B 239 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   TYR B 272 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   PHE B 241 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   PHE B 291 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR B 316 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET B 293 " --> pdb=" O   THR B 316 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   LEU B 318 " --> pdb=" O   MET B 293 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE B 295 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   VAL B 313 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   ASN B 345 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL B 315 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL B 347 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA B 317 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE B 344 " --> pdb=" O   ASN B 373 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   SER B 375 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL B 346 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE B 372 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   SER B 406 " --> pdb=" O   ILE B 372 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU B 374 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 222 through 224
      removed outlier: 6.866A  pdb=" N   PHE B 223 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER B 246 " --> pdb=" O   GLN B 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 284 through 286
      removed outlier: 5.994A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 306 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE B 305 " --> pdb=" O   GLU B 335 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE B 334 " --> pdb=" O   HIS B 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 442 through 445
      removed outlier: 3.754A  pdb=" N   VAL B 476 " --> pdb=" O   THR B 559 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B 559 " --> pdb=" O   VAL B 476 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY B 522 " --> pdb=" O   TYR B 513 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 455 through 456
      removed outlier: 3.728A  pdb=" N   LEU B 456 " --> pdb=" O   VAL B 466 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR B 567 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE B 570 " --> pdb=" O   SER B 494 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER B 494 " --> pdb=" O   ILE B 570 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 17 through 19
      removed outlier: 6.352A  pdb=" N   TRP C  17 " --> pdb=" O   PHE C  39 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU C  53 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87
      removed outlier: 6.755A  pdb=" N   ILE C  86 " --> pdb=" O   PHE C 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 136
      removed outlier: 7.116A  pdb=" N   GLY C 198 " --> pdb=" O   TYR C 160 " (cutoff:3.500A)
      removed outlier: 8.670A  pdb=" N   ARG C 231 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU C 199 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ILE C 230 " --> pdb=" O   TYR C 257 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 151
    Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 184
      removed outlier: 6.132A  pdb=" N   LEU C 183 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   THR C 216 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR C 242 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE C 218 " --> pdb=" O   TYR C 242 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE C 239 " --> pdb=" O   THR C 270 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   TYR C 272 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   PHE C 241 " --> pdb=" O   TYR C 272 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   PHE C 291 " --> pdb=" O   SER C 314 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR C 316 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET C 293 " --> pdb=" O   THR C 316 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   LEU C 318 " --> pdb=" O   MET C 293 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE C 295 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   VAL C 313 " --> pdb=" O   ILE C 343 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ASN C 345 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL C 315 " --> pdb=" O   ASN C 345 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL C 347 " --> pdb=" O   VAL C 315 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA C 317 " --> pdb=" O   VAL C 347 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE C 344 " --> pdb=" O   ASN C 373 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   SER C 375 " --> pdb=" O   PHE C 344 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL C 346 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE C 372 " --> pdb=" O   SER C 404 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   SER C 406 " --> pdb=" O   ILE C 372 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU C 374 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 222 through 224
      removed outlier: 6.866A  pdb=" N   PHE C 223 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER C 246 " --> pdb=" O   GLN C 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'C' and resid 284 through 286
      removed outlier: 5.994A  pdb=" N   ILE C 284 " --> pdb=" O   THR C 306 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE C 305 " --> pdb=" O   GLU C 335 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE C 334 " --> pdb=" O   HIS C 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'C' and resid 442 through 445
      removed outlier: 3.754A  pdb=" N   VAL C 476 " --> pdb=" O   THR C 559 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR C 559 " --> pdb=" O   VAL C 476 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLY C 522 " --> pdb=" O   TYR C 513 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 455 through 456
      removed outlier: 3.727A  pdb=" N   LEU C 456 " --> pdb=" O   VAL C 466 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR C 567 " --> pdb=" O   LEU C 467 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE C 570 " --> pdb=" O   SER C 494 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER C 494 " --> pdb=" O   ILE C 570 " (cutoff:3.500A)

    210 hydrogen bonds defined for protein.
    513 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.23

  Time building geometry restraints manager: 3.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4143
        1.35 -     1.46: 3170
        1.46 -     1.58: 5500
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 12888
  Sorted by residual:
  bond pdb=" CA  TYR B 176 "
       pdb=" CB  TYR B 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.62e-02 3.81e+03 2.19e+00
  bond pdb=" CA  TYR C 176 "
       pdb=" CB  TYR C 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.62e-02 3.81e+03 2.18e+00
  bond pdb=" CA  TYR A 176 "
       pdb=" CB  TYR A 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.62e-02 3.81e+03 2.17e+00
  bond pdb=" N   GLY B 233 "
       pdb=" CA  GLY B 233 "
    ideal  model  delta    sigma   weight residual
    1.442  1.450 -0.008 7.70e-03 1.69e+04 1.10e+00
  bond pdb=" N   GLY A 233 "
       pdb=" CA  GLY A 233 "
    ideal  model  delta    sigma   weight residual
    1.442  1.450 -0.008 7.70e-03 1.69e+04 1.08e+00
  ... (remaining 12883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 16816
        1.32 -     2.64: 537
        2.64 -     3.95: 117
        3.95 -     5.27: 44
        5.27 -     6.59: 15
  Bond angle restraints: 17529
  Sorted by residual:
  angle pdb=" CA  ILE C 268 "
        pdb=" CB  ILE C 268 "
        pdb=" CG2 ILE C 268 "
      ideal   model   delta    sigma   weight residual
     110.50  115.24   -4.74 1.70e+00 3.46e-01 7.78e+00
  angle pdb=" CA  ILE A 268 "
        pdb=" CB  ILE A 268 "
        pdb=" CG2 ILE A 268 "
      ideal   model   delta    sigma   weight residual
     110.50  115.24   -4.74 1.70e+00 3.46e-01 7.76e+00
  angle pdb=" CA  ILE B 268 "
        pdb=" CB  ILE B 268 "
        pdb=" CG2 ILE B 268 "
      ideal   model   delta    sigma   weight residual
     110.50  115.23   -4.73 1.70e+00 3.46e-01 7.74e+00
  angle pdb=" C   ASP C 263 "
        pdb=" N   ASP C 264 "
        pdb=" CA  ASP C 264 "
      ideal   model   delta    sigma   weight residual
     121.54  126.80   -5.26 1.91e+00 2.74e-01 7.59e+00
  angle pdb=" C   SER C 447 "
        pdb=" CA  SER C 447 "
        pdb=" CB  SER C 447 "
      ideal   model   delta    sigma   weight residual
     110.42  115.89   -5.47 1.99e+00 2.53e-01 7.55e+00
  ... (remaining 17524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 6752
       16.50 -    32.99: 540
       32.99 -    49.49: 127
       49.49 -    65.99: 9
       65.99 -    82.48: 30
  Dihedral angle restraints: 7458
    sinusoidal: 2685
      harmonic: 4773
  Sorted by residual:
  dihedral pdb=" CA  LYS B 115 "
           pdb=" C   LYS B 115 "
           pdb=" N   LEU B 116 "
           pdb=" CA  LEU B 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.96  -15.04     0      5.00e+00 4.00e-02 9.05e+00
  dihedral pdb=" CA  LYS A 115 "
           pdb=" C   LYS A 115 "
           pdb=" N   LEU A 116 "
           pdb=" CA  LEU A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.98  -15.02     0      5.00e+00 4.00e-02 9.02e+00
  dihedral pdb=" CA  LYS C 115 "
           pdb=" C   LYS C 115 "
           pdb=" N   LEU C 116 "
           pdb=" CA  LEU C 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.02  -14.98     0      5.00e+00 4.00e-02 8.98e+00
  ... (remaining 7455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1584
       0.054 -    0.108: 327
       0.108 -    0.162: 72
       0.162 -    0.216: 0
       0.216 -    0.270: 3
  Chirality restraints: 1986
  Sorted by residual:
  chirality pdb=" CB  ILE C 268 "
            pdb=" CA  ILE C 268 "
            pdb=" CG1 ILE C 268 "
            pdb=" CG2 ILE C 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CB  ILE B 268 "
            pdb=" CA  ILE B 268 "
            pdb=" CG1 ILE B 268 "
            pdb=" CG2 ILE B 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  ILE A 268 "
            pdb=" CA  ILE A 268 "
            pdb=" CG1 ILE A 268 "
            pdb=" CG2 ILE A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1983 not shown)

  Planarity restraints: 2268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 448 "   -0.052 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO C 449 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO C 449 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 449 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 448 "   -0.052 5.00e-02 4.00e+02   7.96e-02 1.01e+01
        pdb=" N   PRO A 449 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 449 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 449 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 448 "    0.052 5.00e-02 4.00e+02   7.96e-02 1.01e+01
        pdb=" N   PRO B 449 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.043 5.00e-02 4.00e+02
  ... (remaining 2265 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2059
        2.77 -     3.30: 12265
        3.30 -     3.83: 20182
        3.83 -     4.37: 23268
        4.37 -     4.90: 41722
  Nonbonded interactions: 99496
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 205 "
            pdb=" OD1 ASP A 207 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR B 205 "
            pdb=" OD1 ASP B 207 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR C 205 "
            pdb=" OD1 ASP C 207 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE C 336 "
            pdb=" OG  SER C 367 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ILE B 336 "
            pdb=" OG  SER B 367 "
     model   vdw
     2.289 3.040
  ... (remaining 99491 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'
  selection = chain 'B'
  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 group one per residue
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:                  0.010
  Normalize map: mean=0, sd=1:             0.400
  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:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.080
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12888  Z= 0.153
  Angle     :  0.631   6.591  17529  Z= 0.341
  Chirality :  0.046   0.270   1986
  Planarity :  0.004   0.080   2268
  Dihedral  : 13.853  82.483   4446
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.14 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.18), residues: 1680
  helix:  2.87 (0.70), residues: 63
  sheet:  0.40 (0.23), residues: 462
  loop : -2.30 (0.15), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 237 
 HIS   0.004   0.001   HIS B 468 
 PHE   0.014   0.001   PHE C 300 
 TYR   0.018   0.001   TYR B 176 
 ARG   0.002   0.000   ARG B 543 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.306 
Fit side-chains
REVERT: A  375 SER cc_start: 0.8872 (m) cc_final: 0.8670 (m)
REVERT: A  454 GLU cc_start: 0.7416 (pp20) cc_final: 0.7094 (pt0)
REVERT: B   83 ASP cc_start: 0.7603 (t0) cc_final: 0.7385 (t0)
REVERT: B  375 SER cc_start: 0.8955 (m) cc_final: 0.8658 (m)
REVERT: C   83 ASP cc_start: 0.7412 (t0) cc_final: 0.7054 (t0)
REVERT: C  268 ILE cc_start: 0.8651 (tp) cc_final: 0.8450 (tp)
REVERT: C  454 GLU cc_start: 0.7465 (pp20) cc_final: 0.7092 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1871
  time to fit residues: 61.8182
Evaluate side-chains
  150 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.8980
   chunk 127 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 131 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 152 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 387 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN
B 387 GLN
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 ASN
C 387 GLN
** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12888  Z= 0.324
  Angle     :  0.650   6.372  17529  Z= 0.344
  Chirality :  0.049   0.249   1986
  Planarity :  0.004   0.055   2268
  Dihedral  :  4.734  17.859   1812
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.51 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.36 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.19), residues: 1680
  helix:  2.45 (0.72), residues: 63
  sheet: -0.20 (0.22), residues: 552
  loop : -2.27 (0.16), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 237 
 HIS   0.006   0.001   HIS C 468 
 PHE   0.011   0.002   PHE C 322 
 TYR   0.020   0.001   TYR B 176 
 ARG   0.003   0.001   ARG C  80 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.455 
Fit side-chains
REVERT: A  496 MET cc_start: 0.9020 (mmm) cc_final: 0.8780 (mmm)
REVERT: B   83 ASP cc_start: 0.7508 (t0) cc_final: 0.7303 (t70)
REVERT: B  232 MET cc_start: 0.8534 (mmt) cc_final: 0.8253 (mmt)
REVERT: C   83 ASP cc_start: 0.7352 (t0) cc_final: 0.7031 (t0)
REVERT: C  268 ILE cc_start: 0.9105 (tp) cc_final: 0.8866 (tp)
REVERT: C  370 ASN cc_start: 0.8099 (m-40) cc_final: 0.7827 (m110)
  outliers start: 29
  outliers final: 21
  residues processed: 168
  average time/residue: 0.1899
  time to fit residues: 51.9016
Evaluate side-chains
  146 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  235 ASN
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  467 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 84 optimal weight:    0.0870
   chunk 47 optimal weight:    7.9990
   chunk 126 optimal weight:    5.9990
   chunk 103 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 152 optimal weight:    0.9980
   chunk 165 optimal weight:    5.9990
   chunk 136 optimal weight:    0.0980
   chunk 151 optimal weight:    0.0770
   chunk 52 optimal weight:    6.9990
   chunk 122 optimal weight:    0.6980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
A 273 HIS
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 HIS
B 370 ASN
B 573 ASN
C 273 HIS
** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12888  Z= 0.151
  Angle     :  0.557   5.978  17529  Z= 0.292
  Chirality :  0.046   0.234   1986
  Planarity :  0.003   0.042   2268
  Dihedral  :  4.345  17.427   1812
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.87 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.19), residues: 1680
  helix:  2.71 (0.71), residues: 63
  sheet: -0.06 (0.22), residues: 552
  loop : -2.24 (0.16), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 237 
 HIS   0.005   0.001   HIS C 422 
 PHE   0.007   0.001   PHE B 322 
 TYR   0.014   0.001   TYR A 176 
 ARG   0.003   0.000   ARG C  80 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 1.487 
Fit side-chains
REVERT: A  180 SER cc_start: 0.8961 (p) cc_final: 0.8345 (m)
REVERT: A  496 MET cc_start: 0.9023 (mmm) cc_final: 0.8765 (mmm)
REVERT: B  137 ASP cc_start: 0.8010 (t70) cc_final: 0.7502 (t0)
REVERT: B  180 SER cc_start: 0.9023 (p) cc_final: 0.8495 (m)
REVERT: B  224 ASP cc_start: 0.7789 (p0) cc_final: 0.7416 (p0)
REVERT: B  232 MET cc_start: 0.8540 (mmt) cc_final: 0.8148 (mmt)
REVERT: C   83 ASP cc_start: 0.7294 (t0) cc_final: 0.6985 (t0)
REVERT: C  370 ASN cc_start: 0.8105 (m-40) cc_final: 0.7859 (m-40)
REVERT: C  454 GLU cc_start: 0.7469 (pp20) cc_final: 0.7130 (pp20)
  outliers start: 27
  outliers final: 24
  residues processed: 169
  average time/residue: 0.1693
  time to fit residues: 46.8304
Evaluate side-chains
  152 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 79 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 153 optimal weight:    0.9990
   chunk 162 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 145 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
A 273 HIS
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 HIS
C 273 HIS
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  12888  Z= 0.330
  Angle     :  0.622   6.022  17529  Z= 0.333
  Chirality :  0.049   0.286   1986
  Planarity :  0.003   0.049   2268
  Dihedral  :  4.834  17.961   1812
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 14.62 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.19), residues: 1680
  helix:  0.93 (0.64), residues: 81
  sheet: -0.18 (0.22), residues: 552
  loop : -2.36 (0.16), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 237 
 HIS   0.006   0.001   HIS C 468 
 PHE   0.014   0.002   PHE A  54 
 TYR   0.023   0.001   TYR C 176 
 ARG   0.003   0.000   ARG C 238 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 132
  time to evaluate  : 1.400 
Fit side-chains
REVERT: A   43 TRP cc_start: 0.9276 (t60) cc_final: 0.8737 (t60)
REVERT: A  180 SER cc_start: 0.9160 (p) cc_final: 0.8638 (m)
REVERT: A  496 MET cc_start: 0.9070 (mmm) cc_final: 0.8787 (mmm)
REVERT: B  180 SER cc_start: 0.9117 (p) cc_final: 0.8540 (m)
REVERT: B  232 MET cc_start: 0.8590 (mmt) cc_final: 0.8148 (mmt)
REVERT: C   83 ASP cc_start: 0.7394 (t0) cc_final: 0.7065 (t0)
REVERT: C  180 SER cc_start: 0.9082 (p) cc_final: 0.8562 (m)
REVERT: C  370 ASN cc_start: 0.8248 (m-40) cc_final: 0.8034 (m-40)
  outliers start: 59
  outliers final: 38
  residues processed: 177
  average time/residue: 0.1804
  time to fit residues: 51.8763
Evaluate side-chains
  159 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  235 ASN
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 120 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 138 optimal weight:    0.6980
   chunk 112 optimal weight:    0.0870
   chunk 0 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0070
   chunk 145 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 414 ASN
A 498 ASN
A 566 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 468 HIS
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 498 ASN
C 566 GLN
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 573 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12888  Z= 0.175
  Angle     :  0.564   5.958  17529  Z= 0.299
  Chirality :  0.047   0.269   1986
  Planarity :  0.003   0.043   2268
  Dihedral  :  4.511  17.721   1812
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 16.81 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.19), residues: 1680
  helix:  1.14 (0.64), residues: 81
  sheet: -0.41 (0.21), residues: 612
  loop : -2.24 (0.17), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 237 
 HIS   0.007   0.001   HIS C 422 
 PHE   0.011   0.001   PHE A 322 
 TYR   0.016   0.001   TYR B 176 
 ARG   0.002   0.000   ARG C  80 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 136
  time to evaluate  : 1.377 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9019 (p) cc_final: 0.8433 (m)
REVERT: A  496 MET cc_start: 0.8988 (mmm) cc_final: 0.8672 (mmm)
REVERT: B  180 SER cc_start: 0.9054 (p) cc_final: 0.8538 (m)
REVERT: B  232 MET cc_start: 0.8541 (mmt) cc_final: 0.8050 (mmt)
REVERT: B  277 PHE cc_start: 0.8856 (p90) cc_final: 0.8653 (p90)
REVERT: C   83 ASP cc_start: 0.7358 (t0) cc_final: 0.7055 (t0)
REVERT: C  180 SER cc_start: 0.9057 (p) cc_final: 0.8529 (m)
REVERT: C  575 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8210 (tp)
  outliers start: 55
  outliers final: 36
  residues processed: 180
  average time/residue: 0.1774
  time to fit residues: 52.1160
Evaluate side-chains
  166 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  414 ASN
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 146 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 40 optimal weight:    0.3980
   chunk 162 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 414 ASN
A 498 ASN
A 566 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 498 ASN
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12888  Z= 0.281
  Angle     :  0.598   6.061  17529  Z= 0.318
  Chirality :  0.049   0.263   1986
  Planarity :  0.003   0.038   2268
  Dihedral  :  4.675  18.177   1812
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 16.74 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.19), residues: 1680
  helix:  1.02 (0.64), residues: 81
  sheet: -0.39 (0.22), residues: 579
  loop : -2.29 (0.17), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 237 
 HIS   0.006   0.001   HIS C 422 
 PHE   0.014   0.001   PHE A 322 
 TYR   0.017   0.001   TYR B 176 
 ARG   0.003   0.000   ARG C 238 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 138
  time to evaluate  : 1.270 
Fit side-chains
REVERT: A   43 TRP cc_start: 0.9203 (t60) cc_final: 0.8941 (t60)
REVERT: A  180 SER cc_start: 0.9127 (p) cc_final: 0.8563 (m)
REVERT: A  496 MET cc_start: 0.9033 (mmm) cc_final: 0.8827 (mmm)
REVERT: B  180 SER cc_start: 0.9114 (p) cc_final: 0.8557 (m)
REVERT: B  232 MET cc_start: 0.8519 (mmt) cc_final: 0.8064 (mmt)
REVERT: C   83 ASP cc_start: 0.7328 (t0) cc_final: 0.7018 (t0)
REVERT: C  180 SER cc_start: 0.9086 (p) cc_final: 0.8552 (m)
  outliers start: 58
  outliers final: 46
  residues processed: 180
  average time/residue: 0.2007
  time to fit residues: 56.8750
Evaluate side-chains
  177 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  565 VAL
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 92 optimal weight:    0.0040
   chunk 118 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 136 optimal weight:    0.3980
   chunk 90 optimal weight:    0.0020
   chunk 161 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.0804

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 GLN
A 573 ASN
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12888  Z= 0.210
  Angle     :  0.570   7.283  17529  Z= 0.303
  Chirality :  0.048   0.258   1986
  Planarity :  0.003   0.036   2268
  Dihedral  :  4.578  17.329   1812
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 17.47 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.20), residues: 1680
  helix:  1.10 (0.64), residues: 81
  sheet: -0.26 (0.22), residues: 603
  loop : -2.30 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 237 
 HIS   0.006   0.001   HIS C 422 
 PHE   0.013   0.001   PHE A 322 
 TYR   0.013   0.001   TYR B 176 
 ARG   0.002   0.000   ARG C 238 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 129
  time to evaluate  : 1.505 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9108 (p) cc_final: 0.8532 (m)
REVERT: A  496 MET cc_start: 0.9083 (mmm) cc_final: 0.8844 (mmm)
REVERT: B  180 SER cc_start: 0.9074 (p) cc_final: 0.8541 (m)
REVERT: B  232 MET cc_start: 0.8519 (mmt) cc_final: 0.8090 (mmt)
REVERT: C   83 ASP cc_start: 0.7400 (t0) cc_final: 0.7082 (t0)
REVERT: C  180 SER cc_start: 0.9082 (p) cc_final: 0.8556 (m)
  outliers start: 60
  outliers final: 55
  residues processed: 173
  average time/residue: 0.1962
  time to fit residues: 54.2975
Evaluate side-chains
  183 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 128
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0370
   chunk 96 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 102 optimal weight:    7.9990
   chunk 110 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 127 optimal weight:    7.9990
   chunk 147 optimal weight:    0.9980
   overall best weight:    2.0064

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

Flipped N/Q/H residues before XYZ refinement:
A 566 GLN
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12888  Z= 0.324
  Angle     :  0.611   6.116  17529  Z= 0.327
  Chirality :  0.049   0.260   1986
  Planarity :  0.003   0.031   2268
  Dihedral  :  4.857  17.759   1812
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 17.32 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.20), residues: 1680
  helix:  0.88 (0.63), residues: 81
  sheet: -0.33 (0.22), residues: 603
  loop : -2.38 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 237 
 HIS   0.007   0.002   HIS C 422 
 PHE   0.016   0.002   PHE A 276 
 TYR   0.016   0.001   TYR B 176 
 ARG   0.003   0.000   ARG C 238 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 125
  time to evaluate  : 1.387 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9179 (p) cc_final: 0.8588 (m)
REVERT: A  493 MET cc_start: 0.7990 (tpt) cc_final: 0.7733 (tpt)
REVERT: A  496 MET cc_start: 0.9072 (mmm) cc_final: 0.8802 (mmm)
REVERT: B  180 SER cc_start: 0.9132 (p) cc_final: 0.8558 (m)
REVERT: B  232 MET cc_start: 0.8506 (mmt) cc_final: 0.8072 (mmt)
REVERT: C   83 ASP cc_start: 0.7324 (t0) cc_final: 0.7028 (t0)
REVERT: C  180 SER cc_start: 0.9127 (p) cc_final: 0.8667 (m)
REVERT: C  232 MET cc_start: 0.8346 (mmt) cc_final: 0.8106 (mmt)
REVERT: C  486 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7417 (tttp)
  outliers start: 67
  outliers final: 58
  residues processed: 176
  average time/residue: 0.1966
  time to fit residues: 54.9761
Evaluate side-chains
  178 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 120
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 155 optimal weight:    9.9990
   chunk 141 optimal weight:    0.5980
   chunk 150 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0570
   chunk 65 optimal weight:    0.9990
   chunk 118 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 136 optimal weight:    0.0870
   chunk 142 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   chunk 159 optimal weight:    6.9990
   overall best weight:    0.9480

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

Flipped N/Q/H residues before XYZ refinement:
A 566 GLN
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12888  Z= 0.199
  Angle     :  0.567   6.696  17529  Z= 0.300
  Chirality :  0.047   0.261   1986
  Planarity :  0.003   0.033   2268
  Dihedral  :  4.604  17.777   1812
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 18.13 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.19), residues: 1680
  helix:  0.95 (0.64), residues: 81
  sheet: -0.28 (0.22), residues: 603
  loop : -2.34 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 237 
 HIS   0.006   0.001   HIS C 422 
 PHE   0.013   0.001   PHE A 276 
 TYR   0.011   0.001   TYR B 176 
 ARG   0.002   0.000   ARG C  80 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 127
  time to evaluate  : 1.355 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9077 (p) cc_final: 0.8469 (m)
REVERT: A  496 MET cc_start: 0.9056 (mmm) cc_final: 0.8794 (mmm)
REVERT: B  180 SER cc_start: 0.9077 (p) cc_final: 0.8507 (m)
REVERT: B  232 MET cc_start: 0.8477 (mmt) cc_final: 0.8121 (mmt)
REVERT: B  575 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8087 (tp)
REVERT: C   83 ASP cc_start: 0.7370 (t0) cc_final: 0.7072 (t0)
REVERT: C  180 SER cc_start: 0.9080 (p) cc_final: 0.8549 (m)
  outliers start: 65
  outliers final: 60
  residues processed: 175
  average time/residue: 0.1996
  time to fit residues: 55.6418
Evaluate side-chains
  184 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 123
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 97 optimal weight:    0.1980
   chunk 75 optimal weight:    0.7980
   chunk 110 optimal weight:    6.9990
   chunk 167 optimal weight:    0.7980
   chunk 154 optimal weight:    5.9990
   chunk 133 optimal weight:    0.0770
   chunk 13 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 141 optimal weight:    0.8980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12888  Z= 0.164
  Angle     :  0.555   6.809  17529  Z= 0.293
  Chirality :  0.047   0.262   1986
  Planarity :  0.003   0.032   2268
  Dihedral  :  4.471  17.049   1812
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.45 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 18.35 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.20), residues: 1680
  helix:  1.07 (0.63), residues: 81
  sheet: -0.25 (0.22), residues: 603
  loop : -2.29 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 237 
 HIS   0.005   0.001   HIS C 422 
 PHE   0.013   0.001   PHE A 276 
 TYR   0.014   0.001   TYR B  33 
 ARG   0.002   0.000   ARG C  80 

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 132
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 SER cc_start: 0.9038 (p) cc_final: 0.8425 (m)
REVERT: B  180 SER cc_start: 0.8997 (p) cc_final: 0.8437 (m)
REVERT: B  232 MET cc_start: 0.8471 (mmt) cc_final: 0.8107 (mmt)
REVERT: B  575 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8070 (tp)
REVERT: C   83 ASP cc_start: 0.7347 (t0) cc_final: 0.7045 (t0)
REVERT: C  180 SER cc_start: 0.9053 (p) cc_final: 0.8533 (m)
  outliers start: 58
  outliers final: 56
  residues processed: 175
  average time/residue: 0.2006
  time to fit residues: 56.1758
Evaluate side-chains
  185 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 128
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  237 TRP
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 133 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0060
   chunk 137 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 117 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0970
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** 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 = 0.3167 r_free = 0.3167 target = 0.110325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.091902 restraints weight = 18755.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.093697 restraints weight = 12994.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.094916 restraints weight = 10101.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12888  Z= 0.175
  Angle     :  0.554   7.462  17529  Z= 0.292
  Chirality :  0.047   0.263   1986
  Planarity :  0.003   0.033   2268
  Dihedral  :  4.407  16.841   1812
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.63 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 18.20 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.20), residues: 1680
  helix:  1.17 (0.63), residues: 81
  sheet: -0.10 (0.22), residues: 582
  loop : -2.33 (0.17), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 237 
 HIS   0.005   0.001   HIS C 422 
 PHE   0.013   0.001   PHE A 276 
 TYR   0.016   0.001   TYR A 160 
 ARG   0.002   0.000   ARG C  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2302.01 seconds
wall clock time: 43 minutes 27.35 seconds (2607.35 seconds total)