Starting phenix.real_space_refine
on Sun Jun 15 13:23:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhz_43244/06_2025/8vhz_43244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhz_43244/06_2025/8vhz_43244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vhz_43244/06_2025/8vhz_43244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhz_43244/06_2025/8vhz_43244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhz_43244/06_2025/8vhz_43244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhz_43244/06_2025/8vhz_43244.cif"
  }
  resolution = 3.3
  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=   0.001 sd=   0.061
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      87      5.16       5
     C   11280      2.51       5
     N    2856      2.21       5
     O    2985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17208
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 714, 5736
          Classifications: {'peptide': 714}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 666}
          Chain breaks: 2
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 13.56, per 1000 atoms: 0.79
  Number of scatterers: 17208
  At special positions: 0
  Unit cell: (131.76, 135, 104.76, 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      87     16.00
     O    2985      8.00
     N    2856      7.00
     C   11280      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: 4.23
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4002

  Finding SS restraints...
    Secondary structure from input PDB file:
      90 helices and 9 sheets defined
      58.8% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 271 through 298
      Proline residue:  A 277  - end of helix
      removed outlier: 3.625A  pdb=" N   PHE A 291 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE A 292 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLN A 294 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 327
    Processing helix  chain 'A' and resid 338 through 346
      removed outlier: 3.503A  pdb=" N   LEU A 342 " --> pdb=" O   TYR A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 384
      removed outlier: 3.781A  pdb=" N   THR A 375 " --> pdb=" O   PRO A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 390
      No H-bonds generated for 'chain 'A' and resid 388 through 390'
    Processing helix  chain 'A' and resid 402 through 427
      removed outlier: 3.708A  pdb=" N   LYS A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LYS A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      Proline residue:  A 421  - end of helix
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 452 through 477
      removed outlier: 3.598A  pdb=" N   ARG A 457 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 465 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 556
    Processing helix  chain 'A' and resid 574 through 584
      removed outlier: 3.633A  pdb=" N   PHE A 582 " --> pdb=" O   GLU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 620
    Processing helix  chain 'A' and resid 620 through 627
    Processing helix  chain 'A' and resid 642 through 646
      removed outlier: 3.593A  pdb=" N   TYR A 646 " --> pdb=" O   ARG A 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 642 through 646'
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 729 through 737
      removed outlier: 3.697A  pdb=" N   PHE A 737 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 752
      removed outlier: 3.702A  pdb=" N   THR A 751 " --> pdb=" O   ASN A 748 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 752 " --> pdb=" O   PRO A 749 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 748 through 752'
    Processing helix  chain 'A' and resid 753 through 761
      removed outlier: 3.506A  pdb=" N   SER A 761 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 793
      removed outlier: 4.468A  pdb=" N   LEU A 786 " --> pdb=" O   THR A 782 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR A 787 " --> pdb=" O   GLU A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 836
    Processing helix  chain 'A' and resid 850 through 863
    Processing helix  chain 'A' and resid 866 through 883
      Proline residue:  A 877  - end of helix
      removed outlier: 3.573A  pdb=" N   THR A 883 " --> pdb=" O   PHE A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 918
      removed outlier: 4.339A  pdb=" N   TRP A 898 " --> pdb=" O   PHE A 894 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE A 899 " --> pdb=" O   ALA A 895 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER A 910 " --> pdb=" O   ILE A 906 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE A 911 " --> pdb=" O   PHE A 907 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 912 " --> pdb=" O   THR A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 938
      removed outlier: 3.519A  pdb=" N   ALA A 938 " --> pdb=" O   GLY A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 953
    Processing helix  chain 'A' and resid 980 through 982
      No H-bonds generated for 'chain 'A' and resid 980 through 982'
    Processing helix  chain 'A' and resid 983 through 1008
      removed outlier: 3.755A  pdb=" N   THR A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1021
      removed outlier: 3.879A  pdb=" N   LEU A1015 " --> pdb=" O   SER A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1029
      removed outlier: 3.866A  pdb=" N   ILE A1026 " --> pdb=" O   ALA A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1037
    Processing helix  chain 'A' and resid 1044 through 1063
      removed outlier: 3.583A  pdb=" N   ILE A1048 " --> pdb=" O   PRO A1044 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A1063 " --> pdb=" O   SER A1059 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 298
      Proline residue:  B 277  - end of helix
      removed outlier: 3.625A  pdb=" N   PHE B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE B 292 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU B 293 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLN B 294 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 327
    Processing helix  chain 'B' and resid 338 through 346
      removed outlier: 3.503A  pdb=" N   LEU B 342 " --> pdb=" O   TYR B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 384
      removed outlier: 3.780A  pdb=" N   THR B 375 " --> pdb=" O   PRO B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 402 through 427
      removed outlier: 3.708A  pdb=" N   LYS B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LYS B 418 " --> pdb=" O   GLU B 414 " (cutoff:3.500A)
      Proline residue:  B 421  - end of helix
    Processing helix  chain 'B' and resid 432 through 439
    Processing helix  chain 'B' and resid 452 through 477
      removed outlier: 3.598A  pdb=" N   ARG B 457 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU B 465 " --> pdb=" O   ARG B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 556
    Processing helix  chain 'B' and resid 574 through 584
      removed outlier: 3.634A  pdb=" N   PHE B 582 " --> pdb=" O   GLU B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 614 through 620
    Processing helix  chain 'B' and resid 620 through 627
    Processing helix  chain 'B' and resid 642 through 646
      removed outlier: 3.593A  pdb=" N   TYR B 646 " --> pdb=" O   ARG B 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 642 through 646'
    Processing helix  chain 'B' and resid 719 through 726
    Processing helix  chain 'B' and resid 729 through 737
      removed outlier: 3.697A  pdb=" N   PHE B 737 " --> pdb=" O   ILE B 733 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 752
      removed outlier: 3.703A  pdb=" N   THR B 751 " --> pdb=" O   ASN B 748 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU B 752 " --> pdb=" O   PRO B 749 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 748 through 752'
    Processing helix  chain 'B' and resid 753 through 761
      removed outlier: 3.506A  pdb=" N   SER B 761 " --> pdb=" O   ILE B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 793
      removed outlier: 4.468A  pdb=" N   LEU B 786 " --> pdb=" O   THR B 782 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR B 787 " --> pdb=" O   GLU B 783 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 836
    Processing helix  chain 'B' and resid 850 through 863
    Processing helix  chain 'B' and resid 866 through 883
      Proline residue:  B 877  - end of helix
      removed outlier: 3.574A  pdb=" N   THR B 883 " --> pdb=" O   PHE B 879 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 918
      removed outlier: 4.340A  pdb=" N   TRP B 898 " --> pdb=" O   PHE B 894 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE B 899 " --> pdb=" O   ALA B 895 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER B 910 " --> pdb=" O   ILE B 906 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE B 911 " --> pdb=" O   PHE B 907 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B 912 " --> pdb=" O   THR B 908 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 920 through 938
      removed outlier: 3.519A  pdb=" N   ALA B 938 " --> pdb=" O   GLY B 934 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 938 through 953
    Processing helix  chain 'B' and resid 980 through 982
      No H-bonds generated for 'chain 'B' and resid 980 through 982'
    Processing helix  chain 'B' and resid 983 through 1008
      removed outlier: 3.755A  pdb=" N   THR B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1011 through 1021
      removed outlier: 3.879A  pdb=" N   LEU B1015 " --> pdb=" O   SER B1011 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1022 through 1029
      removed outlier: 3.866A  pdb=" N   ILE B1026 " --> pdb=" O   ALA B1022 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1029 through 1037
    Processing helix  chain 'B' and resid 1044 through 1063
      removed outlier: 3.583A  pdb=" N   ILE B1048 " --> pdb=" O   PRO B1044 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL B1063 " --> pdb=" O   SER B1059 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 298
      Proline residue:  C 277  - end of helix
      removed outlier: 3.625A  pdb=" N   PHE C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE C 292 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU C 293 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLN C 294 " --> pdb=" O   GLY C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 327
    Processing helix  chain 'C' and resid 338 through 346
      removed outlier: 3.502A  pdb=" N   LEU C 342 " --> pdb=" O   TYR C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 384
      removed outlier: 3.780A  pdb=" N   THR C 375 " --> pdb=" O   PRO C 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 388 through 390
      No H-bonds generated for 'chain 'C' and resid 388 through 390'
    Processing helix  chain 'C' and resid 402 through 427
      removed outlier: 3.708A  pdb=" N   LYS C 417 " --> pdb=" O   ALA C 413 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LYS C 418 " --> pdb=" O   GLU C 414 " (cutoff:3.500A)
      Proline residue:  C 421  - end of helix
    Processing helix  chain 'C' and resid 432 through 439
    Processing helix  chain 'C' and resid 452 through 477
      removed outlier: 3.598A  pdb=" N   ARG C 457 " --> pdb=" O   VAL C 453 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU C 465 " --> pdb=" O   ARG C 461 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 540 through 556
    Processing helix  chain 'C' and resid 574 through 584
      removed outlier: 3.634A  pdb=" N   PHE C 582 " --> pdb=" O   GLU C 578 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 614 through 620
    Processing helix  chain 'C' and resid 620 through 627
    Processing helix  chain 'C' and resid 642 through 646
      removed outlier: 3.593A  pdb=" N   TYR C 646 " --> pdb=" O   ARG C 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 642 through 646'
    Processing helix  chain 'C' and resid 719 through 726
    Processing helix  chain 'C' and resid 729 through 737
      removed outlier: 3.698A  pdb=" N   PHE C 737 " --> pdb=" O   ILE C 733 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 748 through 752
      removed outlier: 3.703A  pdb=" N   THR C 751 " --> pdb=" O   ASN C 748 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU C 752 " --> pdb=" O   PRO C 749 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 748 through 752'
    Processing helix  chain 'C' and resid 753 through 761
      removed outlier: 3.507A  pdb=" N   SER C 761 " --> pdb=" O   ILE C 757 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 782 through 793
      removed outlier: 4.467A  pdb=" N   LEU C 786 " --> pdb=" O   THR C 782 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR C 787 " --> pdb=" O   GLU C 783 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 815 through 836
    Processing helix  chain 'C' and resid 850 through 863
    Processing helix  chain 'C' and resid 866 through 883
      Proline residue:  C 877  - end of helix
      removed outlier: 3.574A  pdb=" N   THR C 883 " --> pdb=" O   PHE C 879 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 918
      removed outlier: 4.339A  pdb=" N   TRP C 898 " --> pdb=" O   PHE C 894 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE C 899 " --> pdb=" O   ALA C 895 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER C 910 " --> pdb=" O   ILE C 906 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE C 911 " --> pdb=" O   PHE C 907 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU C 912 " --> pdb=" O   THR C 908 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 920 through 938
      removed outlier: 3.519A  pdb=" N   ALA C 938 " --> pdb=" O   GLY C 934 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 938 through 953
    Processing helix  chain 'C' and resid 980 through 982
      No H-bonds generated for 'chain 'C' and resid 980 through 982'
    Processing helix  chain 'C' and resid 983 through 1008
      removed outlier: 3.755A  pdb=" N   THR C 987 " --> pdb=" O   LEU C 983 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1011 through 1021
      removed outlier: 3.879A  pdb=" N   LEU C1015 " --> pdb=" O   SER C1011 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1022 through 1029
      removed outlier: 3.866A  pdb=" N   ILE C1026 " --> pdb=" O   ALA C1022 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1029 through 1037
    Processing helix  chain 'C' and resid 1044 through 1063
      removed outlier: 3.583A  pdb=" N   ILE C1048 " --> pdb=" O   PRO C1044 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL C1063 " --> pdb=" O   SER C1059 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269
    Processing sheet with id=AA2, first strand: chain 'A' and resid 504 through 507
      removed outlier: 4.003A  pdb=" N   ARG A 524 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   VAL A 358 " --> pdb=" O   SER A 393 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   TYR A 395 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL A 360 " --> pdb=" O   TYR A 395 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   VAL A 362 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASP A 359 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS A 638 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   CYS A 593 " --> pdb=" O   ASN A 641 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   ILE A 799 " --> pdb=" O   CYS A 593 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL A 595 " --> pdb=" O   ILE A 799 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 570
      removed outlier: 6.697A  pdb=" N   ARG A 600 " --> pdb=" O   GLY A 810 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 269
    Processing sheet with id=AA5, first strand: chain 'B' and resid 504 through 507
      removed outlier: 4.003A  pdb=" N   ARG B 524 " --> pdb=" O   VAL B 392 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL B 358 " --> pdb=" O   SER B 393 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   TYR B 395 " --> pdb=" O   VAL B 358 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL B 360 " --> pdb=" O   TYR B 395 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   SER B 397 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   VAL B 362 " --> pdb=" O   SER B 397 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASP B 359 " --> pdb=" O   LEU B 562 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS B 638 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   CYS B 593 " --> pdb=" O   ASN B 641 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   ILE B 799 " --> pdb=" O   CYS B 593 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL B 595 " --> pdb=" O   ILE B 799 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 569 through 570
      removed outlier: 6.698A  pdb=" N   ARG B 600 " --> pdb=" O   GLY B 810 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 269
    Processing sheet with id=AA8, first strand: chain 'C' and resid 504 through 507
      removed outlier: 4.003A  pdb=" N   ARG C 524 " --> pdb=" O   VAL C 392 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL C 358 " --> pdb=" O   SER C 393 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   TYR C 395 " --> pdb=" O   VAL C 358 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   VAL C 360 " --> pdb=" O   TYR C 395 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   SER C 397 " --> pdb=" O   VAL C 360 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL C 362 " --> pdb=" O   SER C 397 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASP C 359 " --> pdb=" O   LEU C 562 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   CYS C 638 " --> pdb=" O   ASN C 563 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   CYS C 593 " --> pdb=" O   ASN C 641 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   ILE C 799 " --> pdb=" O   CYS C 593 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   VAL C 595 " --> pdb=" O   ILE C 799 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 569 through 570
      removed outlier: 6.697A  pdb=" N   ARG C 600 " --> pdb=" O   GLY C 810 " (cutoff:3.500A)

    858 hydrogen bonds defined for protein.
    2556 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: 6.10

  Time building geometry restraints manager: 5.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5328
        1.34 -     1.46: 4332
        1.46 -     1.58: 7929
        1.58 -     1.70: 0
        1.70 -     1.82: 135
  Bond restraints: 17724
  Sorted by residual:
  bond pdb=" CG  PRO B 864 "
       pdb=" CD  PRO B 864 "
    ideal  model  delta    sigma   weight residual
    1.503  1.549 -0.046 3.40e-02 8.65e+02 1.83e+00
  bond pdb=" CG  PRO C 864 "
       pdb=" CD  PRO C 864 "
    ideal  model  delta    sigma   weight residual
    1.503  1.549 -0.046 3.40e-02 8.65e+02 1.83e+00
  bond pdb=" CG  PRO A 864 "
       pdb=" CD  PRO A 864 "
    ideal  model  delta    sigma   weight residual
    1.503  1.549 -0.046 3.40e-02 8.65e+02 1.80e+00
  bond pdb=" CB  LYS B 369 "
       pdb=" CG  LYS B 369 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.04e+00
  bond pdb=" CB  LYS A 369 "
       pdb=" CG  LYS A 369 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.93e-01
  ... (remaining 17719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 23777
        1.97 -     3.94: 274
        3.94 -     5.91: 48
        5.91 -     7.88: 18
        7.88 -     9.85: 12
  Bond angle restraints: 24129
  Sorted by residual:
  angle pdb=" CA  PRO C 864 "
        pdb=" N   PRO C 864 "
        pdb=" CD  PRO C 864 "
      ideal   model   delta    sigma   weight residual
     112.00  106.04    5.96 1.40e+00 5.10e-01 1.81e+01
  angle pdb=" CA  PRO B 864 "
        pdb=" N   PRO B 864 "
        pdb=" CD  PRO B 864 "
      ideal   model   delta    sigma   weight residual
     112.00  106.04    5.96 1.40e+00 5.10e-01 1.81e+01
  angle pdb=" CA  PRO A 864 "
        pdb=" N   PRO A 864 "
        pdb=" CD  PRO A 864 "
      ideal   model   delta    sigma   weight residual
     112.00  106.05    5.95 1.40e+00 5.10e-01 1.80e+01
  angle pdb=" CB  LYS B 369 "
        pdb=" CG  LYS B 369 "
        pdb=" CD  LYS B 369 "
      ideal   model   delta    sigma   weight residual
     111.30  119.20   -7.90 2.30e+00 1.89e-01 1.18e+01
  angle pdb=" CB  LYS A 369 "
        pdb=" CG  LYS A 369 "
        pdb=" CD  LYS A 369 "
      ideal   model   delta    sigma   weight residual
     111.30  119.18   -7.88 2.30e+00 1.89e-01 1.18e+01
  ... (remaining 24124 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 9154
       16.59 -    33.18: 930
       33.18 -    49.78: 248
       49.78 -    66.37: 60
       66.37 -    82.96: 15
  Dihedral angle restraints: 10407
    sinusoidal: 4185
      harmonic: 6222
  Sorted by residual:
  dihedral pdb=" CA  TYR C 863 "
           pdb=" C   TYR C 863 "
           pdb=" N   PRO C 864 "
           pdb=" CA  PRO C 864 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.50   19.50     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  TYR B 863 "
           pdb=" C   TYR B 863 "
           pdb=" N   PRO B 864 "
           pdb=" CA  PRO B 864 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.51   19.49     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  TYR A 863 "
           pdb=" C   TYR A 863 "
           pdb=" N   PRO A 864 "
           pdb=" CA  PRO A 864 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.53   19.47     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 10404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 2140
       0.048 -    0.095: 389
       0.095 -    0.143: 105
       0.143 -    0.190: 0
       0.190 -    0.238: 6
  Chirality restraints: 2640
  Sorted by residual:
  chirality pdb=" CB  THR B 782 "
            pdb=" CA  THR B 782 "
            pdb=" OG1 THR B 782 "
            pdb=" CG2 THR B 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  THR C 782 "
            pdb=" CA  THR C 782 "
            pdb=" OG1 THR C 782 "
            pdb=" CG2 THR C 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  THR A 782 "
            pdb=" CA  THR A 782 "
            pdb=" OG1 THR A 782 "
            pdb=" CG2 THR A 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 2637 not shown)

  Planarity restraints: 3030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 863 "   -0.077 5.00e-02 4.00e+02   1.14e-01 2.08e+01
        pdb=" N   PRO B 864 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO B 864 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO B 864 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 863 "   -0.077 5.00e-02 4.00e+02   1.14e-01 2.07e+01
        pdb=" N   PRO A 864 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 863 "    0.077 5.00e-02 4.00e+02   1.14e-01 2.07e+01
        pdb=" N   PRO C 864 "   -0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO C 864 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO C 864 "    0.062 5.00e-02 4.00e+02
  ... (remaining 3027 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 4285
        2.80 -     3.32: 16310
        3.32 -     3.85: 27873
        3.85 -     4.37: 31520
        4.37 -     4.90: 54621
  Nonbonded interactions: 134609
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 904 "
            pdb=" OG1 THR A 908 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   VAL C 904 "
            pdb=" OG1 THR C 908 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   VAL B 904 "
            pdb=" OG1 THR B 908 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG  SER B 867 "
            pdb=" O   GLY B 935 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG  SER C 867 "
            pdb=" O   GLY C 935 "
     model   vdw
     2.280 3.040
  ... (remaining 134604 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             19.670
  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:          0.710
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     43.830
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
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   0.046  17724  Z= 0.100
  Angle     :  0.558   9.847  24129  Z= 0.273
  Chirality :  0.040   0.238   2640
  Planarity :  0.005   0.114   3030
  Dihedral  : 14.895  82.960   6405
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 12.84 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.54 (0.19), residues: 2124
  helix:  1.82 (0.16), residues: 1128
  sheet:  2.20 (0.44), residues: 141
  loop : -0.24 (0.21), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 925 
 HIS   0.001   0.000   HIS C 539 
 PHE   0.015   0.001   PHE A 903 
 TYR   0.010   0.001   TYR B 594 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11641 (  858)
  hydrogen bonds       : angle       5.34190 ( 2556)
  covalent geometry    : bond        0.00223 (17724)
  covalent geometry    : angle       0.55780 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 227
  time to evaluate  : 2.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  578 GLU cc_start: 0.7446 (tt0) cc_final: 0.7103 (tt0)
REVERT: B  403 MET cc_start: 0.8136 (tpt) cc_final: 0.7921 (tpp)
REVERT: B  791 MET cc_start: 0.7756 (ttm) cc_final: 0.7308 (mtm)
REVERT: C  300 PRO cc_start: 0.6484 (Cg_endo) cc_final: 0.6260 (Cg_exo)
REVERT: C  499 ARG cc_start: 0.7355 (mpt-90) cc_final: 0.7099 (mpp80)
REVERT: C  825 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8070 (ttp80)
REVERT: C  843 TYR cc_start: 0.7081 (t80) cc_final: 0.4668 (m-10)
REVERT: C  845 TYR cc_start: 0.5847 (m-80) cc_final: 0.5624 (m-80)
  outliers start: 3
  outliers final: 1
  residues processed: 228
  average time/residue: 0.3224
  time to fit residues: 109.4910
Evaluate side-chains
  185 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 1.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 179 optimal weight:    0.1980
   chunk 161 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 166 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9990
   chunk 193 optimal weight:    6.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 557 ASN
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.188226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.147736 restraints weight = 22361.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 4.14
r_work: 0.3491 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17724  Z= 0.142
  Angle     :  0.576   9.973  24129  Z= 0.282
  Chirality :  0.042   0.178   2640
  Planarity :  0.005   0.080   3030
  Dihedral  :  3.836  50.178   2324
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 10.49 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.55 (0.18), residues: 2124
  helix:  1.88 (0.16), residues: 1143
  sheet:  2.12 (0.43), residues: 138
  loop : -0.33 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 925 
 HIS   0.003   0.001   HIS B 939 
 PHE   0.021   0.001   PHE C1032 
 TYR   0.031   0.001   TYR B 863 
 ARG   0.005   0.000   ARG C 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  858)
  hydrogen bonds       : angle       4.10624 ( 2556)
  covalent geometry    : bond        0.00323 (17724)
  covalent geometry    : angle       0.57553 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 208
  time to evaluate  : 1.880 
Fit side-chains
REVERT: A  619 ASP cc_start: 0.8370 (t0) cc_final: 0.8114 (m-30)
REVERT: A  926 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7158 (mmm-85)
REVERT: B  791 MET cc_start: 0.7970 (ttm) cc_final: 0.7672 (mtm)
REVERT: B  931 TRP cc_start: 0.7997 (t60) cc_final: 0.7706 (t60)
REVERT: C  300 PRO cc_start: 0.6664 (Cg_endo) cc_final: 0.6413 (Cg_exo)
REVERT: C  565 ASP cc_start: 0.8386 (t0) cc_final: 0.7842 (t0)
REVERT: C  825 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8189 (ttp80)
REVERT: C  843 TYR cc_start: 0.7073 (t80) cc_final: 0.4879 (m-10)
REVERT: C  926 ARG cc_start: 0.7549 (tpp80) cc_final: 0.6954 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8296 (t0) cc_final: 0.7966 (t0)
  outliers start: 50
  outliers final: 19
  residues processed: 244
  average time/residue: 0.3229
  time to fit residues: 118.6460
Evaluate side-chains
  206 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 2.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  921 ILE
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  921 ILE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  841 LEU
Chi-restraints excluded: chain C residue  870 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 91 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 174 optimal weight:    1.9990
   chunk 155 optimal weight:    0.7980
   chunk 140 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0870
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0170
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 815 ASN
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.189045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.134120 restraints weight = 22352.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.43
r_work: 0.3620 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  17724  Z= 0.110
  Angle     :  0.538  12.638  24129  Z= 0.260
  Chirality :  0.041   0.218   2640
  Planarity :  0.004   0.073   3030
  Dihedral  :  3.747  51.412   2324
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.84 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.67 (0.18), residues: 2124
  helix:  1.96 (0.16), residues: 1149
  sheet:  2.03 (0.43), residues: 138
  loop : -0.24 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 925 
 HIS   0.002   0.000   HIS C1028 
 PHE   0.018   0.001   PHE A 292 
 TYR   0.023   0.001   TYR A 863 
 ARG   0.006   0.000   ARG C 805 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  858)
  hydrogen bonds       : angle       3.84534 ( 2556)
  covalent geometry    : bond        0.00244 (17724)
  covalent geometry    : angle       0.53782 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 201
  time to evaluate  : 2.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  619 ASP cc_start: 0.8377 (t0) cc_final: 0.8170 (m-30)
REVERT: B  791 MET cc_start: 0.7796 (ttm) cc_final: 0.7519 (mtm)
REVERT: B  902 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4693 (tp)
REVERT: C  300 PRO cc_start: 0.6560 (Cg_endo) cc_final: 0.6302 (Cg_exo)
REVERT: C  825 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8207 (ttp80)
REVERT: C  843 TYR cc_start: 0.6989 (t80) cc_final: 0.4927 (m-10)
REVERT: C  927 ASN cc_start: 0.8300 (t0) cc_final: 0.8040 (t0)
  outliers start: 34
  outliers final: 23
  residues processed: 231
  average time/residue: 0.3349
  time to fit residues: 117.8907
Evaluate side-chains
  209 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 1.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  783 GLU
Chi-restraints excluded: chain B residue  902 LEU
Chi-restraints excluded: chain B residue  909 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  861 ILE
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 176 optimal weight:    0.0970
   chunk 122 optimal weight:    8.9990
   chunk 177 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 179 optimal weight:    2.9990
   chunk 195 optimal weight:    0.9980
   chunk 152 optimal weight:    2.9990
   chunk 174 optimal weight:    0.0370
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.187918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.147564 restraints weight = 22273.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 4.03
r_work: 0.3503 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  17724  Z= 0.118
  Angle     :  0.529  12.004  24129  Z= 0.257
  Chirality :  0.041   0.185   2640
  Planarity :  0.004   0.065   3030
  Dihedral  :  3.697  52.406   2324
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.22 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.60 (0.18), residues: 2124
  helix:  1.96 (0.16), residues: 1167
  sheet:  2.25 (0.44), residues: 123
  loop : -0.43 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 925 
 HIS   0.003   0.000   HIS B 511 
 PHE   0.017   0.001   PHE A 930 
 TYR   0.010   0.001   TYR C 463 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  858)
  hydrogen bonds       : angle       3.71012 ( 2556)
  covalent geometry    : bond        0.00271 (17724)
  covalent geometry    : angle       0.52895 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 204
  time to evaluate  : 1.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  619 ASP cc_start: 0.8456 (t0) cc_final: 0.8164 (m-30)
REVERT: B  791 MET cc_start: 0.7956 (ttm) cc_final: 0.7710 (mtm)
REVERT: B  902 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4740 (tp)
REVERT: B  930 PHE cc_start: 0.8362 (t80) cc_final: 0.8086 (t80)
REVERT: C  300 PRO cc_start: 0.6502 (Cg_endo) cc_final: 0.6212 (Cg_exo)
REVERT: C  825 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8249 (ttp80)
REVERT: C  927 ASN cc_start: 0.8290 (t0) cc_final: 0.8032 (t0)
  outliers start: 44
  outliers final: 28
  residues processed: 242
  average time/residue: 0.2975
  time to fit residues: 108.2506
Evaluate side-chains
  216 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 1.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  902 LEU
Chi-restraints excluded: chain B residue  945 GLN
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  841 LEU
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 210 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 168 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 193 optimal weight:    7.9990
   chunk 197 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 557 ASN
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.183399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.126840 restraints weight = 22611.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.42
r_work: 0.3518 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  17724  Z= 0.211
  Angle     :  0.598  13.365  24129  Z= 0.296
  Chirality :  0.044   0.255   2640
  Planarity :  0.005   0.060   3030
  Dihedral  :  3.959  52.823   2324
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.95 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.39 (0.18), residues: 2124
  helix:  1.86 (0.16), residues: 1146
  sheet:  1.67 (0.45), residues: 123
  loop : -0.48 (0.21), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 925 
 HIS   0.002   0.001   HIS B 792 
 PHE   0.022   0.002   PHE A 930 
 TYR   0.014   0.001   TYR B 463 
 ARG   0.008   0.001   ARG B 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04220 (  858)
  hydrogen bonds       : angle       3.91234 ( 2556)
  covalent geometry    : bond        0.00509 (17724)
  covalent geometry    : angle       0.59775 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 209
  time to evaluate  : 1.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7655 (tt0)
REVERT: B  937 SER cc_start: 0.9019 (m) cc_final: 0.8752 (p)
REVERT: C  594 TYR cc_start: 0.8881 (p90) cc_final: 0.8514 (p90)
REVERT: C  825 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8364 (ttp80)
REVERT: C  926 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7018 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8398 (t0) cc_final: 0.8099 (t0)
  outliers start: 64
  outliers final: 35
  residues processed: 266
  average time/residue: 0.2829
  time to fit residues: 113.9298
Evaluate side-chains
  227 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 192
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  909 THR
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  487 MET
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  861 ILE
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  945 GLN
Chi-restraints excluded: chain C residue  991 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 174 optimal weight:    0.6980
   chunk 207 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 202 optimal weight:    0.6980
   chunk 204 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0060
   chunk 139 optimal weight:    1.9990
   chunk 128 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0070
   overall best weight:    0.4214

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

Flipped N/Q/H residues before XYZ refinement:
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.186382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.130608 restraints weight = 22439.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.45
r_work: 0.3569 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17724  Z= 0.110
  Angle     :  0.539  12.733  24129  Z= 0.262
  Chirality :  0.041   0.198   2640
  Planarity :  0.004   0.054   3030
  Dihedral  :  3.798  53.877   2324
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.39 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.57 (0.19), residues: 2124
  helix:  2.04 (0.16), residues: 1134
  sheet:  1.46 (0.44), residues: 138
  loop : -0.40 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 925 
 HIS   0.002   0.000   HIS A1028 
 PHE   0.013   0.001   PHE A 930 
 TYR   0.010   0.001   TYR C 305 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03412 (  858)
  hydrogen bonds       : angle       3.66597 ( 2556)
  covalent geometry    : bond        0.00252 (17724)
  covalent geometry    : angle       0.53866 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 199
  time to evaluate  : 2.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  871 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7352 (tp)
REVERT: A  937 SER cc_start: 0.8921 (m) cc_final: 0.8599 (p)
REVERT: B  791 MET cc_start: 0.7994 (mtm) cc_final: 0.7688 (mtm)
REVERT: B  937 SER cc_start: 0.8858 (m) cc_final: 0.8649 (p)
REVERT: C  307 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6424 (tt)
REVERT: C  594 TYR cc_start: 0.8854 (p90) cc_final: 0.8503 (p90)
REVERT: C  825 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8294 (ttp80)
REVERT: C  926 ARG cc_start: 0.7511 (tpp80) cc_final: 0.7011 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8398 (t0) cc_final: 0.8102 (t0)
  outliers start: 50
  outliers final: 32
  residues processed: 242
  average time/residue: 0.3083
  time to fit residues: 113.7548
Evaluate side-chains
  221 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 187
  time to evaluate  : 1.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  584 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  307 LEU
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  861 ILE
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 83 optimal weight:    0.1980
   chunk 103 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 136 optimal weight:   10.0000
   chunk 166 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0870
   chunk 95 optimal weight:    0.9990
   chunk 178 optimal weight:    4.9990
   chunk 132 optimal weight:    0.9990
   chunk 160 optimal weight:    1.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A 557 ASN
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.186174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.130347 restraints weight = 22461.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.44
r_work: 0.3568 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  17724  Z= 0.124
  Angle     :  0.553  12.283  24129  Z= 0.268
  Chirality :  0.042   0.279   2640
  Planarity :  0.004   0.053   3030
  Dihedral  :  3.764  54.885   2324
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.23 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.66 (0.19), residues: 2124
  helix:  2.07 (0.16), residues: 1152
  sheet:  1.26 (0.44), residues: 135
  loop : -0.27 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 925 
 HIS   0.001   0.000   HIS C 539 
 PHE   0.013   0.001   PHE A 930 
 TYR   0.010   0.001   TYR A 463 
 ARG   0.006   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  858)
  hydrogen bonds       : angle       3.62464 ( 2556)
  covalent geometry    : bond        0.00294 (17724)
  covalent geometry    : angle       0.55277 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 189
  time to evaluate  : 2.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8125 (mm-30)
REVERT: A  937 SER cc_start: 0.9011 (m) cc_final: 0.8789 (p)
REVERT: B  327 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7104 (t80)
REVERT: B  791 MET cc_start: 0.7976 (mtm) cc_final: 0.7618 (mtm)
REVERT: C  307 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6431 (tt)
REVERT: C  594 TYR cc_start: 0.8855 (p90) cc_final: 0.8539 (p90)
REVERT: C  825 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8390 (ttp80)
REVERT: C  926 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7070 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8401 (t0) cc_final: 0.8090 (t0)
  outliers start: 57
  outliers final: 38
  residues processed: 240
  average time/residue: 0.3816
  time to fit residues: 139.3047
Evaluate side-chains
  227 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 187
  time to evaluate  : 1.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  584 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  902 LEU
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  307 LEU
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  839 CYS
Chi-restraints excluded: chain C residue  861 ILE
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 210 optimal weight:    2.9990
   chunk 200 optimal weight:    6.9990
   chunk 183 optimal weight:    0.0870
   chunk 90 optimal weight:    0.5980
   chunk 155 optimal weight:    1.9990
   chunk 159 optimal weight:    0.0970
   chunk 100 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 175 optimal weight:    0.8980
   chunk 156 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.186298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.130580 restraints weight = 22322.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.44
r_work: 0.3568 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  17724  Z= 0.118
  Angle     :  0.551  12.997  24129  Z= 0.266
  Chirality :  0.042   0.231   2640
  Planarity :  0.004   0.047   3030
  Dihedral  :  3.748  55.464   2324
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.87 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.70 (0.19), residues: 2124
  helix:  2.15 (0.16), residues: 1134
  sheet:  1.30 (0.44), residues: 135
  loop : -0.29 (0.21), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 925 
 HIS   0.001   0.000   HIS B 939 
 PHE   0.012   0.001   PHE A 930 
 TYR   0.009   0.001   TYR A 463 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  858)
  hydrogen bonds       : angle       3.56489 ( 2556)
  covalent geometry    : bond        0.00280 (17724)
  covalent geometry    : angle       0.55066 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 195
  time to evaluate  : 2.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8356 (tpp) cc_final: 0.8023 (mtp)
REVERT: A  307 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6191 (tt)
REVERT: A  937 SER cc_start: 0.8969 (m) cc_final: 0.8617 (p)
REVERT: B  307 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6375 (tt)
REVERT: B  327 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7109 (t80)
REVERT: C  307 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6482 (tt)
REVERT: C  480 MET cc_start: 0.8689 (tpp) cc_final: 0.8279 (tpt)
REVERT: C  594 TYR cc_start: 0.8865 (p90) cc_final: 0.8537 (p90)
REVERT: C  825 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8268 (ttp80)
REVERT: C  926 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7067 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8420 (t0) cc_final: 0.8140 (t0)
  outliers start: 53
  outliers final: 40
  residues processed: 243
  average time/residue: 0.4284
  time to fit residues: 158.8414
Evaluate side-chains
  230 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 186
  time to evaluate  : 1.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  584 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  902 LEU
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  307 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  839 CYS
Chi-restraints excluded: chain C residue  861 ILE
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  902 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 195 optimal weight:    1.9990
   chunk 196 optimal weight:    0.0470
   chunk 194 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 118 optimal weight:    0.8980
   chunk 184 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 929 GLN
** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.185651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.129625 restraints weight = 22592.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.44
r_work: 0.3554 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  17724  Z= 0.132
  Angle     :  0.557  12.893  24129  Z= 0.271
  Chirality :  0.042   0.221   2640
  Planarity :  0.004   0.045   3030
  Dihedral  :  3.765  54.964   2324
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.66 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.70 (0.19), residues: 2124
  helix:  2.11 (0.16), residues: 1152
  sheet:  1.30 (0.44), residues: 138
  loop : -0.29 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP B 925 
 HIS   0.001   0.000   HIS A 838 
 PHE   0.012   0.001   PHE A 930 
 TYR   0.025   0.001   TYR B 594 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  858)
  hydrogen bonds       : angle       3.59676 ( 2556)
  covalent geometry    : bond        0.00315 (17724)
  covalent geometry    : angle       0.55715 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 192
  time to evaluate  : 2.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8400 (tpp) cc_final: 0.8174 (mtp)
REVERT: A  307 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6217 (tt)
REVERT: A  926 ARG cc_start: 0.7789 (tpp80) cc_final: 0.6986 (tpp80)
REVERT: A  937 SER cc_start: 0.8953 (m) cc_final: 0.8624 (p)
REVERT: B  307 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6365 (tt)
REVERT: B  327 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7108 (t80)
REVERT: C  307 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6440 (tt)
REVERT: C  480 MET cc_start: 0.8693 (tpp) cc_final: 0.8304 (tpt)
REVERT: C  594 TYR cc_start: 0.8873 (p90) cc_final: 0.8533 (p90)
REVERT: C  738 MET cc_start: 0.8516 (mmt) cc_final: 0.8087 (mmt)
REVERT: C  825 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8354 (ttp80)
REVERT: C  926 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7048 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8462 (t0) cc_final: 0.8160 (t0)
  outliers start: 52
  outliers final: 43
  residues processed: 237
  average time/residue: 0.2982
  time to fit residues: 107.5425
Evaluate side-chains
  238 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 191
  time to evaluate  : 1.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  584 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  841 LEU
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  902 LEU
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  307 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  753 LEU
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  839 CYS
Chi-restraints excluded: chain C residue  861 ILE
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  902 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 172 optimal weight:    0.8980
   chunk 149 optimal weight:    0.5980
   chunk 116 optimal weight:    0.0670
   chunk 9 optimal weight:    0.5980
   chunk 141 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0870
   chunk 147 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 164 optimal weight:    0.0470
   chunk 91 optimal weight:    1.9990
   chunk 178 optimal weight:    0.5980
   overall best weight:    0.2794

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

Flipped N/Q/H residues before XYZ refinement:
A 929 GLN
C 929 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.189346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.136537 restraints weight = 22419.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 3.12
r_work: 0.3556 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  17724  Z= 0.104
  Angle     :  0.555  12.948  24129  Z= 0.268
  Chirality :  0.041   0.217   2640
  Planarity :  0.004   0.044   3030
  Dihedral  :  3.723  55.888   2324
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.57 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  1.83 (0.19), residues: 2124
  helix:  2.25 (0.16), residues: 1134
  sheet:  1.25 (0.40), residues: 165
  loop : -0.25 (0.22), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.001   TRP B 925 
 HIS   0.001   0.000   HIS C 539 
 PHE   0.012   0.001   PHE C 903 
 TYR   0.029   0.001   TYR A 594 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03096 (  858)
  hydrogen bonds       : angle       3.48594 ( 2556)
  covalent geometry    : bond        0.00239 (17724)
  covalent geometry    : angle       0.55491 (24129)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 196
  time to evaluate  : 2.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8351 (tpp) cc_final: 0.8066 (mtt)
REVERT: A  307 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6221 (tt)
REVERT: A  937 SER cc_start: 0.8914 (m) cc_final: 0.8600 (p)
REVERT: B  307 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6320 (tt)
REVERT: B  327 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: B  819 ARG cc_start: 0.7632 (ttt90) cc_final: 0.7359 (tpt-90)
REVERT: C  307 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6476 (tt)
REVERT: C  480 MET cc_start: 0.8684 (tpp) cc_final: 0.8335 (tpt)
REVERT: C  825 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8424 (ttp80)
REVERT: C  926 ARG cc_start: 0.7533 (tpp80) cc_final: 0.6979 (tpp80)
REVERT: C  927 ASN cc_start: 0.8434 (t0) cc_final: 0.8181 (t0)
  outliers start: 38
  outliers final: 31
  residues processed: 228
  average time/residue: 0.3315
  time to fit residues: 114.1783
Evaluate side-chains
  219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 1.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  584 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  307 LEU
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  902 LEU
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  307 LEU
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  839 CYS
Chi-restraints excluded: chain C residue  881 LEU
Chi-restraints excluded: chain C residue  902 LEU
Chi-restraints excluded: chain C residue  945 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 134 optimal weight:    0.0370
   chunk 156 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 157 optimal weight:    1.9990
   chunk 163 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 184 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 211 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    0.7258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.186186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.130160 restraints weight = 22385.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.43
r_work: 0.3559 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  17724  Z= 0.138
  Angle     :  0.564  12.799  24129  Z= 0.275
  Chirality :  0.042   0.208   2640
  Planarity :  0.004   0.044   3030
  Dihedral  :  3.755  55.897   2324
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.57 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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 (0.19), residues: 2124
  helix:  2.23 (0.16), residues: 1134
  sheet:  1.08 (0.40), residues: 165
  loop : -0.25 (0.22), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.001   TRP B 925 
 HIS   0.001   0.000   HIS A 838 
 PHE   0.011   0.001   PHE A 903 
 TYR   0.019   0.001   TYR A 594 
 ARG   0.007   0.000   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  858)
  hydrogen bonds       : angle       3.56339 ( 2556)
  covalent geometry    : bond        0.00333 (17724)
  covalent geometry    : angle       0.56430 (24129)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9030.69 seconds
wall clock time: 158 minutes 28.45 seconds (9508.45 seconds total)