Starting phenix.real_space_refine
on Sun Aug 24 05:43:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhz_43244/08_2025/8vhz_43244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhz_43244/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhz_43244/08_2025/8vhz_43244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhz_43244/08_2025/8vhz_43244.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vhz_43244/08_2025/8vhz_43244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhz_43244/08_2025/8vhz_43244.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 5.14, per 1000 atoms: 0.30
  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: 1.26
  Conformation dependent library (CDL) restraints added in 626.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.43
  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: 2.72

  Time building geometry restraints manager: 1.63 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.800
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.520
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.110
-------------------------------------------------------------------------------
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 : 6.32
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG B 348 
 TYR   0.010   0.001   TYR B 594 
 PHE   0.015   0.001   PHE A 903 
 TRP   0.013   0.001   TRP B 925 
 HIS   0.001   0.000   HIS C 539 

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

*********************** 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  : 0.423 
Fit side-chains
   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)
REVERT: C  926 ARG cc_start: 0.7147 (tpp80) cc_final: 0.6423 (mmm-85)
  outliers start: 3
  outliers final: 1
  residues processed: 228
  average time/residue: 0.1254
  time to fit residues: 42.9409
Evaluate side-chains
  187 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
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 98 optimal weight:    1.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.2980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 200 optimal weight:    4.9990
   chunk 212 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 929 GLN
** 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 = 0.4375 r_free = 0.4375 target = 0.185265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.129279 restraints weight = 22494.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.43
r_work: 0.3553 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  17724  Z= 0.194
  Angle     :  0.614  10.084  24129  Z= 0.306
  Chirality :  0.044   0.178   2640
  Planarity :  0.005   0.082   3030
  Dihedral  :  3.986  50.002   2324
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 10.70 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.18), residues: 2124
  helix:  1.75 (0.16), residues: 1140
  sheet:  1.68 (0.43), residues: 138
  loop : -0.40 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 926 
 TYR   0.027   0.002   TYR B 863 
 PHE   0.019   0.002   PHE A 930 
 TRP   0.020   0.001   TRP B 925 
 HIS   0.003   0.001   HIS B 939 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (17724)
  covalent geometry    : angle       0.61387 (24129)
  hydrogen bonds       : bond        0.04655 (  858)
  hydrogen bonds       : angle       4.24486 ( 2556)

*********************** 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
  279 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 217
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A  926 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7100 (mmm-85)
REVERT: B  791 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7672 (mtm)
REVERT: B  926 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7421 (mmm-85)
REVERT: C  300 PRO cc_start: 0.6478 (Cg_endo) cc_final: 0.6211 (Cg_exo)
REVERT: C  462 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7929 (mt-10)
REVERT: C  565 ASP cc_start: 0.8373 (t0) cc_final: 0.7915 (t0)
REVERT: C  791 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7708 (mtm)
REVERT: C  825 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8150 (ttp80)
REVERT: C  926 ARG cc_start: 0.7506 (tpp80) cc_final: 0.6890 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8297 (t0) cc_final: 0.7960 (t0)
  outliers start: 62
  outliers final: 26
  residues processed: 262
  average time/residue: 0.1244
  time to fit residues: 49.1999
Evaluate side-chains
  223 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
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  487 MET
Chi-restraints excluded: chain A residue  581 CYS
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  861 ILE
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  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  791 MET
Chi-restraints excluded: chain B residue  870 LEU
Chi-restraints excluded: chain B residue  921 ILE
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  462 GLU
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  791 MET
Chi-restraints excluded: chain C residue  797 ILE
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 23 optimal weight:    0.0270
   chunk 164 optimal weight:    0.9980
   chunk 137 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 91 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0370
   chunk 144 optimal weight:    5.9990
   chunk 160 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
A 557 ASN
B 557 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.187580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132359 restraints weight = 22437.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.44
r_work: 0.3592 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17724  Z= 0.112
  Angle     :  0.541  10.873  24129  Z= 0.264
  Chirality :  0.041   0.180   2640
  Planarity :  0.004   0.073   3030
  Dihedral  :  3.841  51.529   2324
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.11 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.18), residues: 2124
  helix:  1.90 (0.16), residues: 1131
  sheet:  1.76 (0.43), residues: 138
  loop : -0.37 (0.21), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 805 
 TYR   0.024   0.001   TYR A 863 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.022   0.001   TRP C 925 
 HIS   0.004   0.001   HIS A1028 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (17724)
  covalent geometry    : angle       0.54083 (24129)
  hydrogen bonds       : bond        0.03801 (  858)
  hydrogen bonds       : angle       3.90110 ( 2556)

*********************** 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
  243 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 203
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  791 MET cc_start: 0.7849 (ttm) cc_final: 0.7530 (mtm)
REVERT: B  902 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4769 (tp)
REVERT: C  300 PRO cc_start: 0.6413 (Cg_endo) cc_final: 0.6130 (Cg_exo)
REVERT: C  462 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7820 (mt-10)
REVERT: C  825 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8211 (ttp80)
REVERT: C  927 ASN cc_start: 0.8308 (t0) cc_final: 0.8053 (t0)
  outliers start: 40
  outliers final: 21
  residues processed: 237
  average time/residue: 0.1292
  time to fit residues: 46.3656
Evaluate side-chains
  205 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
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  855 LEU
Chi-restraints excluded: chain B residue  282 ILE
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  902 LEU
Chi-restraints excluded: chain B residue  909 THR
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  462 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 168 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0870
   chunk 202 optimal weight:    0.8980
   chunk 162 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 161 optimal weight:    0.6980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4398 r_free = 0.4398 target = 0.188793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.136517 restraints weight = 22688.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 3.11
r_work: 0.3552 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1742

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= 0.118
  Angle     :  0.530   8.549  24129  Z= 0.258
  Chirality :  0.041   0.230   2640
  Planarity :  0.004   0.066   3030
  Dihedral  :  3.751  53.062   2324
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.43 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.18), residues: 2124
  helix:  1.98 (0.16), residues: 1152
  sheet:  1.76 (0.44), residues: 138
  loop : -0.29 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 348 
 TYR   0.032   0.001   TYR B 863 
 PHE   0.019   0.001   PHE A 930 
 TRP   0.021   0.001   TRP C 925 
 HIS   0.002   0.000   HIS A1028 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (17724)
  covalent geometry    : angle       0.53027 (24129)
  hydrogen bonds       : bond        0.03511 (  858)
  hydrogen bonds       : angle       3.71316 ( 2556)

*********************** 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
  243 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 199
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  791 MET cc_start: 0.7946 (ttm) cc_final: 0.7695 (mtm)
REVERT: B  902 LEU cc_start: 0.5092 (OUTLIER) cc_final: 0.4788 (tp)
REVERT: C  300 PRO cc_start: 0.6344 (Cg_endo) cc_final: 0.6042 (Cg_exo)
REVERT: C  462 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7838 (mt-10)
REVERT: C  825 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8270 (ttp80)
REVERT: C  927 ASN cc_start: 0.8373 (t0) cc_final: 0.8144 (t0)
  outliers start: 44
  outliers final: 25
  residues processed: 239
  average time/residue: 0.1388
  time to fit residues: 50.1820
Evaluate side-chains
  213 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 186
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
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  855 LEU
Chi-restraints excluded: chain A residue  861 ILE
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  945 GLN
Chi-restraints excluded: chain B residue  282 ILE
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  902 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  487 MET
Chi-restraints excluded: chain C residue  628 VAL
Chi-restraints excluded: chain C residue  797 ILE
Chi-restraints excluded: chain C residue  798 SER
Chi-restraints excluded: chain C residue  841 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0870
   chunk 184 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0070
   chunk 156 optimal weight:    0.5980
   chunk 136 optimal weight:    0.9990
   chunk 140 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0030
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.2586

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

Flipped N/Q/H residues before XYZ refinement:
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 557 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 = 0.4414 r_free = 0.4414 target = 0.190141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.138235 restraints weight = 22483.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 3.12
r_work: 0.3558 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  17724  Z= 0.099
  Angle     :  0.517   8.770  24129  Z= 0.251
  Chirality :  0.040   0.189   2640
  Planarity :  0.004   0.061   3030
  Dihedral  :  3.668  54.297   2324
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.91 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.19), residues: 2124
  helix:  2.12 (0.16), residues: 1134
  sheet:  1.84 (0.44), residues: 138
  loop : -0.28 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 348 
 TYR   0.010   0.001   TYR C 305 
 PHE   0.020   0.001   PHE A 930 
 TRP   0.022   0.001   TRP C 925 
 HIS   0.001   0.000   HIS C 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (17724)
  covalent geometry    : angle       0.51703 (24129)
  hydrogen bonds       : bond        0.03174 (  858)
  hydrogen bonds       : angle       3.58190 ( 2556)

*********************** 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
  252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 203
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  327 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7112 (t80)
REVERT: B  791 MET cc_start: 0.7821 (ttm) cc_final: 0.7565 (mtm)
REVERT: B  937 SER cc_start: 0.8903 (m) cc_final: 0.8670 (p)
REVERT: C  300 PRO cc_start: 0.6394 (Cg_endo) cc_final: 0.6078 (Cg_exo)
REVERT: C  462 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7774 (mt-10)
REVERT: C  594 TYR cc_start: 0.8906 (p90) cc_final: 0.8576 (p90)
REVERT: C  791 MET cc_start: 0.7725 (ttm) cc_final: 0.7482 (mtt)
REVERT: C  825 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8362 (ttp80)
REVERT: C  927 ASN cc_start: 0.8333 (t0) cc_final: 0.8110 (t0)
  outliers start: 49
  outliers final: 21
  residues processed: 247
  average time/residue: 0.1276
  time to fit residues: 47.8502
Evaluate side-chains
  206 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  628 VAL
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  945 GLN
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 C residue  267 VAL
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  462 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 189 optimal weight:    0.5980
   chunk 148 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0670
   chunk 4 optimal weight:    0.0670
   chunk 23 optimal weight:    0.0170
   chunk 183 optimal weight:    0.2980
   chunk 91 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    0.3980
   chunk 133 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.1694

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

Flipped N/Q/H residues before XYZ refinement:
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 557 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 = 0.4416 r_free = 0.4416 target = 0.189273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.149244 restraints weight = 22357.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 4.13
r_work: 0.3513 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  17724  Z= 0.097
  Angle     :  0.524  11.880  24129  Z= 0.251
  Chirality :  0.040   0.188   2640
  Planarity :  0.004   0.057   3030
  Dihedral  :  3.590  55.545   2324
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.50 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.19), residues: 2124
  helix:  2.24 (0.16), residues: 1134
  sheet:  1.79 (0.45), residues: 135
  loop : -0.19 (0.21), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 348 
 TYR   0.025   0.001   TYR B 594 
 PHE   0.017   0.001   PHE A 930 
 TRP   0.023   0.001   TRP B 925 
 HIS   0.002   0.000   HIS B 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (17724)
  covalent geometry    : angle       0.52399 (24129)
  hydrogen bonds       : bond        0.02992 (  858)
  hydrogen bonds       : angle       3.48885 ( 2556)

*********************** 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
  237 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 195
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A  619 ASP cc_start: 0.8368 (t0) cc_final: 0.8159 (m-30)
REVERT: A  622 MET cc_start: 0.8364 (mmm) cc_final: 0.8084 (mmm)
REVERT: A  930 PHE cc_start: 0.7905 (t80) cc_final: 0.7312 (t80)
REVERT: A  937 SER cc_start: 0.8959 (m) cc_final: 0.8706 (p)
REVERT: B  327 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: B  791 MET cc_start: 0.7841 (ttm) cc_final: 0.7569 (mtm)
REVERT: B  926 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7278 (mmm-85)
REVERT: C  300 PRO cc_start: 0.6346 (Cg_endo) cc_final: 0.6038 (Cg_exo)
REVERT: C  462 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7761 (mt-10)
REVERT: C  791 MET cc_start: 0.7722 (ttm) cc_final: 0.7492 (mtt)
REVERT: C  825 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8365 (ttp80)
REVERT: C  926 ARG cc_start: 0.7468 (tpp80) cc_final: 0.6949 (mmm-85)
REVERT: C  927 ASN cc_start: 0.8379 (t0) cc_final: 0.8108 (t0)
  outliers start: 42
  outliers final: 28
  residues processed: 234
  average time/residue: 0.1260
  time to fit residues: 44.9060
Evaluate side-chains
  213 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 183
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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  370 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  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  945 GLN
Chi-restraints excluded: chain B residue  282 ILE
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  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  783 GLU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  581 CYS
Chi-restraints excluded: chain C residue  628 VAL
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 11 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 183 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 194 optimal weight:    0.0670
   chunk 31 optimal weight:    0.4980
   chunk 93 optimal weight:    5.9990
   chunk 144 optimal weight:    0.0050
   chunk 74 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    0.6334

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4395 r_free = 0.4395 target = 0.188306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.135680 restraints weight = 22446.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 3.04
r_work: 0.3548 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  17724  Z= 0.126
  Angle     :  0.532  12.068  24129  Z= 0.260
  Chirality :  0.041   0.195   2640
  Planarity :  0.004   0.055   3030
  Dihedral  :  3.636  55.879   2324
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.19), residues: 2124
  helix:  2.23 (0.16), residues: 1134
  sheet:  1.76 (0.45), residues: 138
  loop : -0.26 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 819 
 TYR   0.014   0.001   TYR B 594 
 PHE   0.016   0.001   PHE A 930 
 TRP   0.026   0.001   TRP B 925 
 HIS   0.001   0.000   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (17724)
  covalent geometry    : angle       0.53215 (24129)
  hydrogen bonds       : bond        0.03255 (  858)
  hydrogen bonds       : angle       3.54910 ( 2556)

*********************** 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
  251 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 197
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8305 (tpp) cc_final: 0.8019 (mtp)
REVERT: A  307 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6166 (tt)
REVERT: A  937 SER cc_start: 0.9009 (m) cc_final: 0.8741 (p)
REVERT: B  307 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6377 (tt)
REVERT: B  327 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7120 (t80)
REVERT: B  791 MET cc_start: 0.7927 (ttm) cc_final: 0.7708 (mtm)
REVERT: C  300 PRO cc_start: 0.6262 (Cg_endo) cc_final: 0.5894 (Cg_exo)
REVERT: C  462 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7688 (mt-10)
REVERT: C  480 MET cc_start: 0.8783 (tpt) cc_final: 0.8161 (tpt)
REVERT: C  594 TYR cc_start: 0.8912 (p90) cc_final: 0.8558 (p90)
REVERT: C  825 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8376 (ttp80)
REVERT: C  926 ARG cc_start: 0.7532 (tpp80) cc_final: 0.7018 (tpp80)
REVERT: C  927 ASN cc_start: 0.8399 (t0) cc_final: 0.8156 (t0)
  outliers start: 54
  outliers final: 35
  residues processed: 245
  average time/residue: 0.1307
  time to fit residues: 48.5084
Evaluate side-chains
  228 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 189
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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  581 CYS
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  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  852 LEU
Chi-restraints excluded: chain B residue  881 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  327 PHE
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  551 VAL
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  902 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 59 optimal weight:    4.9990
   chunk 160 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 193 optimal weight:    1.9990
   chunk 207 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 164 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4381 r_free = 0.4381 target = 0.186025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.130111 restraints weight = 22391.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.44
r_work: 0.3567 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17724  Z= 0.137
  Angle     :  0.553   9.967  24129  Z= 0.269
  Chirality :  0.042   0.200   2640
  Planarity :  0.004   0.053   3030
  Dihedral  :  3.720  55.905   2324
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.66 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.19), residues: 2124
  helix:  2.20 (0.16), residues: 1134
  sheet:  1.60 (0.44), residues: 138
  loop : -0.27 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 819 
 TYR   0.024   0.001   TYR C 594 
 PHE   0.018   0.001   PHE C 930 
 TRP   0.034   0.001   TRP B 925 
 HIS   0.001   0.000   HIS C 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (17724)
  covalent geometry    : angle       0.55312 (24129)
  hydrogen bonds       : bond        0.03374 (  858)
  hydrogen bonds       : angle       3.58721 ( 2556)

*********************** 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
  247 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 196
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6160 (tt)
REVERT: A  937 SER cc_start: 0.8983 (m) cc_final: 0.8609 (p)
REVERT: B  307 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6371 (tt)
REVERT: B  327 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7094 (t80)
REVERT: B  937 SER cc_start: 0.8893 (m) cc_final: 0.8514 (p)
REVERT: C  462 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7694 (mt-10)
REVERT: C  825 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8338 (ttp80)
REVERT: C  926 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7062 (tpp80)
REVERT: C  927 ASN cc_start: 0.8440 (t0) cc_final: 0.8187 (t0)
  outliers start: 51
  outliers final: 39
  residues processed: 241
  average time/residue: 0.1165
  time to fit residues: 42.9912
Evaluate side-chains
  234 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 191
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  628 VAL
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  841 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  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
Chi-restraints excluded: chain B residue  881 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  327 PHE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  370 GLU
Chi-restraints excluded: chain C residue  462 GLU
Chi-restraints excluded: chain C residue  551 VAL
Chi-restraints excluded: chain C residue  566 CYS
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  945 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 105 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 123 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 141 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 144 optimal weight:    3.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 557 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 = 0.4345 r_free = 0.4345 target = 0.182481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.125735 restraints weight = 22613.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.44
r_work: 0.3505 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  17724  Z= 0.243
  Angle     :  0.612   9.476  24129  Z= 0.309
  Chirality :  0.045   0.207   2640
  Planarity :  0.005   0.050   3030
  Dihedral  :  4.039  54.934   2324
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.19), residues: 2124
  helix:  1.89 (0.16), residues: 1149
  sheet:  0.82 (0.40), residues: 168
  loop : -0.34 (0.22), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 819 
 TYR   0.032   0.002   TYR C 594 
 PHE   0.016   0.002   PHE A 406 
 TRP   0.042   0.002   TRP B 925 
 HIS   0.004   0.001   HIS B 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (17724)
  covalent geometry    : angle       0.61184 (24129)
  hydrogen bonds       : bond        0.04259 (  858)
  hydrogen bonds       : angle       3.85678 ( 2556)

*********************** 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
  252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 196
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  937 SER cc_start: 0.8995 (m) cc_final: 0.8777 (p)
REVERT: B  307 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6526 (tt)
REVERT: B  791 MET cc_start: 0.8057 (mtm) cc_final: 0.7853 (mtp)
REVERT: B  926 ARG cc_start: 0.7558 (tpp80) cc_final: 0.6593 (tpp80)
REVERT: B  937 SER cc_start: 0.8906 (m) cc_final: 0.8533 (p)
REVERT: B  949 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7792 (mttt)
REVERT: C  462 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7846 (mt-10)
REVERT: C  825 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8403 (ttp80)
  outliers start: 56
  outliers final: 44
  residues processed: 245
  average time/residue: 0.1185
  time to fit residues: 44.3855
Evaluate side-chains
  235 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 189
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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  344 LEU
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  628 VAL
Chi-restraints excluded: chain A residue  791 MET
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  841 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  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  564 VAL
Chi-restraints excluded: chain B residue  604 ILE
Chi-restraints excluded: chain B residue  628 VAL
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  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  462 GLU
Chi-restraints excluded: chain C residue  566 CYS
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  839 CYS
Chi-restraints excluded: chain C residue  861 ILE
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 61 optimal weight:    0.9980
   chunk 125 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 207 optimal weight:    9.9990
   chunk 2 optimal weight:    0.0170
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 121 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 204 optimal weight:    2.9990
   overall best weight:    0.5018

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.185565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.134289 restraints weight = 22317.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.68
r_work: 0.3547 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2579

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= 0.121
  Angle     :  0.573  11.075  24129  Z= 0.281
  Chirality :  0.042   0.303   2640
  Planarity :  0.004   0.046   3030
  Dihedral  :  3.915  55.664   2324
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.84 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.19), residues: 2124
  helix:  2.06 (0.16), residues: 1134
  sheet:  0.92 (0.40), residues: 168
  loop : -0.37 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 819 
 TYR   0.028   0.001   TYR C 594 
 PHE   0.018   0.001   PHE C 930 
 TRP   0.042   0.001   TRP B 925 
 HIS   0.002   0.000   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (17724)
  covalent geometry    : angle       0.57320 (24129)
  hydrogen bonds       : bond        0.03411 (  858)
  hydrogen bonds       : angle       3.64799 ( 2556)

********************** 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
  232 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 188
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 MET cc_start: 0.8386 (tpp) cc_final: 0.8079 (mtp)
REVERT: A  937 SER cc_start: 0.8945 (m) cc_final: 0.8604 (p)
REVERT: B  307 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6350 (tt)
REVERT: B  327 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7120 (t80)
REVERT: B  791 MET cc_start: 0.7984 (mtm) cc_final: 0.7557 (mtm)
REVERT: B  926 ARG cc_start: 0.7491 (tpp80) cc_final: 0.6630 (tpp80)
REVERT: B  937 SER cc_start: 0.8845 (m) cc_final: 0.8489 (p)
REVERT: B  944 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8178 (t80)
REVERT: B  949 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7808 (mttt)
REVERT: C  462 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7701 (mt-10)
REVERT: C  480 MET cc_start: 0.8123 (tpt) cc_final: 0.7493 (tpt)
REVERT: C  825 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8357 (ttp80)
REVERT: C  927 ASN cc_start: 0.8582 (t0) cc_final: 0.8349 (t0)
  outliers start: 44
  outliers final: 33
  residues processed: 227
  average time/residue: 0.1187
  time to fit residues: 41.3539
Evaluate side-chains
  219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 182
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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  486 THR
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  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  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  564 VAL
Chi-restraints excluded: chain B residue  628 VAL
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  944 PHE
Chi-restraints excluded: chain B residue  992 VAL
Chi-restraints excluded: chain C residue  267 VAL
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  462 GLU
Chi-restraints excluded: chain C residue  566 CYS
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  861 ILE
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 103 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 189 optimal weight:    0.9990
   chunk 206 optimal weight:    1.9990
   chunk 146 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   chunk 195 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4362 r_free = 0.4362 target = 0.184268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.127749 restraints weight = 22448.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.44
r_work: 0.3530 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  17724  Z= 0.166
  Angle     :  0.582  10.646  24129  Z= 0.290
  Chirality :  0.043   0.287   2640
  Planarity :  0.004   0.048   3030
  Dihedral  :  3.958  56.040   2324
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.57 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.18), residues: 2124
  helix:  2.00 (0.16), residues: 1134
  sheet:  0.68 (0.40), residues: 168
  loop : -0.38 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 819 
 TYR   0.031   0.001   TYR C 594 
 PHE   0.017   0.001   PHE C 930 
 TRP   0.043   0.001   TRP B 925 
 HIS   0.002   0.001   HIS B 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (17724)
  covalent geometry    : angle       0.58182 (24129)
  hydrogen bonds       : bond        0.03670 (  858)
  hydrogen bonds       : angle       3.71181 ( 2556)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3764.40 seconds
wall clock time: 65 minutes 16.26 seconds (3916.26 seconds total)