Starting phenix.real_space_refine
on Fri Jun 20 16:09:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5xlr_6732/06_2025/5xlr_6732.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5xlr_6732/06_2025/5xlr_6732.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5xlr_6732/06_2025/5xlr_6732.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5xlr_6732/06_2025/5xlr_6732.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5xlr_6732/06_2025/5xlr_6732.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5xlr_6732/06_2025/5xlr_6732.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     132      5.16       5
     C   15279      2.51       5
     N    3954      2.21       5
     O    4536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.12s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 23901
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1022, 7967
          Classifications: {'peptide': 1022}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 973}
          Chain breaks: 6
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 19.92, per 1000 atoms: 0.83
  Number of scatterers: 23901
  At special positions: 0
  Unit cell: (132, 133.32, 163.68, 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     132     16.00
     O    4536      8.00
     N    3954      7.00
     C   15279      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=42, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 366 " - pdb=" SG  CYS A 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 378 " - pdb=" SG  CYS A 511 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 467 " - pdb=" SG  CYS A 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 576 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS A 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 648 " - pdb=" SG  CYS A 657 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 720 " - pdb=" SG  CYS A 742 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 725 " - pdb=" SG  CYS A 731 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 822 " - pdb=" SG  CYS A 833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1014 " - pdb=" SG  CYS A1025 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1064 " - pdb=" SG  CYS A1108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 278 " - pdb=" SG  CYS C 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 278 " - pdb=" SG  CYS B 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 323 " - pdb=" SG  CYS C 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 323 " - pdb=" SG  CYS B 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 366 " - pdb=" SG  CYS C 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 366 " - pdb=" SG  CYS B 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 378 " - pdb=" SG  CYS C 511 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 378 " - pdb=" SG  CYS B 511 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 467 " - pdb=" SG  CYS C 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 467 " - pdb=" SG  CYS B 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 524 " - pdb=" SG  CYS C 576 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 524 " - pdb=" SG  CYS B 576 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 603 " - pdb=" SG  CYS C 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 603 " - pdb=" SG  CYS B 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 648 " - pdb=" SG  CYS C 657 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 648 " - pdb=" SG  CYS B 657 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 720 " - pdb=" SG  CYS C 742 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 720 " - pdb=" SG  CYS B 742 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 725 " - pdb=" SG  CYS C 731 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 725 " - pdb=" SG  CYS B 731 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 822 " - pdb=" SG  CYS C 833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 822 " - pdb=" SG  CYS B 833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1014 " - pdb=" SG  CYS C1025 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1014 " - pdb=" SG  CYS B1025 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1064 " - pdb=" SG  CYS C1108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1064 " - pdb=" SG  CYS B1108 " distance=2.03

  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: 5.92
  Conformation dependent library (CDL) restraints added in 3.1 seconds
  

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5736

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 39 sheets defined
      23.4% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 267 through 271
      removed outlier: 4.059A  pdb=" N   THR A 271 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 291
      removed outlier: 3.513A  pdb=" N   LYS A 291 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 390 through 397
      removed outlier: 4.215A  pdb=" N   ARG A 395 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'A' and resid 729 through 739
      removed outlier: 3.503A  pdb=" N   GLY A 739 " --> pdb=" O   LEU A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 765
      removed outlier: 3.809A  pdb=" N   ASP A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 810
    Processing helix  chain 'A' and resid 815 through 820
      removed outlier: 4.197A  pdb=" N   TYR A 819 " --> pdb=" O   PHE A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 848 through 865
    Processing helix  chain 'A' and resid 879 through 892
    Processing helix  chain 'A' and resid 895 through 901
      removed outlier: 3.541A  pdb=" N   ASN A 901 " --> pdb=" O   VAL A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 920
    Processing helix  chain 'A' and resid 927 through 949
      removed outlier: 3.665A  pdb=" N   GLN A 931 " --> pdb=" O   LEU A 927 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 934 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A 949 " --> pdb=" O   VAL A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 966
    Processing helix  chain 'A' and resid 971 through 1015
      removed outlier: 4.020A  pdb=" N   ARG A 977 " --> pdb=" O   VAL A 973 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG A 982 " --> pdb=" O   LEU A 978 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1102
    Processing helix  chain 'B' and resid 267 through 271
      removed outlier: 4.059A  pdb=" N   THR B 271 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 291
      removed outlier: 3.512A  pdb=" N   LYS B 291 " --> pdb=" O   LYS B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 390 through 397
      removed outlier: 4.214A  pdb=" N   ARG B 395 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 409
    Processing helix  chain 'B' and resid 603 through 611
    Processing helix  chain 'B' and resid 729 through 739
      removed outlier: 3.505A  pdb=" N   GLY B 739 " --> pdb=" O   LEU B 735 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 765
      removed outlier: 3.811A  pdb=" N   ASP B 757 " --> pdb=" O   ALA B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 798 through 810
    Processing helix  chain 'B' and resid 815 through 820
      removed outlier: 4.197A  pdb=" N   TYR B 819 " --> pdb=" O   PHE B 815 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 848 through 865
    Processing helix  chain 'B' and resid 879 through 892
    Processing helix  chain 'B' and resid 895 through 901
      removed outlier: 3.540A  pdb=" N   ASN B 901 " --> pdb=" O   VAL B 897 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 901 through 920
    Processing helix  chain 'B' and resid 927 through 949
      removed outlier: 3.665A  pdb=" N   GLN B 931 " --> pdb=" O   LEU B 927 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL B 934 " --> pdb=" O   LEU B 930 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER B 949 " --> pdb=" O   VAL B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 961 through 966
    Processing helix  chain 'B' and resid 971 through 1015
      removed outlier: 4.019A  pdb=" N   ARG B 977 " --> pdb=" O   VAL B 973 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B 982 " --> pdb=" O   LEU B 978 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1098 through 1102
    Processing helix  chain 'C' and resid 267 through 271
      removed outlier: 4.059A  pdb=" N   THR C 271 " --> pdb=" O   GLU C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 291
      removed outlier: 3.513A  pdb=" N   LYS C 291 " --> pdb=" O   LYS C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 330
    Processing helix  chain 'C' and resid 390 through 397
      removed outlier: 4.214A  pdb=" N   ARG C 395 " --> pdb=" O   ASP C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 409
    Processing helix  chain 'C' and resid 603 through 611
    Processing helix  chain 'C' and resid 729 through 739
      removed outlier: 3.504A  pdb=" N   GLY C 739 " --> pdb=" O   LEU C 735 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 740 through 765
      removed outlier: 3.810A  pdb=" N   ASP C 757 " --> pdb=" O   ALA C 753 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 798 through 810
    Processing helix  chain 'C' and resid 815 through 820
      removed outlier: 4.197A  pdb=" N   TYR C 819 " --> pdb=" O   PHE C 815 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 848 through 865
    Processing helix  chain 'C' and resid 879 through 892
    Processing helix  chain 'C' and resid 895 through 901
      removed outlier: 3.541A  pdb=" N   ASN C 901 " --> pdb=" O   VAL C 897 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 901 through 920
    Processing helix  chain 'C' and resid 927 through 949
      removed outlier: 3.665A  pdb=" N   GLN C 931 " --> pdb=" O   LEU C 927 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL C 934 " --> pdb=" O   LEU C 930 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER C 949 " --> pdb=" O   VAL C 945 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 961 through 966
    Processing helix  chain 'C' and resid 971 through 1015
      removed outlier: 4.019A  pdb=" N   ARG C 977 " --> pdb=" O   VAL C 973 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG C 982 " --> pdb=" O   LEU C 978 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1098 through 1102
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36
      removed outlier: 7.145A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   TYR A 256 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166
    Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 306
      removed outlier: 3.859A  pdb=" N   GLY A 298 " --> pdb=" O   THR A 585 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR A 585 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 581 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN A 304 " --> pdb=" O   GLY A 579 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   GLY A 579 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315
      removed outlier: 3.625A  pdb=" N   GLY A 311 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 537 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A 570 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345
      removed outlier: 5.031A  pdb=" N   ASN A 381 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   GLU A 502 " --> pdb=" O   ASN A 381 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441
    Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652
    Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 696
    Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 710
    Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 718
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1063 through 1064
      removed outlier: 3.582A  pdb=" N   ILE A1063 " --> pdb=" O   TYR A1070 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1077 through 1079
    Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 36
      removed outlier: 7.145A  pdb=" N   ASN B  65 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   TYR B 256 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 55
    Processing sheet with id=AB7, first strand: chain 'B' and resid 164 through 166
    Processing sheet with id=AB8, first strand: chain 'B' and resid 298 through 306
      removed outlier: 3.859A  pdb=" N   GLY B 298 " --> pdb=" O   THR B 585 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR B 585 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL B 581 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASN B 304 " --> pdb=" O   GLY B 579 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY B 579 " --> pdb=" O   ASN B 304 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 315
      removed outlier: 3.625A  pdb=" N   GLY B 311 " --> pdb=" O   CYS B 524 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 537 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE B 570 " --> pdb=" O   VAL B 562 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 341 through 345
      removed outlier: 5.030A  pdb=" N   ASN B 381 " --> pdb=" O   GLU B 502 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   GLU B 502 " --> pdb=" O   ASN B 381 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 439 through 441
    Processing sheet with id=AC3, first strand: chain 'B' and resid 650 through 652
    Processing sheet with id=AC4, first strand: chain 'B' and resid 694 through 696
    Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 710
    Processing sheet with id=AC6, first strand: chain 'B' and resid 716 through 718
    Processing sheet with id=AC7, first strand: chain 'B' and resid 1063 through 1064
      removed outlier: 3.582A  pdb=" N   ILE B1063 " --> pdb=" O   TYR B1070 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 1077 through 1079
    Processing sheet with id=AC9, first strand: chain 'C' and resid 34 through 36
      removed outlier: 7.145A  pdb=" N   ASN C  65 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   TYR C 256 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 55
    Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 166
    Processing sheet with id=AD3, first strand: chain 'C' and resid 298 through 306
      removed outlier: 3.857A  pdb=" N   GLY C 298 " --> pdb=" O   THR C 585 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR C 585 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL C 581 " --> pdb=" O   THR C 302 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN C 304 " --> pdb=" O   GLY C 579 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   GLY C 579 " --> pdb=" O   ASN C 304 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 315
      removed outlier: 3.625A  pdb=" N   GLY C 311 " --> pdb=" O   CYS C 524 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL C 537 " --> pdb=" O   ILE C 573 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE C 570 " --> pdb=" O   VAL C 562 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 341 through 345
      removed outlier: 5.030A  pdb=" N   ASN C 381 " --> pdb=" O   GLU C 502 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   GLU C 502 " --> pdb=" O   ASN C 381 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 439 through 441
    Processing sheet with id=AD7, first strand: chain 'C' and resid 650 through 652
    Processing sheet with id=AD8, first strand: chain 'C' and resid 694 through 696
    Processing sheet with id=AD9, first strand: chain 'C' and resid 701 through 710
    Processing sheet with id=AE1, first strand: chain 'C' and resid 716 through 718
    Processing sheet with id=AE2, first strand: chain 'C' and resid 1063 through 1064
      removed outlier: 3.582A  pdb=" N   ILE C1063 " --> pdb=" O   TYR C1070 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 1077 through 1079

    894 hydrogen bonds defined for protein.
    2358 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: 8.90

  Time building geometry restraints manager: 7.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 7555
        1.34 -     1.46: 5559
        1.46 -     1.58: 11159
        1.58 -     1.70: 0
        1.70 -     1.82: 180
  Bond restraints: 24453
  Sorted by residual:
  bond pdb=" C   LYS B 411 "
       pdb=" N   LEU B 412 "
    ideal  model  delta    sigma   weight residual
    1.331  1.239  0.091 3.12e-02 1.03e+03 8.59e+00
  bond pdb=" C   LYS C 411 "
       pdb=" N   LEU C 412 "
    ideal  model  delta    sigma   weight residual
    1.331  1.239  0.091 3.12e-02 1.03e+03 8.59e+00
  bond pdb=" C   LYS A 411 "
       pdb=" N   LEU A 412 "
    ideal  model  delta    sigma   weight residual
    1.331  1.239  0.091 3.12e-02 1.03e+03 8.58e+00
  bond pdb=" C   ILE B 787 "
       pdb=" N   LEU B 788 "
    ideal  model  delta    sigma   weight residual
    1.331  1.251  0.080 2.83e-02 1.25e+03 7.90e+00
  bond pdb=" C   LEU A1031 "
       pdb=" N   MET A1032 "
    ideal  model  delta    sigma   weight residual
    1.330  1.355 -0.025 1.19e-02 7.06e+03 4.30e+00
  ... (remaining 24448 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 31604
        2.44 -     4.87: 1386
        4.87 -     7.31: 217
        7.31 -     9.75: 36
        9.75 -    12.18: 12
  Bond angle restraints: 33255
  Sorted by residual:
  angle pdb=" N   ASN A 227 "
        pdb=" CA  ASN A 227 "
        pdb=" C   ASN A 227 "
      ideal   model   delta    sigma   weight residual
     107.73  115.58   -7.85 1.34e+00 5.57e-01 3.43e+01
  angle pdb=" N   ASN B 227 "
        pdb=" CA  ASN B 227 "
        pdb=" C   ASN B 227 "
      ideal   model   delta    sigma   weight residual
     107.73  115.58   -7.85 1.34e+00 5.57e-01 3.43e+01
  angle pdb=" N   ASN C 227 "
        pdb=" CA  ASN C 227 "
        pdb=" C   ASN C 227 "
      ideal   model   delta    sigma   weight residual
     107.73  115.56   -7.83 1.34e+00 5.57e-01 3.42e+01
  angle pdb=" C   LYS A 566 "
        pdb=" N   THR A 567 "
        pdb=" CA  THR A 567 "
      ideal   model   delta    sigma   weight residual
     122.78  130.94   -8.16 1.52e+00 4.33e-01 2.88e+01
  angle pdb=" C   LYS C 566 "
        pdb=" N   THR C 567 "
        pdb=" CA  THR C 567 "
      ideal   model   delta    sigma   weight residual
     122.78  130.91   -8.13 1.52e+00 4.33e-01 2.86e+01
  ... (remaining 33250 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 13700
       16.27 -    32.55: 719
       32.55 -    48.82: 122
       48.82 -    65.09: 12
       65.09 -    81.36: 6
  Dihedral angle restraints: 14559
    sinusoidal: 5634
      harmonic: 8925
  Sorted by residual:
  dihedral pdb=" CA  ILE B 573 "
           pdb=" C   ILE B 573 "
           pdb=" N   SER B 574 "
           pdb=" CA  SER B 574 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.44  -47.56     0      5.00e+00 4.00e-02 9.05e+01
  dihedral pdb=" CA  ILE C 573 "
           pdb=" C   ILE C 573 "
           pdb=" N   SER C 574 "
           pdb=" CA  SER C 574 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.49  -47.51     0      5.00e+00 4.00e-02 9.03e+01
  dihedral pdb=" CA  ILE A 573 "
           pdb=" C   ILE A 573 "
           pdb=" N   SER A 574 "
           pdb=" CA  SER A 574 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.51  -47.49     0      5.00e+00 4.00e-02 9.02e+01
  ... (remaining 14556 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 2522
       0.057 -    0.113: 929
       0.113 -    0.170: 266
       0.170 -    0.227: 39
       0.227 -    0.284: 6
  Chirality restraints: 3762
  Sorted by residual:
  chirality pdb=" CA  THR B 567 "
            pdb=" N   THR B 567 "
            pdb=" C   THR B 567 "
            pdb=" CB  THR B 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CA  THR A 567 "
            pdb=" N   THR A 567 "
            pdb=" C   THR A 567 "
            pdb=" CB  THR A 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  THR C 567 "
            pdb=" N   THR C 567 "
            pdb=" C   THR C 567 "
            pdb=" CB  THR C 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 3759 not shown)

  Planarity restraints: 4302
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 502 "   -0.031 2.00e-02 2.50e+03   6.17e-02 3.81e+01
        pdb=" C   GLU C 502 "    0.107 2.00e-02 2.50e+03
        pdb=" O   GLU C 502 "   -0.041 2.00e-02 2.50e+03
        pdb=" N   LEU C 503 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 502 "   -0.031 2.00e-02 2.50e+03   6.16e-02 3.79e+01
        pdb=" C   GLU A 502 "    0.107 2.00e-02 2.50e+03
        pdb=" O   GLU A 502 "   -0.040 2.00e-02 2.50e+03
        pdb=" N   LEU A 503 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 502 "    0.031 2.00e-02 2.50e+03   6.14e-02 3.77e+01
        pdb=" C   GLU B 502 "   -0.106 2.00e-02 2.50e+03
        pdb=" O   GLU B 502 "    0.040 2.00e-02 2.50e+03
        pdb=" N   LEU B 503 "    0.035 2.00e-02 2.50e+03
  ... (remaining 4299 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 794
        2.69 -     3.24: 22807
        3.24 -     3.80: 36940
        3.80 -     4.35: 46462
        4.35 -     4.90: 77525
  Nonbonded interactions: 184528
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 549 "
            pdb=" OE1 GLU C  45 "
     model   vdw
     2.139 3.120
  nonbonded pdb=" ND2 ASN A 304 "
            pdb=" OD1 ASP C 719 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" OD1 ASP A 719 "
            pdb=" ND2 ASN B 304 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   PHE C 805 "
            pdb=" OG1 THR C 809 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   PHE A 805 "
            pdb=" OG1 THR A 809 "
     model   vdw
     2.215 3.040
  ... (remaining 184523 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: 0.16
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  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:          0.970
  Check model and map are aligned:         0.180
  Set scattering table:                    0.230
  Process input model:                     59.850
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
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      :  0.008   0.091  24495  Z= 0.371
  Angle     :  1.179  12.182  33339  Z= 0.672
  Chirality :  0.063   0.284   3762
  Planarity :  0.009   0.108   4302
  Dihedral  :  9.811  55.170   8697
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 14.55 %
    Favored  : 85.15 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  2.35 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.62 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.45 (0.12), residues: 3024
  helix: -2.64 (0.13), residues: 699
  sheet: -1.59 (0.21), residues: 516
  loop : -3.71 (0.12), residues: 1809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 423 
 HIS   0.021   0.004   HIS A1030 
 PHE   0.047   0.004   PHE A 193 
 TYR   0.030   0.004   TYR B 886 
 ARG   0.007   0.001   ARG A 315 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11736 (  894)
  hydrogen bonds       : angle      10.64314 ( 2358)
  SS BOND              : bond        0.00468 (   42)
  SS BOND              : angle       3.02750 (   84)
  covalent geometry    : bond        0.00819 (24453)
  covalent geometry    : angle       1.17081 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  718 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 708
  time to evaluate  : 2.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 PHE cc_start: 0.6028 (t80) cc_final: 0.5759 (t80)
REVERT: A  216 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5522 (pp)
REVERT: A  220 PHE cc_start: 0.5276 (t80) cc_final: 0.4948 (t80)
REVERT: A  301 GLN cc_start: 0.8708 (tt0) cc_final: 0.8348 (tm-30)
REVERT: A  850 ASP cc_start: 0.8968 (m-30) cc_final: 0.8553 (t0)
REVERT: A  884 MET cc_start: 0.6871 (mmm) cc_final: 0.6550 (mmt)
REVERT: A  899 TYR cc_start: 0.5974 (t80) cc_final: 0.5646 (t80)
REVERT: A  948 LEU cc_start: 0.9482 (tp) cc_final: 0.9262 (tt)
REVERT: A 1027 LYS cc_start: 0.8705 (tttt) cc_final: 0.8481 (tppt)
REVERT: B  216 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5295 (pp)
REVERT: B  220 PHE cc_start: 0.5563 (t80) cc_final: 0.5336 (t80)
REVERT: B  301 GLN cc_start: 0.8901 (tt0) cc_final: 0.8642 (tm-30)
REVERT: B  405 ILE cc_start: 0.7880 (mm) cc_final: 0.7583 (mp)
REVERT: B  850 ASP cc_start: 0.9121 (m-30) cc_final: 0.8817 (p0)
REVERT: B  894 THR cc_start: 0.8161 (m) cc_final: 0.7954 (p)
REVERT: B  973 VAL cc_start: 0.8782 (p) cc_final: 0.8569 (m)
REVERT: C   89 PHE cc_start: 0.6230 (t80) cc_final: 0.5898 (t80)
REVERT: C  220 PHE cc_start: 0.5565 (t80) cc_final: 0.5328 (t80)
REVERT: C  301 GLN cc_start: 0.8787 (tt0) cc_final: 0.8398 (tm-30)
REVERT: C  532 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7085 (tm)
REVERT: C  733 ASN cc_start: 0.7955 (m-40) cc_final: 0.7567 (m-40)
REVERT: C  850 ASP cc_start: 0.9232 (m-30) cc_final: 0.8700 (t0)
REVERT: C  868 TRP cc_start: 0.6833 (p-90) cc_final: 0.6417 (p-90)
REVERT: C  973 VAL cc_start: 0.8757 (p) cc_final: 0.8375 (m)
  outliers start: 10
  outliers final: 1
  residues processed: 718
  average time/residue: 0.3868
  time to fit residues: 413.2129
Evaluate side-chains
  381 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 377
  time to evaluate  : 2.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  532 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 258 optimal weight:    0.8980
   chunk 231 optimal weight:    5.9990
   chunk 128 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 156 optimal weight:    3.9990
   chunk 123 optimal weight:    0.8980
   chunk 239 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9990
   chunk 145 optimal weight:    3.9990
   chunk 178 optimal weight:    0.9990
   chunk 277 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
A 149 HIS
A 201 GLN
A 214 ASN
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 GLN
A 883 GLN
A 889 ASN
A 904 GLN
B 109 ASN
B 129 ASN
B 149 HIS
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN
B 214 ASN
B 769 GLN
B 883 GLN
B 889 ASN
B 904 GLN
B 984 GLN
B1046 HIS
C 149 HIS
** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 GLN
C 214 ASN
C 769 GLN
C 883 GLN
C 889 ASN
C 904 GLN
C1090 ASN

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.132247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.101965 restraints weight = 56517.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.104714 restraints weight = 32529.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.106566 restraints weight = 22212.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  24495  Z= 0.181
  Angle     :  0.831  10.933  33339  Z= 0.436
  Chirality :  0.049   0.270   3762
  Planarity :  0.007   0.103   4302
  Dihedral  :  7.535  42.487   3301
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 11.28 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 10.10 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.10 (0.14), residues: 3024
  helix:  0.05 (0.19), residues: 687
  sheet: -1.06 (0.22), residues: 525
  loop : -3.46 (0.13), residues: 1812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1084 
 HIS   0.009   0.001   HIS A1065 
 PHE   0.039   0.002   PHE C 262 
 TYR   0.026   0.002   TYR C 886 
 ARG   0.020   0.001   ARG C1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04537 (  894)
  hydrogen bonds       : angle       7.45173 ( 2358)
  SS BOND              : bond        0.00478 (   42)
  SS BOND              : angle       2.52504 (   84)
  covalent geometry    : bond        0.00410 (24453)
  covalent geometry    : angle       0.82253 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  536 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 463
  time to evaluate  : 2.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TRP cc_start: 0.8240 (m100) cc_final: 0.7771 (m100)
REVERT: A  183 ARG cc_start: 0.6081 (mmt180) cc_final: 0.5874 (mmt180)
REVERT: A  216 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6662 (pp)
REVERT: A  220 PHE cc_start: 0.6733 (t80) cc_final: 0.6258 (t80)
REVERT: A  395 ARG cc_start: 0.7644 (tmm160) cc_final: 0.7441 (tmm160)
REVERT: A  441 ARG cc_start: 0.6684 (mtp85) cc_final: 0.6260 (mtp85)
REVERT: A  491 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5772 (m-10)
REVERT: A  899 TYR cc_start: 0.6128 (t80) cc_final: 0.4742 (t80)
REVERT: A  956 SER cc_start: 0.8988 (t) cc_final: 0.8779 (p)
REVERT: A  966 LEU cc_start: 0.8898 (mp) cc_final: 0.8693 (mm)
REVERT: B   49 SER cc_start: 0.8549 (t) cc_final: 0.8328 (t)
REVERT: B  185 PHE cc_start: 0.8306 (m-80) cc_final: 0.8032 (m-80)
REVERT: B  191 ASP cc_start: 0.7996 (t0) cc_final: 0.7326 (t70)
REVERT: B  216 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6908 (pp)
REVERT: B  346 SER cc_start: 0.8653 (p) cc_final: 0.7819 (m)
REVERT: B  381 ASN cc_start: 0.8141 (m-40) cc_final: 0.7708 (m-40)
REVERT: B  405 ILE cc_start: 0.8810 (mm) cc_final: 0.8221 (mp)
REVERT: B  440 TYR cc_start: 0.7630 (p90) cc_final: 0.6668 (p90)
REVERT: B  515 LEU cc_start: 0.8923 (mt) cc_final: 0.8580 (tp)
REVERT: B  558 PHE cc_start: 0.7710 (m-80) cc_final: 0.7186 (m-80)
REVERT: B  894 THR cc_start: 0.8517 (m) cc_final: 0.7783 (p)
REVERT: B 1011 MET cc_start: 0.8869 (ttm) cc_final: 0.8529 (ttm)
REVERT: B 1118 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.5781 (m)
REVERT: C   89 PHE cc_start: 0.7416 (t80) cc_final: 0.7105 (t80)
REVERT: C  185 PHE cc_start: 0.8571 (m-80) cc_final: 0.8026 (m-10)
REVERT: C  220 PHE cc_start: 0.6747 (t80) cc_final: 0.6457 (t80)
REVERT: C  224 LEU cc_start: 0.7703 (mt) cc_final: 0.7118 (mt)
REVERT: C  257 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7195 (pp)
REVERT: C  515 LEU cc_start: 0.8870 (mt) cc_final: 0.8640 (tp)
REVERT: C  532 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7647 (tm)
REVERT: C  558 PHE cc_start: 0.7696 (m-80) cc_final: 0.7457 (m-80)
REVERT: C  818 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7428 (mp10)
REVERT: C 1089 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6946 (mtt90)
  outliers start: 73
  outliers final: 43
  residues processed: 511
  average time/residue: 0.3484
  time to fit residues: 278.0548
Evaluate side-chains
  416 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 366
  time to evaluate  : 2.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  157 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  360 PHE
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue 1087 THR
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  263 MET
Chi-restraints excluded: chain B residue  360 PHE
Chi-restraints excluded: chain B residue  444 ARG
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1087 THR
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1118 THR
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  360 PHE
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  849 ASP
Chi-restraints excluded: chain C residue  878 ILE
Chi-restraints excluded: chain C residue  894 THR
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1089 ARG
Chi-restraints excluded: chain C residue 1092 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 148 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0770
   chunk 104 optimal weight:    3.9990
   chunk 283 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 163 optimal weight:    1.9990
   chunk 246 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 300 optimal weight:    0.2980
   chunk 255 optimal weight:    4.9990
   chunk 290 optimal weight:    3.9990
   overall best weight:    1.2742

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 GLN
A 947 GLN
A1046 HIS
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 838 ASN
B 984 GLN
B1090 ASN
C 109 ASN
C 129 ASN
** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 818 GLN
C 883 GLN
C 939 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.131269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.101062 restraints weight = 56130.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.103783 restraints weight = 32147.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.105623 restraints weight = 21916.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  24495  Z= 0.187
  Angle     :  0.787  19.107  33339  Z= 0.409
  Chirality :  0.049   0.258   3762
  Planarity :  0.006   0.094   4302
  Dihedral  :  7.023  38.473   3301
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 12.83 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 12.83 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.69 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.15), residues: 3024
  helix:  0.99 (0.20), residues: 669
  sheet: -0.86 (0.22), residues: 552
  loop : -3.33 (0.13), residues: 1803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 101 
 HIS   0.008   0.002   HIS A1065 
 PHE   0.036   0.002   PHE C 262 
 TYR   0.037   0.002   TYR B 886 
 ARG   0.011   0.001   ARG C1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  894)
  hydrogen bonds       : angle       6.93859 ( 2358)
  SS BOND              : bond        0.00587 (   42)
  SS BOND              : angle       2.26965 (   84)
  covalent geometry    : bond        0.00428 (24453)
  covalent geometry    : angle       0.77926 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  483 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 391
  time to evaluate  : 2.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 HIS cc_start: 0.4368 (t-90) cc_final: 0.3975 (t-90)
REVERT: A  183 ARG cc_start: 0.6176 (mmt180) cc_final: 0.5838 (mmt180)
REVERT: A  184 GLU cc_start: 0.6565 (tt0) cc_final: 0.6298 (tt0)
REVERT: A  216 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6793 (pp)
REVERT: A  220 PHE cc_start: 0.6585 (t80) cc_final: 0.6175 (t80)
REVERT: A  441 ARG cc_start: 0.6753 (mtp85) cc_final: 0.5945 (mtp85)
REVERT: A  491 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5991 (m-10)
REVERT: A  558 PHE cc_start: 0.7423 (m-80) cc_final: 0.6806 (m-80)
REVERT: A  837 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7394 (m-80)
REVERT: A  886 TYR cc_start: 0.7715 (t80) cc_final: 0.7389 (t80)
REVERT: B  191 ASP cc_start: 0.7983 (t0) cc_final: 0.7296 (t70)
REVERT: B  216 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5920 (pp)
REVERT: B  220 PHE cc_start: 0.6623 (t80) cc_final: 0.6275 (t80)
REVERT: B  373 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7957 (mtmt)
REVERT: B  405 ILE cc_start: 0.8794 (mm) cc_final: 0.8314 (mp)
REVERT: B  440 TYR cc_start: 0.7581 (p90) cc_final: 0.6615 (p90)
REVERT: B  558 PHE cc_start: 0.7995 (m-80) cc_final: 0.7340 (m-80)
REVERT: B 1011 MET cc_start: 0.8723 (ttm) cc_final: 0.8230 (ttm)
REVERT: C   89 PHE cc_start: 0.7564 (t80) cc_final: 0.7166 (t80)
REVERT: C  216 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6544 (pp)
REVERT: C  220 PHE cc_start: 0.6555 (t80) cc_final: 0.6252 (t80)
REVERT: C  348 CYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7677 (t)
REVERT: C  373 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7784 (mtmm)
REVERT: C  532 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7762 (tm)
REVERT: C  818 GLN cc_start: 0.7709 (mm110) cc_final: 0.7365 (mp10)
REVERT: C  966 LEU cc_start: 0.8915 (mt) cc_final: 0.8549 (mm)
  outliers start: 92
  outliers final: 53
  residues processed: 448
  average time/residue: 0.3319
  time to fit residues: 236.5176
Evaluate side-chains
  403 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 343
  time to evaluate  : 2.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  360 PHE
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  744 GLN
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  894 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  360 PHE
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  896 ASN
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  360 PHE
Chi-restraints excluded: chain C residue  386 SER
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  849 ASP
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 187 optimal weight:    4.9990
   chunk 244 optimal weight:    0.0170
   chunk 158 optimal weight:    0.2980
   chunk 291 optimal weight:    3.9990
   chunk 147 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 173 optimal weight:    3.9990
   chunk 220 optimal weight:    7.9990
   chunk 128 optimal weight:    7.9990
   chunk 165 optimal weight:    0.8980
   overall best weight:    1.2422

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 GLN
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 GLN
A 904 GLN
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 947 GLN
B 984 GLN
** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 939 GLN
** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.131092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.100927 restraints weight = 56987.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103544 restraints weight = 33403.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.105315 restraints weight = 23038.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098  24495  Z= 0.180
  Angle     :  0.778  17.249  33339  Z= 0.401
  Chirality :  0.049   0.267   3762
  Planarity :  0.006   0.102   4302
  Dihedral  :  6.738  36.766   3300
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.33 %
    Favored  : 87.60 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.38 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.15), residues: 3024
  helix:  1.07 (0.20), residues: 705
  sheet: -0.95 (0.21), residues: 582
  loop : -3.31 (0.13), residues: 1737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 101 
 HIS   0.007   0.001   HIS A1065 
 PHE   0.037   0.002   PHE C 262 
 TYR   0.022   0.002   TYR C 723 
 ARG   0.011   0.001   ARG C1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  894)
  hydrogen bonds       : angle       6.58150 ( 2358)
  SS BOND              : bond        0.00872 (   42)
  SS BOND              : angle       2.78563 (   84)
  covalent geometry    : bond        0.00409 (24453)
  covalent geometry    : angle       0.76656 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  465 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 372
  time to evaluate  : 2.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.8678 (m-80) cc_final: 0.8456 (m-10)
REVERT: A  216 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6867 (pp)
REVERT: A  220 PHE cc_start: 0.6385 (t80) cc_final: 0.5971 (t80)
REVERT: A  441 ARG cc_start: 0.6662 (mtp85) cc_final: 0.5870 (mtp85)
REVERT: A  491 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5688 (m-10)
REVERT: A  554 ASP cc_start: 0.5797 (t0) cc_final: 0.5490 (t0)
REVERT: A  558 PHE cc_start: 0.7228 (m-80) cc_final: 0.6931 (m-80)
REVERT: A  837 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7551 (m-80)
REVERT: A  963 LEU cc_start: 0.8134 (mp) cc_final: 0.7931 (mp)
REVERT: A  976 ASP cc_start: 0.8653 (p0) cc_final: 0.8346 (p0)
REVERT: B  191 ASP cc_start: 0.7989 (t0) cc_final: 0.7293 (t70)
REVERT: B  216 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6270 (pp)
REVERT: B  220 PHE cc_start: 0.6627 (t80) cc_final: 0.6375 (t80)
REVERT: B  373 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7867 (mtmt)
REVERT: B  405 ILE cc_start: 0.8775 (mm) cc_final: 0.8438 (mp)
REVERT: B  558 PHE cc_start: 0.7887 (m-80) cc_final: 0.7246 (m-80)
REVERT: B  818 GLN cc_start: 0.7488 (mp10) cc_final: 0.7207 (mp10)
REVERT: B 1011 MET cc_start: 0.8682 (ttm) cc_final: 0.8225 (ttm)
REVERT: B 1073 ARG cc_start: 0.8041 (tmm160) cc_final: 0.7680 (tmm160)
REVERT: B 1076 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7095 (t)
REVERT: C   89 PHE cc_start: 0.7658 (t80) cc_final: 0.7406 (t80)
REVERT: C  220 PHE cc_start: 0.6228 (t80) cc_final: 0.5856 (t80)
REVERT: C  258 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8536 (mtmm)
REVERT: C  348 CYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7666 (t)
REVERT: C  373 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7788 (mtmm)
REVERT: C  393 ASP cc_start: 0.8742 (p0) cc_final: 0.8529 (p0)
REVERT: C  405 ILE cc_start: 0.8953 (mp) cc_final: 0.8672 (mp)
REVERT: C  532 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7674 (tm)
REVERT: C  818 GLN cc_start: 0.7751 (mm110) cc_final: 0.7389 (mp10)
REVERT: C  966 LEU cc_start: 0.8934 (mt) cc_final: 0.8506 (mm)
REVERT: C 1013 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7451 (mt-10)
  outliers start: 93
  outliers final: 66
  residues processed: 423
  average time/residue: 0.3272
  time to fit residues: 221.5218
Evaluate side-chains
  416 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 343
  time to evaluate  : 2.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  360 PHE
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1092 PHE
Chi-restraints excluded: chain A residue 1093 SER
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  263 MET
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  360 PHE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  555 VAL
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  605 ASP
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  722 MET
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  878 ILE
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1076 VAL
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  359 THR
Chi-restraints excluded: chain C residue  360 PHE
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  548 PHE
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  848 THR
Chi-restraints excluded: chain C residue  849 ASP
Chi-restraints excluded: chain C residue  896 ASN
Chi-restraints excluded: chain C residue  898 LEU
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1089 ARG
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 248 optimal weight:    0.9990
   chunk 301 optimal weight:    2.9990
   chunk 174 optimal weight:    4.9990
   chunk 173 optimal weight:    0.7980
   chunk 294 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 171 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 133 optimal weight:    0.8980
   chunk 204 optimal weight:    8.9990
   chunk 281 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 904 GLN
** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 HIS
C 550 GLN
C 904 GLN
C1046 HIS
** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.130909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.100841 restraints weight = 56947.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103466 restraints weight = 33514.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105242 restraints weight = 23092.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  24495  Z= 0.169
  Angle     :  0.766  15.847  33339  Z= 0.396
  Chirality :  0.048   0.301   3762
  Planarity :  0.006   0.106   4302
  Dihedral  :  6.583  37.978   3300
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 12.83 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 14.57 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.69 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.15), residues: 3024
  helix:  1.19 (0.21), residues: 708
  sheet: -0.94 (0.21), residues: 582
  loop : -3.22 (0.14), residues: 1734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 101 
 HIS   0.006   0.001   HIS A1065 
 PHE   0.036   0.002   PHE C 262 
 TYR   0.029   0.002   TYR C 886 
 ARG   0.011   0.000   ARG C1073 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  894)
  hydrogen bonds       : angle       6.41735 ( 2358)
  SS BOND              : bond        0.00444 (   42)
  SS BOND              : angle       3.30185 (   84)
  covalent geometry    : bond        0.00380 (24453)
  covalent geometry    : angle       0.74886 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  467 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 104
    poor density    : 363
  time to evaluate  : 2.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ARG cc_start: 0.6315 (mmt180) cc_final: 0.5910 (mmt180)
REVERT: A  220 PHE cc_start: 0.6274 (t80) cc_final: 0.5877 (t80)
REVERT: A  441 ARG cc_start: 0.6595 (mtp85) cc_final: 0.5843 (mtp85)
REVERT: A  491 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5847 (m-10)
REVERT: A  503 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7547 (mm)
REVERT: A  545 PHE cc_start: 0.6387 (m-80) cc_final: 0.6108 (m-80)
REVERT: A  558 PHE cc_start: 0.7122 (m-80) cc_final: 0.6866 (m-80)
REVERT: A  735 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9014 (tt)
REVERT: A  837 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7721 (m-80)
REVERT: A  976 ASP cc_start: 0.8654 (p0) cc_final: 0.8336 (p0)
REVERT: B   42 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.5920 (t80)
REVERT: B  107 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6132 (mmp)
REVERT: B  191 ASP cc_start: 0.7967 (t0) cc_final: 0.7261 (t70)
REVERT: B  216 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6297 (pp)
REVERT: B  346 SER cc_start: 0.8586 (p) cc_final: 0.7817 (m)
REVERT: B  373 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7851 (mtmt)
REVERT: B  405 ILE cc_start: 0.8778 (mm) cc_final: 0.8245 (mp)
REVERT: B  440 TYR cc_start: 0.7557 (p90) cc_final: 0.6647 (p90)
REVERT: B  558 PHE cc_start: 0.7843 (m-80) cc_final: 0.7208 (m-80)
REVERT: B  896 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8471 (p0)
REVERT: B  992 GLN cc_start: 0.8618 (mt0) cc_final: 0.8384 (mm-40)
REVERT: C  220 PHE cc_start: 0.6032 (t80) cc_final: 0.5592 (t80)
REVERT: C  348 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7680 (t)
REVERT: C  373 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7905 (mtmm)
REVERT: C  441 ARG cc_start: 0.6700 (mtp85) cc_final: 0.6346 (ttm-80)
REVERT: C  532 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7864 (tm)
REVERT: C  966 LEU cc_start: 0.8987 (mt) cc_final: 0.8569 (mm)
REVERT: C 1013 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7558 (mt-10)
  outliers start: 104
  outliers final: 67
  residues processed: 426
  average time/residue: 0.3693
  time to fit residues: 253.2791
Evaluate side-chains
  405 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 328
  time to evaluate  : 2.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  360 PHE
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  894 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1023 ASP
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1110 VAL
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  263 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  360 PHE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  441 ARG
Chi-restraints excluded: chain B residue  444 ARG
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  605 ASP
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  878 ILE
Chi-restraints excluded: chain B residue  896 ASN
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  925 THR
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1110 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  359 THR
Chi-restraints excluded: chain C residue  360 PHE
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  548 PHE
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  849 ASP
Chi-restraints excluded: chain C residue  898 LEU
Chi-restraints excluded: chain C residue 1087 THR
Chi-restraints excluded: chain C residue 1089 ARG
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1110 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 180 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 207 optimal weight:    5.9990
   chunk 165 optimal weight:    1.9990
   chunk 173 optimal weight:    3.9990
   chunk 174 optimal weight:    6.9990
   chunk 269 optimal weight:    0.9980
   chunk 248 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 889 ASN
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 627 ASN
C 733 ASN
C 744 GLN
** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.131089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.101093 restraints weight = 56714.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.103735 restraints weight = 33471.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.105485 restraints weight = 23074.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  24495  Z= 0.155
  Angle     :  0.747  14.599  33339  Z= 0.382
  Chirality :  0.047   0.198   3762
  Planarity :  0.005   0.108   4302
  Dihedral  :  6.365  39.339   3298
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  : 12.27 %
    Favored  : 87.70 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.63 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.69 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.15), residues: 3024
  helix:  1.48 (0.21), residues: 687
  sheet: -0.82 (0.21), residues: 561
  loop : -3.19 (0.13), residues: 1776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 101 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.038   0.002   PHE A 231 
 TYR   0.030   0.001   TYR B 886 
 ARG   0.007   0.000   ARG C1073 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  894)
  hydrogen bonds       : angle       6.27741 ( 2358)
  SS BOND              : bond        0.00394 (   42)
  SS BOND              : angle       2.76158 (   84)
  covalent geometry    : bond        0.00350 (24453)
  covalent geometry    : angle       0.73472 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 104
    poor density    : 352
  time to evaluate  : 2.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 MET cc_start: 0.5162 (mpp) cc_final: 0.4793 (mmt)
REVERT: A  183 ARG cc_start: 0.6377 (mmt180) cc_final: 0.5949 (mmt180)
REVERT: A  220 PHE cc_start: 0.6320 (t80) cc_final: 0.5859 (t80)
REVERT: A  441 ARG cc_start: 0.6570 (mtp85) cc_final: 0.5841 (mtp85)
REVERT: A  491 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5906 (m-10)
REVERT: A  503 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7746 (mm)
REVERT: A  548 PHE cc_start: 0.7680 (m-80) cc_final: 0.7437 (m-80)
REVERT: A  554 ASP cc_start: 0.5769 (t0) cc_final: 0.5311 (t0)
REVERT: A  558 PHE cc_start: 0.7200 (m-80) cc_final: 0.6944 (m-80)
REVERT: A  837 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7877 (m-80)
REVERT: A  976 ASP cc_start: 0.8635 (p0) cc_final: 0.8289 (p0)
REVERT: B   42 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.5701 (t80)
REVERT: B  107 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6012 (mmp)
REVERT: B  191 ASP cc_start: 0.7932 (t0) cc_final: 0.7259 (t70)
REVERT: B  216 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6605 (pp)
REVERT: B  257 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6597 (mp)
REVERT: B  346 SER cc_start: 0.8547 (p) cc_final: 0.7889 (m)
REVERT: B  373 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7800 (mtmt)
REVERT: B  405 ILE cc_start: 0.8771 (mm) cc_final: 0.8257 (mp)
REVERT: B  440 TYR cc_start: 0.7613 (p90) cc_final: 0.6749 (p90)
REVERT: B  558 PHE cc_start: 0.7799 (m-80) cc_final: 0.7180 (m-80)
REVERT: B  818 GLN cc_start: 0.7485 (mp10) cc_final: 0.7170 (mp10)
REVERT: B  992 GLN cc_start: 0.8594 (mt0) cc_final: 0.8393 (mm-40)
REVERT: C   42 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.5023 (t80)
REVERT: C  197 TYR cc_start: 0.7924 (m-10) cc_final: 0.7610 (m-80)
REVERT: C  348 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7678 (t)
REVERT: C  373 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7922 (mtmm)
REVERT: C  532 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7823 (tm)
REVERT: C  837 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7778 (m-80)
REVERT: C  966 LEU cc_start: 0.9018 (mt) cc_final: 0.8578 (mm)
REVERT: C 1013 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7562 (mt-10)
  outliers start: 104
  outliers final: 67
  residues processed: 423
  average time/residue: 0.3529
  time to fit residues: 240.3975
Evaluate side-chains
  412 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 334
  time to evaluate  : 2.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  193 PHE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  360 PHE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  419 CYS
Chi-restraints excluded: chain B residue  441 ARG
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  735 LEU
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  848 THR
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  925 THR
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1093 SER
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1110 VAL
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  359 THR
Chi-restraints excluded: chain C residue  360 PHE
Chi-restraints excluded: chain C residue  386 SER
Chi-restraints excluded: chain C residue  532 LEU
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  596 VAL
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  767 VAL
Chi-restraints excluded: chain C residue  823 LEU
Chi-restraints excluded: chain C residue  837 PHE
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  848 THR
Chi-restraints excluded: chain C residue  896 ASN
Chi-restraints excluded: chain C residue  922 THR
Chi-restraints excluded: chain C residue 1089 ARG
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Chi-restraints excluded: chain C residue 1110 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 280 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 295 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0270
   chunk 138 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 947 GLN
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.132184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102370 restraints weight = 57366.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.105000 restraints weight = 33784.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.106785 restraints weight = 23296.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  24495  Z= 0.137
  Angle     :  0.733  14.357  33339  Z= 0.372
  Chirality :  0.047   0.193   3762
  Planarity :  0.005   0.111   4302
  Dihedral  :  6.157  41.188   3298
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.65 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.15), residues: 3024
  helix:  1.57 (0.21), residues: 687
  sheet: -0.81 (0.21), residues: 561
  loop : -3.11 (0.14), residues: 1776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C 101 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.039   0.002   PHE A 231 
 TYR   0.028   0.001   TYR B 886 
 ARG   0.011   0.001   ARG B1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  894)
  hydrogen bonds       : angle       6.12162 ( 2358)
  SS BOND              : bond        0.00315 (   42)
  SS BOND              : angle       2.67076 (   84)
  covalent geometry    : bond        0.00309 (24453)
  covalent geometry    : angle       0.72109 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  460 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 364
  time to evaluate  : 3.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5716 (t80)
REVERT: A  151 MET cc_start: 0.5119 (mpp) cc_final: 0.4772 (mmt)
REVERT: A  220 PHE cc_start: 0.6287 (t80) cc_final: 0.6069 (t80)
REVERT: A  441 ARG cc_start: 0.6482 (mtp85) cc_final: 0.5736 (mtp85)
REVERT: A  491 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5807 (m-10)
REVERT: A  503 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7788 (mm)
REVERT: A  548 PHE cc_start: 0.7833 (m-80) cc_final: 0.7628 (m-80)
REVERT: A  558 PHE cc_start: 0.7145 (m-80) cc_final: 0.6876 (m-80)
REVERT: A  621 ILE cc_start: 0.8795 (mt) cc_final: 0.8417 (pt)
REVERT: A  755 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7440 (tt0)
REVERT: A  837 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7921 (m-80)
REVERT: A  976 ASP cc_start: 0.8589 (p0) cc_final: 0.8314 (p0)
REVERT: B   42 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5474 (t80)
REVERT: B  107 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6060 (mmp)
REVERT: B  185 PHE cc_start: 0.8395 (m-10) cc_final: 0.7999 (m-10)
REVERT: B  191 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7175 (t70)
REVERT: B  257 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6583 (mp)
REVERT: B  346 SER cc_start: 0.8335 (p) cc_final: 0.7565 (m)
REVERT: B  373 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7840 (mtpp)
REVERT: B  405 ILE cc_start: 0.8754 (mm) cc_final: 0.8226 (mp)
REVERT: B  440 TYR cc_start: 0.7610 (p90) cc_final: 0.6767 (p90)
REVERT: B  558 PHE cc_start: 0.7715 (m-80) cc_final: 0.7146 (m-80)
REVERT: B  818 GLN cc_start: 0.7468 (mp10) cc_final: 0.7166 (mp10)
REVERT: B  899 TYR cc_start: 0.5130 (t80) cc_final: 0.4103 (t80)
REVERT: B  966 LEU cc_start: 0.9126 (mm) cc_final: 0.8863 (mm)
REVERT: B  992 GLN cc_start: 0.8560 (mt0) cc_final: 0.8335 (mm-40)
REVERT: B 1086 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8589 (tp)
REVERT: C   42 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.4822 (t80)
REVERT: C  183 ARG cc_start: 0.6370 (mmt180) cc_final: 0.6068 (mmt180)
REVERT: C  348 CYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7583 (t)
REVERT: C  373 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7900 (mtmm)
REVERT: C  558 PHE cc_start: 0.7170 (m-80) cc_final: 0.6874 (m-80)
REVERT: C  801 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8250 (mt-10)
REVERT: C  837 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7847 (m-80)
REVERT: C  880 PHE cc_start: 0.8756 (t80) cc_final: 0.8463 (t80)
REVERT: C  966 LEU cc_start: 0.9004 (mt) cc_final: 0.8548 (mm)
REVERT: C 1013 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7790 (mt-10)
  outliers start: 96
  outliers final: 61
  residues processed: 429
  average time/residue: 0.3391
  time to fit residues: 235.6842
Evaluate side-chains
  410 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 336
  time to evaluate  : 3.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  193 PHE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  894 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  419 CYS
Chi-restraints excluded: chain B residue  441 ARG
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  925 THR
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1086 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  386 SER
Chi-restraints excluded: chain C residue  555 VAL
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  731 CYS
Chi-restraints excluded: chain C residue  767 VAL
Chi-restraints excluded: chain C residue  823 LEU
Chi-restraints excluded: chain C residue  837 PHE
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  848 THR
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain C residue  896 ASN
Chi-restraints excluded: chain C residue  898 LEU
Chi-restraints excluded: chain C residue  922 THR
Chi-restraints excluded: chain C residue 1089 ARG
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 262 optimal weight:    2.9990
   chunk 301 optimal weight:    2.9990
   chunk 193 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 110 optimal weight:    8.9990
   chunk 49 optimal weight:    0.3980
   chunk 203 optimal weight:    0.4980
   chunk 143 optimal weight:   10.0000
   chunk 174 optimal weight:    1.9990
   chunk 300 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 759 ASN
A 889 ASN
** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 ASN
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN
C 883 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.132778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.102910 restraints weight = 56824.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.105672 restraints weight = 32628.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.107514 restraints weight = 22130.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.5310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  24495  Z= 0.130
  Angle     :  0.738  14.130  33339  Z= 0.372
  Chirality :  0.047   0.194   3762
  Planarity :  0.005   0.113   4302
  Dihedral  :  5.947  32.787   3294
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.31 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.48 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.15), residues: 3024
  helix:  1.59 (0.21), residues: 690
  sheet: -0.76 (0.22), residues: 546
  loop : -3.03 (0.14), residues: 1788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP C 101 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.042   0.002   PHE C 231 
 TYR   0.027   0.001   TYR B 677 
 ARG   0.007   0.000   ARG B1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  894)
  hydrogen bonds       : angle       6.00192 ( 2358)
  SS BOND              : bond        0.00328 (   42)
  SS BOND              : angle       2.68580 (   84)
  covalent geometry    : bond        0.00289 (24453)
  covalent geometry    : angle       0.72602 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 362
  time to evaluate  : 2.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.7279 (ppp) cc_final: 0.6964 (ppp)
REVERT: A   42 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.5583 (t80)
REVERT: A  151 MET cc_start: 0.5121 (mpp) cc_final: 0.4791 (mmt)
REVERT: A  197 TYR cc_start: 0.7580 (m-10) cc_final: 0.7356 (m-80)
REVERT: A  440 TYR cc_start: 0.6716 (p90) cc_final: 0.6305 (p90)
REVERT: A  441 ARG cc_start: 0.6368 (mtp85) cc_final: 0.5677 (mtp85)
REVERT: A  491 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5841 (m-10)
REVERT: A  503 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7767 (mm)
REVERT: A  554 ASP cc_start: 0.6339 (t0) cc_final: 0.5700 (t0)
REVERT: A  558 PHE cc_start: 0.7408 (m-80) cc_final: 0.7096 (m-80)
REVERT: A  621 ILE cc_start: 0.8767 (mt) cc_final: 0.8390 (pt)
REVERT: A  837 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (m-80)
REVERT: A  942 ASN cc_start: 0.8610 (m-40) cc_final: 0.8323 (m-40)
REVERT: A 1023 ASP cc_start: 0.7824 (m-30) cc_final: 0.7048 (m-30)
REVERT: B   42 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5187 (t80)
REVERT: B  107 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.5641 (mmp)
REVERT: B  191 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7232 (t0)
REVERT: B  257 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6361 (mp)
REVERT: B  346 SER cc_start: 0.8368 (p) cc_final: 0.7670 (m)
REVERT: B  373 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7839 (mtpp)
REVERT: B  405 ILE cc_start: 0.8743 (mm) cc_final: 0.8407 (mp)
REVERT: B  440 TYR cc_start: 0.7593 (p90) cc_final: 0.6761 (p90)
REVERT: B  558 PHE cc_start: 0.7714 (m-80) cc_final: 0.7109 (m-80)
REVERT: B  818 GLN cc_start: 0.7464 (mp10) cc_final: 0.7128 (mp10)
REVERT: B  899 TYR cc_start: 0.5378 (t80) cc_final: 0.4424 (t80)
REVERT: B  966 LEU cc_start: 0.9147 (mm) cc_final: 0.8906 (mm)
REVERT: B 1073 ARG cc_start: 0.7972 (tmm160) cc_final: 0.7386 (tmm160)
REVERT: C   42 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.4835 (t80)
REVERT: C  183 ARG cc_start: 0.6429 (mmt180) cc_final: 0.6044 (mmt180)
REVERT: C  348 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7580 (t)
REVERT: C  373 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7903 (mtmm)
REVERT: C  441 ARG cc_start: 0.6764 (mtp85) cc_final: 0.6461 (ttm-80)
REVERT: C  451 PHE cc_start: 0.7302 (m-80) cc_final: 0.6721 (m-10)
REVERT: C  558 PHE cc_start: 0.7070 (m-80) cc_final: 0.6772 (m-80)
REVERT: C  801 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: C  837 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7899 (m-80)
REVERT: C  966 LEU cc_start: 0.9067 (mt) cc_final: 0.8534 (mm)
  outliers start: 94
  outliers final: 64
  residues processed: 425
  average time/residue: 0.4544
  time to fit residues: 316.4870
Evaluate side-chains
  417 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 342
  time to evaluate  : 3.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  193 PHE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  882 MET
Chi-restraints excluded: chain A residue  894 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  657 CYS
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  925 THR
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1086 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  555 VAL
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  767 VAL
Chi-restraints excluded: chain C residue  823 LEU
Chi-restraints excluded: chain C residue  837 PHE
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  848 THR
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain C residue  898 LEU
Chi-restraints excluded: chain C residue  922 THR
Chi-restraints excluded: chain C residue 1089 ARG
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 255 optimal weight:    0.9990
   chunk 142 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9980
   chunk 112 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   chunk 202 optimal weight:    4.9990
   chunk 220 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 274 optimal weight:    3.9990
   chunk 254 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 ASN
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 611 HIS
C 744 GLN
C 883 GLN
C 939 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.130358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.100408 restraints weight = 57288.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.103002 restraints weight = 33799.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.104770 restraints weight = 23301.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  24495  Z= 0.178
  Angle     :  0.765  13.217  33339  Z= 0.389
  Chirality :  0.048   0.206   3762
  Planarity :  0.005   0.110   4302
  Dihedral  :  6.088  32.622   3294
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.13 %
    Favored  : 86.81 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.44 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.15), residues: 3024
  helix:  1.68 (0.21), residues: 669
  sheet: -0.82 (0.22), residues: 546
  loop : -2.99 (0.14), residues: 1809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.001   TRP B 101 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.044   0.002   PHE C 231 
 TYR   0.041   0.002   TYR A  41 
 ARG   0.011   0.001   ARG B1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  894)
  hydrogen bonds       : angle       6.05378 ( 2358)
  SS BOND              : bond        0.00388 (   42)
  SS BOND              : angle       2.77625 (   84)
  covalent geometry    : bond        0.00405 (24453)
  covalent geometry    : angle       0.75361 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  443 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 347
  time to evaluate  : 3.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.5569 (t80)
REVERT: A  151 MET cc_start: 0.5254 (mpp) cc_final: 0.4945 (mmt)
REVERT: A  183 ARG cc_start: 0.6278 (mmt180) cc_final: 0.5895 (mmt180)
REVERT: A  440 TYR cc_start: 0.6742 (p90) cc_final: 0.6356 (p90)
REVERT: A  441 ARG cc_start: 0.6336 (mtp85) cc_final: 0.5663 (mtp85)
REVERT: A  491 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.6038 (m-10)
REVERT: A  503 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7819 (mm)
REVERT: A  558 PHE cc_start: 0.7333 (m-80) cc_final: 0.6977 (m-80)
REVERT: A  621 ILE cc_start: 0.8854 (mt) cc_final: 0.8611 (pt)
REVERT: A  837 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7824 (m-80)
REVERT: A 1011 MET cc_start: 0.9223 (tpp) cc_final: 0.8608 (ttp)
REVERT: A 1023 ASP cc_start: 0.7893 (m-30) cc_final: 0.7178 (m-30)
REVERT: B   42 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.5584 (t80)
REVERT: B  107 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.5499 (mmp)
REVERT: B  151 MET cc_start: 0.5244 (mpp) cc_final: 0.5003 (mmt)
REVERT: B  184 GLU cc_start: 0.7710 (tt0) cc_final: 0.7263 (tt0)
REVERT: B  373 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7755 (mtmt)
REVERT: B  379 PHE cc_start: 0.8240 (m-10) cc_final: 0.8018 (m-80)
REVERT: B  405 ILE cc_start: 0.8746 (mm) cc_final: 0.8385 (mp)
REVERT: B  440 TYR cc_start: 0.7598 (p90) cc_final: 0.6784 (p90)
REVERT: B  451 PHE cc_start: 0.6947 (m-80) cc_final: 0.6687 (m-10)
REVERT: B  558 PHE cc_start: 0.7837 (m-80) cc_final: 0.7215 (m-80)
REVERT: B  818 GLN cc_start: 0.7601 (mp10) cc_final: 0.7232 (mp10)
REVERT: B  899 TYR cc_start: 0.5334 (t80) cc_final: 0.4257 (t80)
REVERT: B  966 LEU cc_start: 0.9179 (mm) cc_final: 0.8948 (mm)
REVERT: C   42 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.5046 (t80)
REVERT: C  183 ARG cc_start: 0.6506 (mmt180) cc_final: 0.6147 (mmt180)
REVERT: C  348 CYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7723 (t)
REVERT: C  373 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7945 (mtmm)
REVERT: C  441 ARG cc_start: 0.6816 (mtp85) cc_final: 0.6526 (ttm-80)
REVERT: C  554 ASP cc_start: 0.6580 (t0) cc_final: 0.6180 (p0)
REVERT: C  801 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: C  837 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7838 (m-80)
REVERT: C  966 LEU cc_start: 0.9120 (mt) cc_final: 0.8580 (mm)
REVERT: C  967 ASP cc_start: 0.7167 (t0) cc_final: 0.6856 (m-30)
REVERT: C 1032 MET cc_start: 0.7870 (ttm) cc_final: 0.7468 (mtm)
  outliers start: 96
  outliers final: 74
  residues processed: 416
  average time/residue: 0.3326
  time to fit residues: 223.0097
Evaluate side-chains
  409 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 326
  time to evaluate  : 2.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  193 PHE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  767 VAL
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  882 MET
Chi-restraints excluded: chain A residue  894 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  419 CYS
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  922 THR
Chi-restraints excluded: chain B residue  925 THR
Chi-restraints excluded: chain B residue  978 LEU
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1086 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1093 SER
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  386 SER
Chi-restraints excluded: chain C residue  555 VAL
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  571 LEU
Chi-restraints excluded: chain C residue  596 VAL
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  731 CYS
Chi-restraints excluded: chain C residue  767 VAL
Chi-restraints excluded: chain C residue  823 LEU
Chi-restraints excluded: chain C residue  837 PHE
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  848 THR
Chi-restraints excluded: chain C residue  876 LEU
Chi-restraints excluded: chain C residue  896 ASN
Chi-restraints excluded: chain C residue  898 LEU
Chi-restraints excluded: chain C residue  922 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 228 optimal weight:    0.0970
   chunk 214 optimal weight:    3.9990
   chunk 299 optimal weight:    0.6980
   chunk 287 optimal weight:    2.9990
   chunk 202 optimal weight:    1.9990
   chunk 222 optimal weight:    2.9990
   chunk 236 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 GLN
** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 ASN
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 744 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.130523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.100607 restraints weight = 57430.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.103313 restraints weight = 33061.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.105110 restraints weight = 22468.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  24495  Z= 0.166
  Angle     :  0.778  16.919  33339  Z= 0.394
  Chirality :  0.048   0.201   3762
  Planarity :  0.005   0.115   4302
  Dihedral  :  6.106  32.822   3294
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.24 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.69 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.15), residues: 3024
  helix:  1.59 (0.21), residues: 687
  sheet: -0.82 (0.22), residues: 531
  loop : -2.98 (0.14), residues: 1806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.001   TRP B 101 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.045   0.002   PHE C 231 
 TYR   0.027   0.002   TYR A  41 
 ARG   0.008   0.000   ARG B1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04103 (  894)
  hydrogen bonds       : angle       6.01361 ( 2358)
  SS BOND              : bond        0.00336 (   42)
  SS BOND              : angle       2.97662 (   84)
  covalent geometry    : bond        0.00381 (24453)
  covalent geometry    : angle       0.76435 (33255)

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

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

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6048 Ramachandran restraints generated.
    3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 335
  time to evaluate  : 2.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.5693 (t80)
REVERT: A  151 MET cc_start: 0.5239 (mpp) cc_final: 0.4934 (mmt)
REVERT: A  216 LEU cc_start: 0.7740 (pp) cc_final: 0.7478 (pp)
REVERT: A  440 TYR cc_start: 0.6728 (p90) cc_final: 0.6344 (p90)
REVERT: A  441 ARG cc_start: 0.6344 (mtp85) cc_final: 0.5692 (mtp85)
REVERT: A  491 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5918 (m-10)
REVERT: A  503 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7838 (mm)
REVERT: A  558 PHE cc_start: 0.7322 (m-80) cc_final: 0.6955 (m-80)
REVERT: A  621 ILE cc_start: 0.8849 (mt) cc_final: 0.8602 (pt)
REVERT: A  837 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7838 (m-80)
REVERT: A 1011 MET cc_start: 0.9244 (tpp) cc_final: 0.8614 (ttp)
REVERT: A 1023 ASP cc_start: 0.7997 (m-30) cc_final: 0.7309 (m-30)
REVERT: B   42 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.5500 (t80)
REVERT: B  107 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.5479 (mmp)
REVERT: B  151 MET cc_start: 0.5236 (mpp) cc_final: 0.4980 (mmt)
REVERT: B  184 GLU cc_start: 0.7667 (tt0) cc_final: 0.7339 (tt0)
REVERT: B  263 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8354 (tmm)
REVERT: B  373 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7959 (mtpp)
REVERT: B  379 PHE cc_start: 0.8254 (m-10) cc_final: 0.8022 (m-80)
REVERT: B  405 ILE cc_start: 0.8770 (mm) cc_final: 0.8375 (mp)
REVERT: B  440 TYR cc_start: 0.7594 (p90) cc_final: 0.6782 (p90)
REVERT: B  548 PHE cc_start: 0.7631 (m-80) cc_final: 0.7398 (m-80)
REVERT: B  558 PHE cc_start: 0.7851 (m-80) cc_final: 0.7202 (m-80)
REVERT: B  627 ASN cc_start: 0.8507 (t0) cc_final: 0.8281 (t0)
REVERT: B  818 GLN cc_start: 0.7633 (mp10) cc_final: 0.7241 (mp10)
REVERT: B  899 TYR cc_start: 0.5398 (t80) cc_final: 0.4392 (t80)
REVERT: B  966 LEU cc_start: 0.9165 (mm) cc_final: 0.8898 (mm)
REVERT: C   42 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.4969 (t80)
REVERT: C  183 ARG cc_start: 0.6491 (mmt180) cc_final: 0.6099 (mmt180)
REVERT: C  348 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7686 (t)
REVERT: C  373 LYS cc_start: 0.8382 (mtpp) cc_final: 0.7947 (mtmm)
REVERT: C  441 ARG cc_start: 0.6850 (mtp85) cc_final: 0.6561 (ttm-80)
REVERT: C  554 ASP cc_start: 0.6882 (t0) cc_final: 0.6088 (p0)
REVERT: C  707 GLU cc_start: 0.7829 (tt0) cc_final: 0.7552 (tt0)
REVERT: C  801 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: C  837 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7876 (m-80)
REVERT: C  966 LEU cc_start: 0.9126 (mt) cc_final: 0.8571 (mm)
REVERT: C  967 ASP cc_start: 0.7429 (t0) cc_final: 0.7020 (m-30)
  outliers start: 86
  outliers final: 70
  residues processed: 396
  average time/residue: 0.3310
  time to fit residues: 213.2329
Evaluate side-chains
  400 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 320
  time to evaluate  : 2.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 TYR
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  193 PHE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  323 CYS
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  386 SER
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain A residue  680 SER
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  733 ASN
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  841 THR
Chi-restraints excluded: chain A residue  882 MET
Chi-restraints excluded: chain A residue  894 THR
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain B residue   42 TYR
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  193 PHE
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  263 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  419 CYS
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  581 VAL
Chi-restraints excluded: chain B residue  632 GLN
Chi-restraints excluded: chain B residue  733 ASN
Chi-restraints excluded: chain B residue  737 GLN
Chi-restraints excluded: chain B residue  770 MET
Chi-restraints excluded: chain B residue  840 LEU
Chi-restraints excluded: chain B residue  841 THR
Chi-restraints excluded: chain B residue  898 LEU
Chi-restraints excluded: chain B residue  919 SER
Chi-restraints excluded: chain B residue  922 THR
Chi-restraints excluded: chain B residue  925 THR
Chi-restraints excluded: chain B residue  979 ILE
Chi-restraints excluded: chain B residue 1086 ILE
Chi-restraints excluded: chain B residue 1092 PHE
Chi-restraints excluded: chain B residue 1093 SER
Chi-restraints excluded: chain B residue 1098 THR
Chi-restraints excluded: chain B residue 1110 VAL
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  323 CYS
Chi-restraints excluded: chain C residue  348 CYS
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  386 SER
Chi-restraints excluded: chain C residue  555 VAL
Chi-restraints excluded: chain C residue  570 ILE
Chi-restraints excluded: chain C residue  577 SER
Chi-restraints excluded: chain C residue  596 VAL
Chi-restraints excluded: chain C residue  680 SER
Chi-restraints excluded: chain C residue  731 CYS
Chi-restraints excluded: chain C residue  767 VAL
Chi-restraints excluded: chain C residue  823 LEU
Chi-restraints excluded: chain C residue  837 PHE
Chi-restraints excluded: chain C residue  840 LEU
Chi-restraints excluded: chain C residue  841 THR
Chi-restraints excluded: chain C residue  848 THR
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain C residue  922 THR
Chi-restraints excluded: chain C residue 1092 PHE
Chi-restraints excluded: chain C residue 1098 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 306
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 230 optimal weight:    0.9990
   chunk 180 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   chunk 130 optimal weight:    6.9990
   chunk 273 optimal weight:    0.3980
   chunk 281 optimal weight:    0.0980
   chunk 169 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 301 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 889 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.132482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.102932 restraints weight = 56998.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.105681 restraints weight = 32753.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107550 restraints weight = 22200.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  24495  Z= 0.133
  Angle     :  0.753  16.606  33339  Z= 0.379
  Chirality :  0.047   0.197   3762
  Planarity :  0.005   0.115   4302
  Dihedral  :  5.910  31.604   3294
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.21 %
    Favored  : 88.79 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.69 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.16), residues: 3024
  helix:  1.83 (0.21), residues: 669
  sheet: -0.76 (0.22), residues: 543
  loop : -2.91 (0.14), residues: 1812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP C 101 
 HIS   0.005   0.001   HIS C1030 
 PHE   0.047   0.002   PHE C 231 
 TYR   0.034   0.001   TYR C 886 
 ARG   0.007   0.001   ARG B1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  894)
  hydrogen bonds       : angle       5.89905 ( 2358)
  SS BOND              : bond        0.00290 (   42)
  SS BOND              : angle       2.81788 (   84)
  covalent geometry    : bond        0.00301 (24453)
  covalent geometry    : angle       0.74052 (33255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8554.32 seconds
wall clock time: 151 minutes 40.84 seconds (9100.84 seconds total)