Starting phenix.real_space_refine
on Fri May 16 06:22:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d81_46624/05_2025/9d81_46624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d81_46624/05_2025/9d81_46624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d81_46624/05_2025/9d81_46624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d81_46624/05_2025/9d81_46624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d81_46624/05_2025/9d81_46624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d81_46624/05_2025/9d81_46624.cif"
  }
  resolution = 2.4
  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
-------------------------------------------------------------------------------
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=   0.015
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      93      5.16       5
     C    9156      2.51       5
     N    2487      2.21       5
     O    2739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14475
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 4825
          Classifications: {'peptide': 625}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 598}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 12.45, per 1000 atoms: 0.86
  Number of scatterers: 14475
  At special positions: 0
  Unit cell: (98.346, 94.802, 129.356, 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      93     16.00
     O    2739      8.00
     N    2487      7.00
     C    9156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 520 " - pdb=" SG  CYS C 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 520 " - pdb=" SG  CYS B 596 " 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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.93
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3342

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 27 sheets defined
      29.3% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 462 through 469
    Processing helix  chain 'A' and resid 470 through 476
      removed outlier: 4.439A  pdb=" N   ALA A 473 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 491
    Processing helix  chain 'A' and resid 492 through 513
    Processing helix  chain 'A' and resid 524 through 529
    Processing helix  chain 'A' and resid 552 through 566
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 580 through 586
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 610 through 614
    Processing helix  chain 'A' and resid 615 through 633
    Processing helix  chain 'A' and resid 652 through 668
      removed outlier: 4.044A  pdb=" N   HIS A 656 " --> pdb=" O   PRO A 652 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR A 668 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 688
    Processing helix  chain 'A' and resid 695 through 712
    Processing helix  chain 'A' and resid 808 through 814
      removed outlier: 4.075A  pdb=" N   GLN A 812 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 885
    Processing helix  chain 'A' and resid 930 through 934
    Processing helix  chain 'A' and resid 938 through 943
    Processing helix  chain 'A' and resid 947 through 951
      removed outlier: 3.940A  pdb=" N   THR A 951 " --> pdb=" O   PHE A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 995
    Processing helix  chain 'A' and resid 1044 through 1048
      removed outlier: 4.136A  pdb=" N   GLY A1047 " --> pdb=" O   SER A1044 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 469
    Processing helix  chain 'B' and resid 470 through 476
      removed outlier: 4.440A  pdb=" N   ALA B 473 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 491
    Processing helix  chain 'B' and resid 492 through 513
    Processing helix  chain 'B' and resid 524 through 529
    Processing helix  chain 'B' and resid 552 through 566
      Proline residue:  B 562  - end of helix
    Processing helix  chain 'B' and resid 580 through 586
    Processing helix  chain 'B' and resid 604 through 609
    Processing helix  chain 'B' and resid 610 through 614
    Processing helix  chain 'B' and resid 615 through 633
    Processing helix  chain 'B' and resid 652 through 668
      removed outlier: 4.044A  pdb=" N   HIS B 656 " --> pdb=" O   PRO B 652 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR B 668 " --> pdb=" O   VAL B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 688
    Processing helix  chain 'B' and resid 695 through 712
    Processing helix  chain 'B' and resid 808 through 814
      removed outlier: 4.075A  pdb=" N   GLN B 812 " --> pdb=" O   PRO B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 881 through 885
    Processing helix  chain 'B' and resid 930 through 934
    Processing helix  chain 'B' and resid 938 through 943
    Processing helix  chain 'B' and resid 947 through 951
      removed outlier: 3.940A  pdb=" N   THR B 951 " --> pdb=" O   PHE B 948 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 991 through 995
    Processing helix  chain 'B' and resid 1044 through 1048
      removed outlier: 4.136A  pdb=" N   GLY B1047 " --> pdb=" O   SER B1044 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 469
    Processing helix  chain 'C' and resid 470 through 476
      removed outlier: 4.439A  pdb=" N   ALA C 473 " --> pdb=" O   THR C 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 491
    Processing helix  chain 'C' and resid 492 through 513
    Processing helix  chain 'C' and resid 524 through 529
    Processing helix  chain 'C' and resid 552 through 566
      Proline residue:  C 562  - end of helix
    Processing helix  chain 'C' and resid 580 through 586
    Processing helix  chain 'C' and resid 604 through 609
    Processing helix  chain 'C' and resid 610 through 614
    Processing helix  chain 'C' and resid 615 through 633
    Processing helix  chain 'C' and resid 652 through 668
      removed outlier: 4.043A  pdb=" N   HIS C 656 " --> pdb=" O   PRO C 652 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR C 668 " --> pdb=" O   VAL C 664 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 683 through 688
    Processing helix  chain 'C' and resid 695 through 712
    Processing helix  chain 'C' and resid 808 through 814
      removed outlier: 4.075A  pdb=" N   GLN C 812 " --> pdb=" O   PRO C 809 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 881 through 885
    Processing helix  chain 'C' and resid 930 through 934
    Processing helix  chain 'C' and resid 938 through 943
    Processing helix  chain 'C' and resid 947 through 951
      removed outlier: 3.940A  pdb=" N   THR C 951 " --> pdb=" O   PHE C 948 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 991 through 995
    Processing helix  chain 'C' and resid 1044 through 1048
      removed outlier: 4.135A  pdb=" N   GLY C1047 " --> pdb=" O   SER C1044 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 568 through 573
      removed outlier: 8.251A  pdb=" N   PHE A 673 " --> pdb=" O   VAL A 637 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL A 639 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 537 through 538
    Processing sheet with id=3, first strand: chain 'A' and resid 726 through 728
    Processing sheet with id=4, first strand: chain 'A' and resid 726 through 728
      removed outlier: 5.384A  pdb=" N   VAL A 872 " --> pdb=" O   ASP A 790 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ASP A 790 " --> pdb=" O   VAL A 872 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   SER A 874 " --> pdb=" O   LYS A 788 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 782 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA A 783 " --> pdb=" O   ARG A 847 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ARG A 847 " --> pdb=" O   ALA A 783 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE A 785 " --> pdb=" O   VAL A 845 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 737 through 741
    Processing sheet with id=6, first strand: chain 'A' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR A 965 " --> pdb=" O   HIS A 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS A 987 " --> pdb=" O   TYR A 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU A 967 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   LEU A 998 " --> pdb=" O   GLY A 982 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'A' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR A 965 " --> pdb=" O   HIS A 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS A 987 " --> pdb=" O   TYR A 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU A 967 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   LEU A 998 " --> pdb=" O   GLY A 982 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'A' and resid 920 through 921
    Processing sheet with id=9, first strand: chain 'A' and resid 1008 through 1011
      removed outlier: 6.801A  pdb=" N   ILE A1025 " --> pdb=" O   ILE A1010 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 568 through 573
      removed outlier: 8.251A  pdb=" N   PHE B 673 " --> pdb=" O   VAL B 637 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL B 639 " --> pdb=" O   PHE B 673 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'B' and resid 537 through 538
    Processing sheet with id=12, first strand: chain 'B' and resid 726 through 728
    Processing sheet with id=13, first strand: chain 'B' and resid 726 through 728
      removed outlier: 5.384A  pdb=" N   VAL B 872 " --> pdb=" O   ASP B 790 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ASP B 790 " --> pdb=" O   VAL B 872 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER B 874 " --> pdb=" O   LYS B 788 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B 782 " --> pdb=" O   ILE B 880 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA B 783 " --> pdb=" O   ARG B 847 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ARG B 847 " --> pdb=" O   ALA B 783 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE B 785 " --> pdb=" O   VAL B 845 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'B' and resid 737 through 741
    Processing sheet with id=15, first strand: chain 'B' and resid 898 through 906
      removed outlier: 6.569A  pdb=" N   TYR B 965 " --> pdb=" O   HIS B 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS B 987 " --> pdb=" O   TYR B 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU B 967 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU B 998 " --> pdb=" O   GLY B 982 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'B' and resid 898 through 906
      removed outlier: 6.569A  pdb=" N   TYR B 965 " --> pdb=" O   HIS B 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS B 987 " --> pdb=" O   TYR B 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU B 967 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU B 998 " --> pdb=" O   GLY B 982 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'B' and resid 920 through 921
    Processing sheet with id=18, first strand: chain 'B' and resid 1008 through 1011
      removed outlier: 6.800A  pdb=" N   ILE B1025 " --> pdb=" O   ILE B1010 " (cutoff:3.500A)
    Processing sheet with id=19, first strand: chain 'C' and resid 568 through 573
      removed outlier: 8.251A  pdb=" N   PHE C 673 " --> pdb=" O   VAL C 637 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL C 639 " --> pdb=" O   PHE C 673 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'C' and resid 537 through 538
    Processing sheet with id=21, first strand: chain 'C' and resid 726 through 728
    Processing sheet with id=22, first strand: chain 'C' and resid 726 through 728
      removed outlier: 5.384A  pdb=" N   VAL C 872 " --> pdb=" O   ASP C 790 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   ASP C 790 " --> pdb=" O   VAL C 872 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER C 874 " --> pdb=" O   LYS C 788 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA C 782 " --> pdb=" O   ILE C 880 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA C 783 " --> pdb=" O   ARG C 847 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ARG C 847 " --> pdb=" O   ALA C 783 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE C 785 " --> pdb=" O   VAL C 845 " (cutoff:3.500A)
    Processing sheet with id=23, first strand: chain 'C' and resid 737 through 741
    Processing sheet with id=24, first strand: chain 'C' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR C 965 " --> pdb=" O   HIS C 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS C 987 " --> pdb=" O   TYR C 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU C 967 " --> pdb=" O   LEU C 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU C 998 " --> pdb=" O   GLY C 982 " (cutoff:3.500A)
    Processing sheet with id=25, first strand: chain 'C' and resid 898 through 906
      removed outlier: 6.568A  pdb=" N   TYR C 965 " --> pdb=" O   HIS C 987 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   HIS C 987 " --> pdb=" O   TYR C 965 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU C 967 " --> pdb=" O   LEU C 985 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU C 998 " --> pdb=" O   GLY C 982 " (cutoff:3.500A)
    Processing sheet with id=26, first strand: chain 'C' and resid 920 through 921
    Processing sheet with id=27, first strand: chain 'C' and resid 1008 through 1011
      removed outlier: 6.800A  pdb=" N   ILE C1025 " --> pdb=" O   ILE C1010 " (cutoff:3.500A)

    702 hydrogen bonds defined for protein.
    1764 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: 5.96

  Time building geometry restraints manager: 4.57 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 2379
        1.30 -     1.43: 4212
        1.43 -     1.55: 8112
        1.55 -     1.68: 0
        1.68 -     1.80: 156
  Bond restraints: 14859
  Sorted by residual:
  bond pdb=" CA  TYR A 835 "
       pdb=" C   TYR A 835 "
    ideal  model  delta    sigma   weight residual
    1.525  1.446  0.079 1.27e-02 6.20e+03 3.85e+01
  bond pdb=" CA  TYR B 835 "
       pdb=" C   TYR B 835 "
    ideal  model  delta    sigma   weight residual
    1.525  1.447  0.079 1.27e-02 6.20e+03 3.83e+01
  bond pdb=" CA  TYR C 835 "
       pdb=" C   TYR C 835 "
    ideal  model  delta    sigma   weight residual
    1.525  1.447  0.078 1.27e-02 6.20e+03 3.82e+01
  bond pdb=" CA  GLY C 837 "
       pdb=" C   GLY C 837 "
    ideal  model  delta    sigma   weight residual
    1.516  1.469  0.046 8.10e-03 1.52e+04 3.28e+01
  bond pdb=" CA  GLY B 837 "
       pdb=" C   GLY B 837 "
    ideal  model  delta    sigma   weight residual
    1.516  1.469  0.046 8.10e-03 1.52e+04 3.27e+01
  ... (remaining 14854 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 19933
        3.09 -     6.18: 215
        6.18 -     9.27: 30
        9.27 -    12.37: 18
       12.37 -    15.46: 6
  Bond angle restraints: 20202
  Sorted by residual:
  angle pdb=" N   PRO C 839 "
        pdb=" CA  PRO C 839 "
        pdb=" CB  PRO C 839 "
      ideal   model   delta    sigma   weight residual
     103.31   96.72    6.59 8.90e-01 1.26e+00 5.48e+01
  angle pdb=" N   PRO A 839 "
        pdb=" CA  PRO A 839 "
        pdb=" CB  PRO A 839 "
      ideal   model   delta    sigma   weight residual
     103.31   96.73    6.58 8.90e-01 1.26e+00 5.46e+01
  angle pdb=" N   PRO B 839 "
        pdb=" CA  PRO B 839 "
        pdb=" CB  PRO B 839 "
      ideal   model   delta    sigma   weight residual
     103.31   96.74    6.57 8.90e-01 1.26e+00 5.45e+01
  angle pdb=" C   LEU C 522 "
        pdb=" N   GLY C 523 "
        pdb=" CA  GLY C 523 "
      ideal   model   delta    sigma   weight residual
     121.70  134.29  -12.59 1.80e+00 3.09e-01 4.90e+01
  angle pdb=" C   LEU B 522 "
        pdb=" N   GLY B 523 "
        pdb=" CA  GLY B 523 "
      ideal   model   delta    sigma   weight residual
     121.70  134.29  -12.59 1.80e+00 3.09e-01 4.89e+01
  ... (remaining 20197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 7537
       16.71 -    33.42: 797
       33.42 -    50.13: 204
       50.13 -    66.84: 36
       66.84 -    83.55: 9
  Dihedral angle restraints: 8583
    sinusoidal: 3261
      harmonic: 5322
  Sorted by residual:
  dihedral pdb=" CA  GLN B1020 "
           pdb=" C   GLN B1020 "
           pdb=" N   PRO B1021 "
           pdb=" CA  PRO B1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.08   50.92     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  GLN C1020 "
           pdb=" C   GLN C1020 "
           pdb=" N   PRO C1021 "
           pdb=" CA  PRO C1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.10   50.90     0      5.00e+00 4.00e-02 1.04e+02
  dihedral pdb=" CA  GLN A1020 "
           pdb=" C   GLN A1020 "
           pdb=" N   PRO A1021 "
           pdb=" CA  PRO A1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.11   50.89     0      5.00e+00 4.00e-02 1.04e+02
  ... (remaining 8580 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1861
       0.070 -    0.140: 248
       0.140 -    0.209: 6
       0.209 -    0.279: 3
       0.279 -    0.349: 3
  Chirality restraints: 2121
  Sorted by residual:
  chirality pdb=" CA  GLU A 836 "
            pdb=" N   GLU A 836 "
            pdb=" C   GLU A 836 "
            pdb=" CB  GLU A 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CA  GLU B 836 "
            pdb=" N   GLU B 836 "
            pdb=" C   GLU B 836 "
            pdb=" CB  GLU B 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CA  GLU C 836 "
            pdb=" N   GLU C 836 "
            pdb=" C   GLU C 836 "
            pdb=" CB  GLU C 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.02e+00
  ... (remaining 2118 not shown)

  Planarity restraints: 2616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 464 "   -0.375 9.50e-02 1.11e+02   1.68e-01 1.74e+01
        pdb=" NE  ARG C 464 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 464 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 464 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 464 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 464 "   -0.375 9.50e-02 1.11e+02   1.68e-01 1.73e+01
        pdb=" NE  ARG B 464 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 464 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 464 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 464 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 464 "    0.375 9.50e-02 1.11e+02   1.68e-01 1.73e+01
        pdb=" NE  ARG A 464 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 464 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 464 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 464 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2613 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.19: 108
        2.19 -     2.87: 6251
        2.87 -     3.55: 23178
        3.55 -     4.22: 43683
        4.22 -     4.90: 71608
  Nonbonded interactions: 144828
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 723 "
            pdb=" ND2 ASN C 724 "
     model   vdw
     1.518 3.120
  nonbonded pdb=" ND2 ASN A 724 "
            pdb=" O   VAL C 723 "
     model   vdw
     1.518 3.120
  nonbonded pdb=" O   VAL A 723 "
            pdb=" ND2 ASN B 724 "
     model   vdw
     1.518 3.120
  nonbonded pdb=" NH2 ARG B 899 "
            pdb=" OE2 GLU C1071 "
     model   vdw
     1.583 3.120
  nonbonded pdb=" OE2 GLU A1071 "
            pdb=" NH2 ARG C 899 "
     model   vdw
     1.584 3.120
  ... (remaining 144823 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: 0.14
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.620
  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:          0.590
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     40.600
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4632
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   0.417  14865  Z= 0.676
  Angle     :  0.891  15.457  20208  Z= 0.504
  Chirality :  0.047   0.349   2121
  Planarity :  0.008   0.168   2616
  Dihedral  : 14.868  83.546   5232
  Min Nonbonded Distance : 1.518

Molprobity Statistics.
  All-atom Clashscore : 75.36
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  3.85 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.84 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.33 %

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: -0.83 (0.19), residues: 1869
  helix: -0.33 (0.24), residues: 471
  sheet:  0.14 (0.26), residues: 402
  loop : -0.91 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 654 
 HIS   0.005   0.002   HIS C 676 
 PHE   0.010   0.002   PHE B 776 
 TYR   0.023   0.002   TYR C1028 
 ARG   0.006   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19200 (  600)
  hydrogen bonds       : angle       8.26620 ( 1764)
  SS BOND              : bond        0.00391 (    3)
  SS BOND              : angle       1.06526 (    6)
  covalent geometry    : bond        0.00569 (14859)
  covalent geometry    : angle       0.89132 (20202)
  Misc. bond           : bond        0.41724 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 321
  time to evaluate  : 1.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8330 (mtp) cc_final: 0.7944 (mtm)
REVERT: A  501 MET cc_start: 0.7471 (mtt) cc_final: 0.6875 (mtt)
REVERT: A  579 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6791 (t80)
REVERT: A  595 ASN cc_start: 0.7708 (m110) cc_final: 0.7458 (m-40)
REVERT: B  462 THR cc_start: 0.5698 (OUTLIER) cc_final: 0.5182 (t)
REVERT: B  464 ARG cc_start: 0.3963 (OUTLIER) cc_final: 0.3306 (ttp-170)
REVERT: C  576 ILE cc_start: 0.5302 (mt) cc_final: 0.4584 (mm)
REVERT: C  663 MET cc_start: 0.2946 (tpt) cc_final: 0.1827 (tpt)
REVERT: C  672 VAL cc_start: 0.3201 (t) cc_final: 0.2973 (t)
  outliers start: 21
  outliers final: 5
  residues processed: 330
  average time/residue: 0.9609
  time to fit residues: 359.7555
Evaluate side-chains
  188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 180
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  579 TYR
Chi-restraints excluded: chain A residue  733 MET
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  733 MET
Chi-restraints excluded: chain C residue  906 MET
Chi-restraints excluded: chain C residue  964 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 140 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 95 optimal weight:    0.2980
   chunk 75 optimal weight:    0.7980
   chunk 145 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 88 optimal weight:    0.1980
   chunk 108 optimal weight:    0.9980
   chunk 168 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 512 HIS
A 513 ASN
A 606 ASN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 676 HIS
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 826 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 ASN
B 595 ASN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 724 ASN
** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 500 ASN
C 513 ASN
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 676 HIS
C 765 GLN
C 826 GLN
C 854 HIS
** C 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 902 HIS
C1020 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.105523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093042 restraints weight = 26774.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.28
r_work: 0.3274 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.8988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.127  14865  Z= 0.392
  Angle     :  1.056  18.142  20208  Z= 0.563
  Chirality :  0.057   0.274   2121
  Planarity :  0.009   0.089   2616
  Dihedral  :  7.810  60.145   2083
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 25.80
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.51 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 15.93 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.39 %

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: -1.65 (0.18), residues: 1869
  helix: -1.06 (0.23), residues: 432
  sheet: -0.26 (0.24), residues: 426
  loop : -1.48 (0.18), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 487 
 HIS   0.017   0.004   HIS B 902 
 PHE   0.034   0.004   PHE B 821 
 TYR   0.028   0.003   TYR A 811 
 ARG   0.013   0.002   ARG C 641 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05816 (  600)
  hydrogen bonds       : angle       6.84742 ( 1764)
  SS BOND              : bond        0.00188 (    3)
  SS BOND              : angle       1.35179 (    6)
  covalent geometry    : bond        0.00710 (14859)
  covalent geometry    : angle       1.05616 (20202)
  Misc. bond           : bond        0.00173 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 297
  time to evaluate  : 1.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8303 (mtp) cc_final: 0.7866 (mtm)
REVERT: A  526 MET cc_start: 0.8591 (mmm) cc_final: 0.8341 (mmm)
REVERT: A  720 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7276 (mppt)
REVERT: B  663 MET cc_start: 0.7885 (tpt) cc_final: 0.7194 (tpt)
REVERT: B  681 ASN cc_start: 0.6880 (m-40) cc_final: 0.6654 (m110)
REVERT: B  709 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7829 (ttp)
REVERT: B  711 MET cc_start: 0.7595 (mtt) cc_final: 0.7379 (mtm)
REVERT: B  765 GLN cc_start: 0.8174 (tt0) cc_final: 0.7932 (pt0)
REVERT: B  781 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7499 (mm-30)
REVERT: C  589 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7524 (tt)
REVERT: C  679 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4918 (ptm)
REVERT: C  803 TRP cc_start: 0.7254 (t60) cc_final: 0.6761 (t60)
REVERT: C  828 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8375 (t)
REVERT: C  847 ARG cc_start: 0.7394 (ptt180) cc_final: 0.7091 (ptt180)
REVERT: C  854 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6903 (t-90)
REVERT: C  856 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.7024 (pt)
REVERT: C  862 LEU cc_start: 0.7288 (mt) cc_final: 0.7028 (mm)
REVERT: C  886 THR cc_start: 0.3840 (t) cc_final: 0.3291 (p)
REVERT: C  889 MET cc_start: 0.7302 (ttp) cc_final: 0.7017 (ttm)
REVERT: C  934 LEU cc_start: 0.6222 (mt) cc_final: 0.5979 (mt)
  outliers start: 79
  outliers final: 15
  residues processed: 346
  average time/residue: 1.0888
  time to fit residues: 420.5414
Evaluate side-chains
  219 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 197
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  664 VAL
Chi-restraints excluded: chain B residue  683 HIS
Chi-restraints excluded: chain B residue  709 MET
Chi-restraints excluded: chain B residue  784 HIS
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  920 VAL
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  589 LEU
Chi-restraints excluded: chain C residue  679 MET
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  841 SER
Chi-restraints excluded: chain C residue  854 HIS
Chi-restraints excluded: chain C residue  856 ILE
Chi-restraints excluded: chain C residue  915 THR
Chi-restraints excluded: chain C residue 1041 THR
Chi-restraints excluded: chain C residue 1079 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    0.7980
   chunk 126 optimal weight:    0.6980
   chunk 144 optimal weight:    0.7980
   chunk 91 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 541 GLN
A 676 HIS
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 819 ASN
** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 683 HIS
B 724 ASN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 826 GLN
B 892 GLN
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 676 HIS
C 683 HIS
C 765 GLN
C 829 ASN
** C 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 863 GLN
** C 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 941 ASN
** C 987 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.079967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.067485 restraints weight = 26822.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 1.99
r_work: 0.2821 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          1.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  14865  Z= 0.262
  Angle     :  0.843  12.699  20208  Z= 0.440
  Chirality :  0.050   0.213   2121
  Planarity :  0.007   0.100   2616
  Dihedral  :  6.547  63.178   2064
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.58 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 18.14 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.33 %

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: -1.28 (0.19), residues: 1869
  helix: -0.59 (0.24), residues: 435
  sheet: -0.59 (0.24), residues: 453
  loop : -1.03 (0.19), residues: 981

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 654 
 HIS   0.055   0.002   HIS C 854 
 PHE   0.024   0.003   PHE B 530 
 TYR   0.021   0.003   TYR C 630 
 ARG   0.014   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04997 (  600)
  hydrogen bonds       : angle       6.10874 ( 1764)
  SS BOND              : bond        0.00080 (    3)
  SS BOND              : angle       0.83303 (    6)
  covalent geometry    : bond        0.00595 (14859)
  covalent geometry    : angle       0.84285 (20202)
  Misc. bond           : bond        0.00307 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 166
  time to evaluate  : 1.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.3517 (mtm180) cc_final: 0.3080 (mtm180)
REVERT: A  482 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7200 (mtm110)
REVERT: A  526 MET cc_start: 0.8738 (mmm) cc_final: 0.8397 (mmm)
REVERT: A  553 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7982 (p90)
REVERT: A  720 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7680 (mtpt)
REVERT: B  623 MET cc_start: 0.7861 (tpt) cc_final: 0.7487 (tpt)
REVERT: B  765 GLN cc_start: 0.7968 (tt0) cc_final: 0.7660 (pt0)
REVERT: B  816 ASP cc_start: 0.7492 (m-30) cc_final: 0.7203 (m-30)
REVERT: C  579 TYR cc_start: 0.5604 (m-10) cc_final: 0.4914 (m-10)
REVERT: C  583 GLN cc_start: 0.7587 (tt0) cc_final: 0.7195 (tt0)
REVERT: C  620 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6055 (tpt)
REVERT: C  621 GLU cc_start: 0.7816 (tt0) cc_final: 0.7566 (tm-30)
REVERT: C  856 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7985 (mt)
REVERT: C  862 LEU cc_start: 0.7849 (mt) cc_final: 0.7616 (mm)
REVERT: C  863 GLN cc_start: 0.8241 (mp10) cc_final: 0.7867 (mm-40)
REVERT: C  927 MET cc_start: 0.8463 (mmm) cc_final: 0.8158 (tpt)
  outliers start: 69
  outliers final: 19
  residues processed: 210
  average time/residue: 1.2552
  time to fit residues: 291.7831
Evaluate side-chains
  152 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  906 MET
Chi-restraints excluded: chain B residue  920 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  598 ILE
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  856 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 183 optimal weight:    0.7980
   chunk 123 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 161 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 139 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 125 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 ASN
A 878 GLN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 HIS
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 513 ASN
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 683 HIS
** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 941 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.067672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.055778 restraints weight = 27580.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 1.93
r_work: 0.2599 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2490 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          1.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  14865  Z= 0.288
  Angle     :  0.811  14.103  20208  Z= 0.425
  Chirality :  0.049   0.230   2121
  Planarity :  0.007   0.081   2616
  Dihedral  :  7.712 178.726   2064
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.96 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.34 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.30 (0.19), residues: 1869
  helix: -0.65 (0.24), residues: 450
  sheet: -0.76 (0.24), residues: 432
  loop : -0.92 (0.20), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 654 
 HIS   0.010   0.002   HIS C 854 
 PHE   0.020   0.003   PHE A 948 
 TYR   0.023   0.003   TYR B 553 
 ARG   0.024   0.001   ARG B 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04869 (  600)
  hydrogen bonds       : angle       5.96267 ( 1764)
  SS BOND              : bond        0.00049 (    3)
  SS BOND              : angle       0.83723 (    6)
  covalent geometry    : bond        0.00633 (14859)
  covalent geometry    : angle       0.81098 (20202)
  Misc. bond           : bond        0.01015 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 124
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4036 (mtm180) cc_final: 0.3613 (mtm180)
REVERT: A  482 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7777 (mtm-85)
REVERT: A  574 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8088 (mtt180)
REVERT: A  781 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8468 (mm-30)
REVERT: B  486 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7439 (mt0)
REVERT: B  487 TRP cc_start: 0.7124 (m100) cc_final: 0.6870 (m100)
REVERT: B  661 MET cc_start: 0.8916 (tmm) cc_final: 0.8566 (tmm)
REVERT: B  682 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8842 (mtt-85)
REVERT: B  697 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8739 (tpt)
REVERT: B  717 ASP cc_start: 0.8028 (t70) cc_final: 0.7827 (t70)
REVERT: B  855 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8799 (m)
REVERT: C  466 GLN cc_start: 0.6694 (mt0) cc_final: 0.6239 (mt0)
REVERT: C  553 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8541 (p90)
REVERT: C  781 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8580 (mm-30)
  outliers start: 52
  outliers final: 18
  residues processed: 156
  average time/residue: 1.3932
  time to fit residues: 238.0723
Evaluate side-chains
  127 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 1.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  697 MET
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  889 MET
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  618 LEU
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 122 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 175 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0870
   chunk 158 optimal weight:    0.4980
   chunk 123 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 146 optimal weight:    0.6980
   chunk 181 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 662 GLN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 799 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.067565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.055761 restraints weight = 27929.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 1.95
r_work: 0.2597 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2489 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          1.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  14865  Z= 0.216
  Angle     :  0.743  14.162  20208  Z= 0.388
  Chirality :  0.047   0.226   2121
  Planarity :  0.007   0.166   2616
  Dihedral  :  7.261 159.623   2064
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.17 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.94 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.25 (0.19), residues: 1869
  helix: -0.56 (0.24), residues: 453
  sheet: -0.80 (0.24), residues: 453
  loop : -0.87 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 654 
 HIS   0.005   0.001   HIS C 512 
 PHE   0.024   0.002   PHE C 496 
 TYR   0.023   0.002   TYR C 553 
 ARG   0.018   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04469 (  600)
  hydrogen bonds       : angle       5.80864 ( 1764)
  SS BOND              : bond        0.00084 (    3)
  SS BOND              : angle       1.09330 (    6)
  covalent geometry    : bond        0.00477 (14859)
  covalent geometry    : angle       0.74314 (20202)
  Misc. bond           : bond        0.00813 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 107
  time to evaluate  : 1.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4050 (mtm180) cc_final: 0.3360 (mtm180)
REVERT: A  482 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7764 (mtm-85)
REVERT: A  720 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7631 (mppt)
REVERT: A  781 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8423 (mm-30)
REVERT: A 1011 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8728 (p)
REVERT: B  486 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7651 (mt0)
REVERT: B  661 MET cc_start: 0.8927 (tmm) cc_final: 0.8544 (tmm)
REVERT: B  682 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8766 (mtt-85)
REVERT: B  717 ASP cc_start: 0.8199 (t70) cc_final: 0.7984 (t70)
REVERT: B  855 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8824 (m)
REVERT: C  466 GLN cc_start: 0.6840 (mt0) cc_final: 0.6434 (mt0)
REVERT: C  499 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8293 (ttmt)
REVERT: C  553 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8581 (p90)
REVERT: C  781 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8590 (mm-30)
  outliers start: 49
  outliers final: 28
  residues processed: 141
  average time/residue: 1.4699
  time to fit residues: 227.9156
Evaluate side-chains
  131 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 1.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  765 GLN
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  889 MET
Chi-restraints excluded: chain B residue  906 MET
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  499 LYS
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 169 optimal weight:    0.0980
   chunk 108 optimal weight:    0.9980
   chunk 178 optimal weight:    0.5980
   chunk 101 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 171 optimal weight:    0.6980
   chunk 159 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 512 HIS
** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.068012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.055954 restraints weight = 27321.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2696 rms_B_bonded: 1.96
r_work: 0.2592 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          1.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  14865  Z= 0.211
  Angle     :  0.735  14.657  20208  Z= 0.384
  Chirality :  0.047   0.226   2121
  Planarity :  0.009   0.296   2616
  Dihedral  :  7.315 164.485   2064
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.01 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.67 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.23 (0.19), residues: 1869
  helix: -0.55 (0.24), residues: 453
  sheet: -0.81 (0.24), residues: 447
  loop : -0.85 (0.20), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 654 
 HIS   0.005   0.001   HIS C 512 
 PHE   0.019   0.002   PHE C 496 
 TYR   0.023   0.002   TYR C 553 
 ARG   0.042   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  600)
  hydrogen bonds       : angle       5.74972 ( 1764)
  SS BOND              : bond        0.00072 (    3)
  SS BOND              : angle       1.10352 (    6)
  covalent geometry    : bond        0.00469 (14859)
  covalent geometry    : angle       0.73490 (20202)
  Misc. bond           : bond        0.00838 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 99
  time to evaluate  : 1.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4256 (mtm180) cc_final: 0.3491 (mtm180)
REVERT: A  482 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7672 (mtm-85)
REVERT: A  720 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7629 (mppt)
REVERT: A  781 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8424 (mm-30)
REVERT: A 1011 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8749 (p)
REVERT: B  486 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7819 (mt0)
REVERT: B  661 MET cc_start: 0.8960 (tmm) cc_final: 0.8617 (tmm)
REVERT: B  682 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8763 (mtt-85)
REVERT: C  466 GLN cc_start: 0.7021 (mt0) cc_final: 0.6719 (mt0)
REVERT: C  490 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7307 (pm20)
REVERT: C  553 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8569 (p90)
REVERT: C  781 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8601 (mm-30)
  outliers start: 46
  outliers final: 27
  residues processed: 133
  average time/residue: 1.4521
  time to fit residues: 211.4067
Evaluate side-chains
  129 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  621 GLU
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  490 GLN
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  497 ARG
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 85 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 160 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 152 optimal weight:    1.9990
   chunk 182 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 GLN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.066449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.054523 restraints weight = 27291.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2663 rms_B_bonded: 1.95
r_work: 0.2559 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2452 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          1.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  14865  Z= 0.236
  Angle     :  0.745  14.220  20208  Z= 0.389
  Chirality :  0.047   0.223   2121
  Planarity :  0.008   0.277   2616
  Dihedral  :  7.362 165.921   2064
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.39 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.54 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.20 (0.19), residues: 1869
  helix: -0.53 (0.24), residues: 453
  sheet: -0.88 (0.24), residues: 453
  loop : -0.77 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 654 
 HIS   0.005   0.001   HIS B 702 
 PHE   0.022   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.048   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  600)
  hydrogen bonds       : angle       5.78429 ( 1764)
  SS BOND              : bond        0.00132 (    3)
  SS BOND              : angle       1.05457 (    6)
  covalent geometry    : bond        0.00524 (14859)
  covalent geometry    : angle       0.74497 (20202)
  Misc. bond           : bond        0.00851 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 1.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4344 (mtm180) cc_final: 0.3548 (mtm180)
REVERT: A  482 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7718 (mtm-85)
REVERT: A  720 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7640 (mppt)
REVERT: A  781 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8423 (mm-30)
REVERT: A 1011 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (p)
REVERT: B  661 MET cc_start: 0.8926 (tmm) cc_final: 0.8638 (tmm)
REVERT: B  682 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8812 (mtt-85)
REVERT: C  466 GLN cc_start: 0.7376 (mt0) cc_final: 0.7133 (mt0)
REVERT: C  490 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7453 (pm20)
REVERT: C  499 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8286 (ttmt)
REVERT: C  553 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8562 (p90)
REVERT: C  781 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8563 (mm-30)
  outliers start: 47
  outliers final: 28
  residues processed: 136
  average time/residue: 1.4762
  time to fit residues: 219.9927
Evaluate side-chains
  128 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 1.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  490 GLN
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  497 ARG
Chi-restraints excluded: chain C residue  499 LYS
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 168 optimal weight:    0.9990
   chunk 182 optimal weight:    0.5980
   chunk 161 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0040
   chunk 54 optimal weight:    0.7980
   chunk 174 optimal weight:    0.5980
   chunk 141 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 110 optimal weight:    0.5980
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.067738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.055842 restraints weight = 27097.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.2690 rms_B_bonded: 1.96
r_work: 0.2586 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          1.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  14865  Z= 0.198
  Angle     :  0.729  18.415  20208  Z= 0.380
  Chirality :  0.046   0.224   2121
  Planarity :  0.010   0.419   2616
  Dihedral  :  7.410 165.056   2064
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.23 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.67 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.18 (0.19), residues: 1869
  helix: -0.50 (0.24), residues: 453
  sheet: -0.85 (0.24), residues: 447
  loop : -0.77 (0.20), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 654 
 HIS   0.004   0.001   HIS B 736 
 PHE   0.013   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.044   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  600)
  hydrogen bonds       : angle       5.73449 ( 1764)
  SS BOND              : bond        0.00172 (    3)
  SS BOND              : angle       1.13827 (    6)
  covalent geometry    : bond        0.00436 (14859)
  covalent geometry    : angle       0.72845 (20202)
  Misc. bond           : bond        0.00818 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 1.746 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4398 (mtm180) cc_final: 0.3580 (mtm180)
REVERT: A  482 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7773 (mtm-85)
REVERT: A  720 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7633 (mppt)
REVERT: A  781 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8426 (mm-30)
REVERT: B  661 MET cc_start: 0.8945 (tmm) cc_final: 0.8573 (tmm)
REVERT: B  682 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8737 (mtt-85)
REVERT: B  967 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8384 (tt0)
REVERT: C  466 GLN cc_start: 0.7436 (mt0) cc_final: 0.7177 (mt0)
REVERT: C  490 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7515 (pm20)
REVERT: C  499 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8323 (ttmt)
REVERT: C  553 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8515 (p90)
REVERT: C  781 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: C  869 ASP cc_start: 0.8471 (m-30) cc_final: 0.8246 (m-30)
  outliers start: 42
  outliers final: 25
  residues processed: 130
  average time/residue: 1.4675
  time to fit residues: 208.8847
Evaluate side-chains
  126 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  490 GLN
Chi-restraints excluded: chain C residue  499 LYS
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 153 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 168 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 145 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 48 optimal weight:    0.4980
   chunk 91 optimal weight:    0.0980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 583 GLN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 805 ASN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.067420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.055454 restraints weight = 27141.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 1.97
r_work: 0.2581 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2474 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          1.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  14865  Z= 0.202
  Angle     :  0.726  16.461  20208  Z= 0.379
  Chirality :  0.046   0.224   2121
  Planarity :  0.011   0.425   2616
  Dihedral  :  7.455 160.135   2064
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.33 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.88 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.17 (0.19), residues: 1869
  helix: -0.46 (0.24), residues: 453
  sheet: -0.94 (0.24), residues: 453
  loop : -0.73 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 654 
 HIS   0.004   0.001   HIS B 702 
 PHE   0.011   0.002   PHE B 776 
 TYR   0.023   0.002   TYR C 553 
 ARG   0.041   0.001   ARG C 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  600)
  hydrogen bonds       : angle       5.71716 ( 1764)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.17224 (    6)
  covalent geometry    : bond        0.00446 (14859)
  covalent geometry    : angle       0.72544 (20202)
  Misc. bond           : bond        0.00753 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 96
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4499 (mtm180) cc_final: 0.3645 (mtm180)
REVERT: A  482 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7835 (mtm-85)
REVERT: A  720 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7622 (mppt)
REVERT: A  781 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8432 (mm-30)
REVERT: B  486 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7797 (mp10)
REVERT: B  661 MET cc_start: 0.8905 (tmm) cc_final: 0.8638 (tmm)
REVERT: B  682 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (mtt-85)
REVERT: B  967 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8399 (tt0)
REVERT: C  466 GLN cc_start: 0.7404 (mt0) cc_final: 0.7145 (mt0)
REVERT: C  490 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7490 (pm20)
REVERT: C  499 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8353 (ttmt)
REVERT: C  553 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8510 (p90)
REVERT: C  781 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8557 (mm-30)
REVERT: C  869 ASP cc_start: 0.8453 (m-30) cc_final: 0.8229 (m-30)
REVERT: C  940 THR cc_start: 0.8766 (m) cc_final: 0.8466 (p)
  outliers start: 38
  outliers final: 26
  residues processed: 125
  average time/residue: 1.4575
  time to fit residues: 200.4625
Evaluate side-chains
  126 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  486 GLN
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  475 MET
Chi-restraints excluded: chain C residue  490 GLN
Chi-restraints excluded: chain C residue  499 LYS
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  816 ASP
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 179 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 152 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 135 optimal weight:    0.6980
   chunk 131 optimal weight:    0.7980
   chunk 137 optimal weight:    0.4980
   chunk 115 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   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 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 490 GLN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.067053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.055153 restraints weight = 27139.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.2678 rms_B_bonded: 1.96
r_work: 0.2573 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2466 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          1.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  14865  Z= 0.208
  Angle     :  0.738  18.462  20208  Z= 0.384
  Chirality :  0.047   0.224   2121
  Planarity :  0.012   0.421   2616
  Dihedral  :  7.895 154.821   2064
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.28 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.34 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    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: -1.18 (0.19), residues: 1869
  helix: -0.46 (0.24), residues: 453
  sheet: -1.01 (0.23), residues: 480
  loop : -0.69 (0.21), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 654 
 HIS   0.005   0.001   HIS B 702 
 PHE   0.012   0.002   PHE C 496 
 TYR   0.022   0.002   TYR C 553 
 ARG   0.044   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  600)
  hydrogen bonds       : angle       5.71968 ( 1764)
  SS BOND              : bond        0.00164 (    3)
  SS BOND              : angle       1.16177 (    6)
  covalent geometry    : bond        0.00460 (14859)
  covalent geometry    : angle       0.73736 (20202)
  Misc. bond           : bond        0.00607 (    3)

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

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

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3738 Ramachandran restraints generated.
    1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.4511 (mtm180) cc_final: 0.3660 (mtm180)
REVERT: A  482 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7705 (mtm-85)
REVERT: A  553 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8264 (p90)
REVERT: A  720 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7620 (mppt)
REVERT: A  781 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8434 (mm-30)
REVERT: B  486 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7782 (mp10)
REVERT: B  490 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7830 (mm-40)
REVERT: B  661 MET cc_start: 0.8932 (tmm) cc_final: 0.8562 (tmm)
REVERT: B  682 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8799 (mtt-85)
REVERT: C  466 GLN cc_start: 0.7535 (mt0) cc_final: 0.7230 (mt0)
REVERT: C  499 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (ttmt)
REVERT: C  553 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8521 (p90)
REVERT: C  781 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8570 (mm-30)
REVERT: C  869 ASP cc_start: 0.8451 (m-30) cc_final: 0.8223 (m-30)
REVERT: C  940 THR cc_start: 0.8764 (m) cc_final: 0.8463 (p)
  outliers start: 33
  outliers final: 26
  residues processed: 123
  average time/residue: 1.4271
  time to fit residues: 192.8613
Evaluate side-chains
  125 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  959 TYR
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain B residue  486 GLN
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  682 ARG
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  795 THR
Chi-restraints excluded: chain B residue  926 GLN
Chi-restraints excluded: chain B residue  959 TYR
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1054 THR
Chi-restraints excluded: chain C residue  499 LYS
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  816 ASP
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  862 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 185 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 146 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 987 HIS
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.067870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.056502 restraints weight = 27085.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 1.73
r_work: 0.2668 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          1.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  14865  Z= 0.256
  Angle     :  0.787  20.831  20208  Z= 0.409
  Chirality :  0.048   0.226   2121
  Planarity :  0.009   0.309   2616
  Dihedral  :  8.762 177.059   2064
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.44 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.08 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

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: -1.21 (0.19), residues: 1869
  helix: -0.53 (0.24), residues: 459
  sheet: -0.99 (0.24), residues: 453
  loop : -0.71 (0.20), residues: 957

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 654 
 HIS   0.006   0.001   HIS B 702 
 PHE   0.014   0.002   PHE C 496 
 TYR   0.023   0.002   TYR B 622 
 ARG   0.016   0.001   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04600 (  600)
  hydrogen bonds       : angle       5.80585 ( 1764)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       1.10289 (    6)
  covalent geometry    : bond        0.00566 (14859)
  covalent geometry    : angle       0.78688 (20202)
  Misc. bond           : bond        0.00835 (    3)

===============================================================================
Job complete
usr+sys time: 10244.98 seconds
wall clock time: 178 minutes 17.58 seconds (10697.58 seconds total)