Starting phenix.real_space_refine
on Thu Sep 18 04:43:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d81_46624/09_2025/9d81_46624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d81_46624/09_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_46624/09_2025/9d81_46624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d81_46624/09_2025/9d81_46624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d81_46624/09_2025/9d81_46624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d81_46624/09_2025/9d81_46624.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 3.38, per 1000 atoms: 0.23
  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 B 520 " - pdb=" SG  CYS B 596 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 520 " - pdb=" SG  CYS C 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: 1.17
  Conformation dependent library (CDL) restraints added in 518.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.51
  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: 3.10

  Time building geometry restraints manager: 1.54 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             15.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.450
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.480
-------------------------------------------------------------------------------
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 : 75.25
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.006   0.001   ARG A 497 
 TYR   0.023   0.002   TYR C1028 
 PHE   0.010   0.002   PHE B 776 
 TRP   0.017   0.002   TRP C 654 
 HIS   0.005   0.002   HIS C 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 (14859)
  covalent geometry    : angle       0.89132 (20202)
  SS BOND              : bond        0.00391 (    3)
  SS BOND              : angle       1.06526 (    6)
  hydrogen bonds       : bond        0.19200 (  600)
  hydrogen bonds       : angle       8.26620 ( 1764)
  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  : 0.412 
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  488 LEU cc_start: 0.8269 (mt) cc_final: 0.8068 (mm)
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: 0.4583 (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: 0.4950
  time to fit residues: 184.6727
Evaluate side-chains
  189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0010
   chunk 10 optimal weight:    0.0030
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.0970
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:    0.0000
   overall best weight:    0.0798

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

Flipped N/Q/H residues before XYZ refinement:
** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 826 GLN
** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
B 510 GLN
B 595 ASN
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 681 ASN
B 724 ASN
** B 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 805 ASN
** B 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1020 GLN
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 724 ASN
** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 826 GLN
** C 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 878 GLN
C1020 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.111905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.101312 restraints weight = 27589.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.11
r_work: 0.3415 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5270
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14865  Z= 0.176
  Angle     :  0.811  13.157  20208  Z= 0.422
  Chirality :  0.048   0.220   2121
  Planarity :  0.007   0.093   2616
  Dihedral  :  7.125  70.884   2083
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 23.47
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.65 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 16.67 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.19), residues: 1869
  helix: -0.17 (0.25), residues: 417
  sheet: -0.25 (0.24), residues: 456
  loop : -0.92 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 497 
 TYR   0.023   0.002   TYR B 949 
 PHE   0.022   0.002   PHE B 948 
 TRP   0.019   0.002   TRP B 487 
 HIS   0.012   0.002   HIS B 902 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (14859)
  covalent geometry    : angle       0.81124 (20202)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       1.21345 (    6)
  hydrogen bonds       : bond        0.04908 (  600)
  hydrogen bonds       : angle       6.40961 ( 1764)
  Misc. bond           : bond        0.00169 (    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
  347 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 287
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8155 (mtp) cc_final: 0.7874 (mtm)
REVERT: A  526 MET cc_start: 0.7719 (mmm) cc_final: 0.7412 (mmm)
REVERT: A  595 ASN cc_start: 0.7969 (m110) cc_final: 0.7702 (m-40)
REVERT: A  599 VAL cc_start: 0.7307 (p) cc_final: 0.7066 (t)
REVERT: A  807 ASN cc_start: 0.7050 (m-40) cc_final: 0.6653 (m110)
REVERT: A  816 ASP cc_start: 0.6284 (OUTLIER) cc_final: 0.5131 (p0)
REVERT: A  826 GLN cc_start: 0.7594 (tp40) cc_final: 0.7168 (tp40)
REVERT: A  900 VAL cc_start: 0.6504 (m) cc_final: 0.5933 (p)
REVERT: B  462 THR cc_start: 0.5386 (OUTLIER) cc_final: 0.5108 (t)
REVERT: B  561 LEU cc_start: 0.6718 (tp) cc_final: 0.6467 (tm)
REVERT: B  585 TYR cc_start: 0.5671 (t80) cc_final: 0.4889 (t80)
REVERT: B  586 GLU cc_start: 0.6904 (pp20) cc_final: 0.6662 (pp20)
REVERT: B  663 MET cc_start: 0.6501 (tpt) cc_final: 0.6061 (tpp)
REVERT: B  678 VAL cc_start: 0.6435 (p) cc_final: 0.5987 (t)
REVERT: B  756 THR cc_start: 0.5723 (p) cc_final: 0.5447 (p)
REVERT: B  764 LEU cc_start: 0.6007 (mt) cc_final: 0.5538 (mt)
REVERT: B 1020 GLN cc_start: 0.5645 (OUTLIER) cc_final: 0.5170 (tt0)
REVERT: B 1065 TYR cc_start: 0.6001 (m-80) cc_final: 0.5771 (m-80)
REVERT: C  625 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6590 (mtmm)
REVERT: C  835 TYR cc_start: 0.5857 (m-80) cc_final: 0.5474 (m-80)
REVERT: C 1027 ASP cc_start: 0.4390 (t0) cc_final: 0.3323 (t0)
  outliers start: 60
  outliers final: 12
  residues processed: 323
  average time/residue: 0.4743
  time to fit residues: 173.1501
Evaluate side-chains
  224 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  516 SER
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  816 ASP
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  971 TYR
Chi-restraints excluded: chain B residue 1020 GLN
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  625 LYS
Chi-restraints excluded: chain C residue  804 ASN
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue 1044 SER
Chi-restraints excluded: chain C residue 1055 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 155 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0980
   chunk 142 optimal weight:    0.6980
   chunk 167 optimal weight:    0.6980
   chunk 174 optimal weight:    0.1980
   chunk 18 optimal weight:    0.0970
   chunk 77 optimal weight:    1.9990
   chunk 175 optimal weight:    0.7980
   overall best weight:    0.2378

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

Flipped N/Q/H residues before XYZ refinement:
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 GLN
** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1078 ASN
B 606 ASN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 688 GLN
B 805 ASN
** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1024 ASN
C 854 HIS
C 861 ASN
C1020 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.105690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.093847 restraints weight = 27679.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.27
r_work: 0.3299 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.6301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  14865  Z= 0.212
  Angle     :  0.819  14.005  20208  Z= 0.430
  Chirality :  0.049   0.250   2121
  Planarity :  0.007   0.079   2616
  Dihedral  :  6.437  52.411   2065
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 22.06
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.28 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.47 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.19), residues: 1869
  helix: -0.33 (0.25), residues: 432
  sheet: -0.50 (0.24), residues: 465
  loop : -1.07 (0.20), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 897 
 TYR   0.040   0.002   TYR B 553 
 PHE   0.017   0.002   PHE B 530 
 TRP   0.028   0.002   TRP B 890 
 HIS   0.011   0.002   HIS A 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (14859)
  covalent geometry    : angle       0.81868 (20202)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       1.22365 (    6)
  hydrogen bonds       : bond        0.04564 (  600)
  hydrogen bonds       : angle       6.23048 ( 1764)
  Misc. bond           : bond        0.00203 (    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
  362 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 279
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8403 (mtp) cc_final: 0.8075 (mtm)
REVERT: A  526 MET cc_start: 0.8359 (mmm) cc_final: 0.7877 (mmm)
REVERT: A  553 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7713 (p90)
REVERT: A  595 ASN cc_start: 0.8096 (m110) cc_final: 0.7775 (m-40)
REVERT: A  720 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7379 (mtpt)
REVERT: A  765 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8036 (mp10)
REVERT: A  807 ASN cc_start: 0.7765 (m-40) cc_final: 0.7471 (m110)
REVERT: A  816 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.5692 (p0)
REVERT: A 1020 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.6194 (tt0)
REVERT: B  563 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6252 (mt-10)
REVERT: B  681 ASN cc_start: 0.6238 (m110) cc_final: 0.5953 (m110)
REVERT: B  736 HIS cc_start: 0.5182 (m-70) cc_final: 0.4952 (m90)
REVERT: B  996 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7180 (Cg_endo)
REVERT: B 1042 ASP cc_start: 0.7393 (m-30) cc_final: 0.7163 (m-30)
REVERT: B 1065 TYR cc_start: 0.7105 (m-80) cc_final: 0.6755 (m-80)
REVERT: C  625 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7147 (mtmm)
REVERT: C  657 TRP cc_start: 0.5787 (m-10) cc_final: 0.5118 (m-10)
REVERT: C  927 MET cc_start: 0.5823 (mmm) cc_final: 0.5556 (mmm)
REVERT: C  975 SER cc_start: 0.6819 (p) cc_final: 0.6534 (t)
  outliers start: 83
  outliers final: 19
  residues processed: 336
  average time/residue: 0.5201
  time to fit residues: 195.1775
Evaluate side-chains
  236 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 210
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  710 LEU
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  765 GLN
Chi-restraints excluded: chain A residue  816 ASP
Chi-restraints excluded: chain A residue 1020 GLN
Chi-restraints excluded: chain A residue 1025 ILE
Chi-restraints excluded: chain B residue  563 GLU
Chi-restraints excluded: chain B residue  726 THR
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  784 HIS
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  979 LYS
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  625 LYS
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  855 THR
Chi-restraints excluded: chain C residue  856 ILE
Chi-restraints excluded: chain C residue  894 GLU
Chi-restraints excluded: chain C residue  951 THR
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 163 optimal weight:    0.9990
   chunk 154 optimal weight:    0.1980
   chunk 60 optimal weight:    0.7980
   chunk 117 optimal weight:    0.0870
   chunk 122 optimal weight:    0.1980
   chunk 184 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 144 optimal weight:    0.5980
   chunk 120 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 160 optimal weight:    1.9990
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 GLN
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 765 GLN
A 878 GLN
B 513 ASN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 HIS
B 805 ASN
B 878 GLN
B 892 GLN
B 941 ASN
** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 662 GLN
C 688 GLN
C 826 GLN
C 931 GLN
** C1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081176 restraints weight = 27430.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.24
r_work: 0.3087 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          1.0081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100  14865  Z= 0.265
  Angle     :  0.855  12.850  20208  Z= 0.448
  Chirality :  0.050   0.236   2121
  Planarity :  0.007   0.091   2616
  Dihedral  :  6.394  60.294   2064
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 20.01
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  5.03 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 18.61 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.19), residues: 1869
  helix: -0.57 (0.24), residues: 426
  sheet: -0.77 (0.22), residues: 498
  loop : -1.15 (0.20), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 899 
 TYR   0.030   0.002   TYR C 553 
 PHE   0.022   0.002   PHE B 530 
 TRP   0.039   0.003   TRP B1057 
 HIS   0.008   0.002   HIS A 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (14859)
  covalent geometry    : angle       0.85507 (20202)
  SS BOND              : bond        0.00231 (    3)
  SS BOND              : angle       0.69636 (    6)
  hydrogen bonds       : bond        0.04560 (  600)
  hydrogen bonds       : angle       6.11992 ( 1764)
  Misc. bond           : bond        0.00291 (    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
  311 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 229
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 MET cc_start: 0.8707 (mmm) cc_final: 0.8269 (mmm)
REVERT: A  553 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7872 (p90)
REVERT: A  573 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7795 (tpt)
REVERT: A  622 TYR cc_start: 0.8635 (m-80) cc_final: 0.8406 (m-80)
REVERT: A  720 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7840 (mtpt)
REVERT: B  513 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7432 (m110)
REVERT: B  622 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6744 (t80)
REVERT: B  628 ARG cc_start: 0.6763 (mtp-110) cc_final: 0.6555 (mtp-110)
REVERT: B  720 LYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5831 (mppt)
REVERT: B  735 ASP cc_start: 0.7000 (m-30) cc_final: 0.6791 (m-30)
REVERT: B  821 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.5964 (t80)
REVERT: B  862 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7607 (mt)
REVERT: C  464 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7103 (ttm170)
REVERT: C  563 GLU cc_start: 0.8297 (tp30) cc_final: 0.7967 (tt0)
REVERT: C  571 ILE cc_start: 0.7909 (mt) cc_final: 0.7687 (mm)
REVERT: C  579 TYR cc_start: 0.4086 (m-10) cc_final: 0.3820 (m-10)
REVERT: C  598 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7810 (mp)
REVERT: C  679 MET cc_start: 0.5571 (ptp) cc_final: 0.5223 (ptm)
REVERT: C  781 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7214 (mm-30)
REVERT: C  862 LEU cc_start: 0.7056 (mt) cc_final: 0.6656 (mm)
REVERT: C  865 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7886 (mt-10)
REVERT: C  959 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (m-80)
  outliers start: 82
  outliers final: 23
  residues processed: 287
  average time/residue: 0.5752
  time to fit residues: 183.1022
Evaluate side-chains
  189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  573 MET
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  976 SER
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  513 ASN
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  622 TYR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  772 CYS
Chi-restraints excluded: chain B residue  784 HIS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  862 LEU
Chi-restraints excluded: chain B residue  943 VAL
Chi-restraints excluded: chain B residue  995 VAL
Chi-restraints excluded: chain B residue 1010 ILE
Chi-restraints excluded: chain B residue 1032 LEU
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  598 ILE
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  764 LEU
Chi-restraints excluded: chain C residue  828 VAL
Chi-restraints excluded: chain C residue  854 HIS
Chi-restraints excluded: chain C residue  856 ILE
Chi-restraints excluded: chain C residue  951 THR
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 132 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 173 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   chunk 160 optimal weight:    0.7980
   chunk 133 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0870
   chunk 47 optimal weight:    0.6980
   chunk 113 optimal weight:    0.7980
   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 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 765 GLN
A 861 ASN
A1020 GLN
B 513 ASN
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 662 GLN
B 724 ASN
B 765 GLN
B 805 ASN
B 807 ASN
** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 513 ASN
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 941 ASN
** C1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.079367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.066240 restraints weight = 26843.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.08
r_work: 0.2793 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          1.2980

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= 0.254
  Angle     :  0.837  12.587  20208  Z= 0.434
  Chirality :  0.050   0.234   2121
  Planarity :  0.007   0.081   2616
  Dihedral  :  6.642  55.770   2064
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.23 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 19.28 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.19), residues: 1869
  helix: -0.59 (0.24), residues: 450
  sheet: -0.69 (0.23), residues: 456
  loop : -1.03 (0.21), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.031   0.001   ARG A 497 
 TYR   0.026   0.002   TYR B 553 
 PHE   0.028   0.003   PHE B 530 
 TRP   0.023   0.002   TRP B1057 
 HIS   0.010   0.002   HIS C 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 (14859)
  covalent geometry    : angle       0.83685 (20202)
  SS BOND              : bond        0.00127 (    3)
  SS BOND              : angle       0.67153 (    6)
  hydrogen bonds       : bond        0.04690 (  600)
  hydrogen bonds       : angle       6.04730 ( 1764)
  Misc. bond           : bond        0.00725 (    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
  246 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 170
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8511 (mtm)
REVERT: A  482 ARG cc_start: 0.8461 (mtm110) cc_final: 0.8173 (mtm110)
REVERT: A  553 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8214 (p90)
REVERT: A  720 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7605 (mppt)
REVERT: A  861 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8669 (t0)
REVERT: B  464 ARG cc_start: 0.5764 (ttt90) cc_final: 0.5442 (ttm170)
REVERT: B  486 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7641 (mt0)
REVERT: B  512 HIS cc_start: 0.8100 (m-70) cc_final: 0.7898 (m-70)
REVERT: B  624 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7534 (mm-30)
REVERT: B  661 MET cc_start: 0.8890 (tmm) cc_final: 0.8583 (tmm)
REVERT: B  697 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8851 (tpt)
REVERT: B  720 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7525 (pttt)
REVERT: B  821 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.6987 (t80)
REVERT: B  868 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8475 (mtmt)
REVERT: B  894 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (pt0)
REVERT: B  895 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8365 (mt-10)
REVERT: B  920 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8639 (m)
REVERT: B  956 LEU cc_start: 0.7820 (mp) cc_final: 0.7105 (mt)
REVERT: B  967 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.6995 (tp30)
REVERT: B 1069 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7886 (mt-10)
REVERT: C  466 GLN cc_start: 0.6383 (mt0) cc_final: 0.5906 (mt0)
REVERT: C  475 MET cc_start: 0.7479 (ppp) cc_final: 0.7259 (pmt)
REVERT: C  518 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7349 (mttt)
REVERT: C  524 ASP cc_start: 0.7599 (p0) cc_final: 0.7376 (p0)
REVERT: C  583 GLN cc_start: 0.7875 (mt0) cc_final: 0.7674 (mt0)
REVERT: C  598 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (mp)
REVERT: C  621 GLU cc_start: 0.8001 (tt0) cc_final: 0.7731 (tm-30)
REVERT: C  622 TYR cc_start: 0.7589 (m-80) cc_final: 0.7110 (m-10)
REVERT: C  625 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7815 (mtpp)
REVERT: C  727 THR cc_start: 0.9080 (t) cc_final: 0.8724 (m)
  outliers start: 76
  outliers final: 11
  residues processed: 213
  average time/residue: 0.6434
  time to fit residues: 150.5637
Evaluate side-chains
  160 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  475 MET
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  861 ASN
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  624 GLU
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  697 MET
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  855 THR
Chi-restraints excluded: chain B residue  868 LYS
Chi-restraints excluded: chain B residue  894 GLU
Chi-restraints excluded: chain B residue  895 GLU
Chi-restraints excluded: chain B residue  906 MET
Chi-restraints excluded: chain B residue  920 VAL
Chi-restraints excluded: chain B residue  967 GLU
Chi-restraints excluded: chain B residue 1009 VAL
Chi-restraints excluded: chain B residue 1069 GLU
Chi-restraints excluded: chain C residue  518 LYS
Chi-restraints excluded: chain C residue  598 ILE
Chi-restraints excluded: chain C residue  625 LYS
Chi-restraints excluded: chain C residue  734 SER
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  805 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 177 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0980
   chunk 68 optimal weight:    0.8980
   chunk 131 optimal weight:    0.0060
   chunk 140 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 171 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 144 optimal weight:    0.7980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 490 GLN
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 799 ASN
B 807 ASN
B 878 GLN
B 941 ASN
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 724 ASN
** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 799 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.063655 restraints weight = 27084.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.05
r_work: 0.2749 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          1.3333

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= 0.191
  Angle     :  0.747  12.414  20208  Z= 0.389
  Chirality :  0.047   0.228   2121
  Planarity :  0.009   0.259   2616
  Dihedral  :  6.373  58.601   2064
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.39 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 20.68 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.19), residues: 1869
  helix: -0.47 (0.24), residues: 447
  sheet: -0.74 (0.23), residues: 459
  loop : -0.94 (0.21), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG B 497 
 TYR   0.025   0.002   TYR B 553 
 PHE   0.025   0.002   PHE B 530 
 TRP   0.018   0.002   TRP B 654 
 HIS   0.008   0.002   HIS C 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (14859)
  covalent geometry    : angle       0.74662 (20202)
  SS BOND              : bond        0.00161 (    3)
  SS BOND              : angle       0.78564 (    6)
  hydrogen bonds       : bond        0.04272 (  600)
  hydrogen bonds       : angle       5.82291 ( 1764)
  Misc. bond           : bond        0.00663 (    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
  190 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 134
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8794 (mtp) cc_final: 0.8577 (mtm)
REVERT: A  482 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8073 (mtm-85)
REVERT: A  553 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8179 (p90)
REVERT: A  574 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7978 (mtt180)
REVERT: A  720 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7729 (mppt)
REVERT: B  464 ARG cc_start: 0.5832 (ttt90) cc_final: 0.5599 (ttm170)
REVERT: B  720 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7812 (pttt)
REVERT: B  868 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8620 (mtmt)
REVERT: B  920 VAL cc_start: 0.8837 (p) cc_final: 0.8605 (m)
REVERT: C  464 ARG cc_start: 0.8074 (ttt-90) cc_final: 0.7283 (mtm180)
REVERT: C  466 GLN cc_start: 0.6253 (mt0) cc_final: 0.5998 (mt0)
REVERT: C  490 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7047 (pm20)
REVERT: C  501 MET cc_start: 0.8763 (mtp) cc_final: 0.8546 (mtp)
REVERT: C  532 ARG cc_start: 0.8277 (mtp85) cc_final: 0.8036 (mtm-85)
REVERT: C  583 GLN cc_start: 0.8205 (mt0) cc_final: 0.7975 (mt0)
REVERT: C  598 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (tp)
REVERT: C  621 GLU cc_start: 0.8138 (tt0) cc_final: 0.7910 (tm-30)
REVERT: C  781 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8386 (mm-30)
REVERT: C  926 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8469 (pm20)
  outliers start: 56
  outliers final: 15
  residues processed: 169
  average time/residue: 0.7067
  time to fit residues: 130.7042
Evaluate side-chains
  145 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  720 LYS
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  976 SER
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  550 SER
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  868 LYS
Chi-restraints excluded: chain B residue  906 MET
Chi-restraints excluded: chain C residue  490 GLN
Chi-restraints excluded: chain C residue  598 ILE
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  784 HIS
Chi-restraints excluded: chain C residue  926 GLN
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 184 optimal weight:    0.5980
   chunk 174 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0770
   chunk 126 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 75 optimal weight:    0.3980
   chunk 91 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 ASN
B 541 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 805 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.072682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.060188 restraints weight = 26994.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 2.02
r_work: 0.2693 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          1.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096  14865  Z= 0.214
  Angle     :  0.757  18.029  20208  Z= 0.396
  Chirality :  0.048   0.228   2121
  Planarity :  0.009   0.323   2616
  Dihedral  :  6.417  57.691   2064
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.55 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.02 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.19), residues: 1869
  helix: -0.52 (0.24), residues: 453
  sheet: -0.82 (0.23), residues: 462
  loop : -0.90 (0.21), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.058   0.001   ARG B 497 
 TYR   0.021   0.002   TYR A 553 
 PHE   0.027   0.002   PHE B 530 
 TRP   0.017   0.002   TRP A 654 
 HIS   0.011   0.002   HIS C 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (14859)
  covalent geometry    : angle       0.75678 (20202)
  SS BOND              : bond        0.00056 (    3)
  SS BOND              : angle       0.80903 (    6)
  hydrogen bonds       : bond        0.04463 (  600)
  hydrogen bonds       : angle       5.82386 ( 1764)
  Misc. bond           : bond        0.01001 (    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
  163 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8769 (mtp) cc_final: 0.8512 (mtp)
REVERT: A  482 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8126 (mtm-85)
REVERT: A  553 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8263 (p90)
REVERT: A  574 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8131 (mtt180)
REVERT: A  720 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7722 (mppt)
REVERT: B  464 ARG cc_start: 0.5925 (ttt90) cc_final: 0.5618 (ttm170)
REVERT: B  490 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6600 (pt0)
REVERT: B  720 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7941 (pttt)
REVERT: B  868 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8567 (mtmt)
REVERT: C  464 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7338 (mtm180)
REVERT: C  582 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7756 (tmtm)
REVERT: C  621 GLU cc_start: 0.8532 (tt0) cc_final: 0.8270 (tm-30)
REVERT: C  781 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: C  868 LYS cc_start: 0.8992 (mttt) cc_final: 0.8546 (mtmm)
REVERT: C  869 ASP cc_start: 0.8518 (m-30) cc_final: 0.8260 (m-30)
REVERT: C  926 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (pm20)
REVERT: C  991 ASP cc_start: 0.8352 (p0) cc_final: 0.8098 (p0)
  outliers start: 40
  outliers final: 15
  residues processed: 150
  average time/residue: 0.7047
  time to fit residues: 115.6669
Evaluate side-chains
  134 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  550 SER
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  868 LYS
Chi-restraints excluded: chain C residue  582 LYS
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  805 ASN
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  926 GLN
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 185 optimal weight:    0.9980
   chunk 111 optimal weight:    0.5980
   chunk 169 optimal weight:    0.0270
   chunk 179 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 128 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 132 optimal weight:    0.9980
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 805 ASN
C 466 GLN
** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 583 GLN
C 805 ASN
C1020 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.071044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.058736 restraints weight = 27217.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 1.99
r_work: 0.2660 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          1.4099

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= 0.219
  Angle     :  0.749  16.434  20208  Z= 0.392
  Chirality :  0.048   0.232   2121
  Planarity :  0.008   0.289   2616
  Dihedral  :  6.349  57.128   2064
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.49 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.55 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.19), residues: 1869
  helix: -0.59 (0.24), residues: 447
  sheet: -0.85 (0.24), residues: 453
  loop : -0.83 (0.21), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.043   0.001   ARG B 497 
 TYR   0.023   0.002   TYR A 553 
 PHE   0.027   0.002   PHE B 530 
 TRP   0.019   0.002   TRP B 654 
 HIS   0.011   0.002   HIS C 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (14859)
  covalent geometry    : angle       0.74895 (20202)
  SS BOND              : bond        0.00089 (    3)
  SS BOND              : angle       1.05165 (    6)
  hydrogen bonds       : bond        0.04465 (  600)
  hydrogen bonds       : angle       5.77796 ( 1764)
  Misc. bond           : bond        0.00750 (    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
  151 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 111
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8773 (mtp) cc_final: 0.8491 (mtp)
REVERT: A  482 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7854 (mtm-85)
REVERT: A  553 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8372 (p90)
REVERT: A  574 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8202 (mtt180)
REVERT: A  720 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7686 (mppt)
REVERT: B  490 GLN cc_start: 0.7535 (mm-40) cc_final: 0.6839 (pt0)
REVERT: B  720 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7934 (pttt)
REVERT: C  464 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7444 (mtm180)
REVERT: C  553 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.8496 (p90)
REVERT: C  602 MET cc_start: 0.8553 (mtm) cc_final: 0.8296 (ttp)
REVERT: C  666 ARG cc_start: 0.8411 (mmp-170) cc_final: 0.8164 (mmm160)
REVERT: C  781 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8640 (mm-30)
REVERT: C  868 LYS cc_start: 0.9050 (mttt) cc_final: 0.8593 (mtmm)
REVERT: C  869 ASP cc_start: 0.8503 (m-30) cc_final: 0.8252 (m-30)
REVERT: C  926 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8483 (pm20)
REVERT: C  991 ASP cc_start: 0.8347 (p0) cc_final: 0.8082 (p0)
  outliers start: 40
  outliers final: 18
  residues processed: 140
  average time/residue: 0.7744
  time to fit residues: 118.1985
Evaluate side-chains
  128 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  574 ARG
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  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  497 ARG
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  951 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  805 ASN
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  926 GLN
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 2 optimal weight:    0.9980
   chunk 146 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 145 optimal weight:    0.0570
   chunk 93 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 127 optimal weight:    0.5980
   chunk 176 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0770
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 805 ASN
C1020 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.071546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.059401 restraints weight = 27197.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 2.00
r_work: 0.2671 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2564 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          1.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092  14865  Z= 0.197
  Angle     :  0.744  16.353  20208  Z= 0.388
  Chirality :  0.047   0.229   2121
  Planarity :  0.010   0.324   2616
  Dihedral  :  6.956 135.344   2064
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.60 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.55 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.19), residues: 1869
  helix: -0.61 (0.24), residues: 456
  sheet: -0.88 (0.24), residues: 453
  loop : -0.83 (0.21), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.001   ARG B 497 
 TYR   0.022   0.002   TYR A 553 
 PHE   0.032   0.002   PHE C 496 
 TRP   0.018   0.002   TRP B 654 
 HIS   0.010   0.001   HIS C 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (14859)
  covalent geometry    : angle       0.74400 (20202)
  SS BOND              : bond        0.00105 (    3)
  SS BOND              : angle       1.02608 (    6)
  hydrogen bonds       : bond        0.04437 (  600)
  hydrogen bonds       : angle       5.76006 ( 1764)
  Misc. bond           : bond        0.00658 (    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
  136 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8759 (mtp) cc_final: 0.8432 (mtp)
REVERT: A  482 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7849 (mtm-85)
REVERT: A  553 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8361 (p90)
REVERT: A  574 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8168 (mtt180)
REVERT: A  720 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7664 (mppt)
REVERT: B  490 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7009 (pt0)
REVERT: B  501 MET cc_start: 0.8415 (mtm) cc_final: 0.8110 (mtp)
REVERT: B  717 ASP cc_start: 0.8324 (m-30) cc_final: 0.8112 (t0)
REVERT: B  720 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7967 (pttt)
REVERT: C  464 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.7385 (mtm180)
REVERT: C  487 TRP cc_start: 0.6564 (t-100) cc_final: 0.6362 (t-100)
REVERT: C  553 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8380 (p90)
REVERT: C  602 MET cc_start: 0.8468 (mtm) cc_final: 0.8224 (ttp)
REVERT: C  666 ARG cc_start: 0.8364 (mmp-170) cc_final: 0.8140 (mmm160)
REVERT: C  781 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8641 (mm-30)
REVERT: C  868 LYS cc_start: 0.9052 (mttt) cc_final: 0.8594 (mtmm)
REVERT: C  869 ASP cc_start: 0.8439 (m-30) cc_final: 0.8195 (m-30)
REVERT: C  926 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8456 (pm20)
REVERT: C  991 ASP cc_start: 0.8336 (p0) cc_final: 0.8068 (p0)
  outliers start: 29
  outliers final: 16
  residues processed: 129
  average time/residue: 0.7563
  time to fit residues: 106.0836
Evaluate side-chains
  123 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  720 LYS
Chi-restraints excluded: chain A residue  838 MET
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  497 ARG
Chi-restraints excluded: chain B residue  550 SER
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  951 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  926 GLN
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 123 optimal weight:    0.5980
   chunk 162 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0870
   chunk 151 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   chunk 130 optimal weight:    0.6980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 GLN
C1020 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.070289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.058269 restraints weight = 27293.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 1.98
r_work: 0.2648 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2542 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          1.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  14865  Z= 0.210
  Angle     :  0.755  16.553  20208  Z= 0.393
  Chirality :  0.047   0.228   2121
  Planarity :  0.010   0.296   2616
  Dihedral  :  7.113 149.486   2064
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.92 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.35 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.19), residues: 1869
  helix: -0.59 (0.24), residues: 450
  sheet: -0.88 (0.24), residues: 453
  loop : -0.80 (0.21), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.042   0.001   ARG B 497 
 TYR   0.022   0.002   TYR A 553 
 PHE   0.030   0.002   PHE C 496 
 TRP   0.018   0.002   TRP B 654 
 HIS   0.011   0.002   HIS C 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (14859)
  covalent geometry    : angle       0.75533 (20202)
  SS BOND              : bond        0.00083 (    3)
  SS BOND              : angle       1.02314 (    6)
  hydrogen bonds       : bond        0.04475 (  600)
  hydrogen bonds       : angle       5.78650 ( 1764)
  Misc. bond           : bond        0.00773 (    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
  136 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 MET cc_start: 0.8785 (mtp) cc_final: 0.8566 (mtp)
REVERT: A  482 ARG cc_start: 0.8349 (mtm110) cc_final: 0.7978 (mtm-85)
REVERT: A  553 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8356 (p90)
REVERT: A  574 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8202 (mtt180)
REVERT: A  720 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7655 (mppt)
REVERT: B  486 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7819 (mp10)
REVERT: B  490 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7492 (mm-40)
REVERT: B  501 MET cc_start: 0.8480 (mtm) cc_final: 0.8173 (mtp)
REVERT: B  717 ASP cc_start: 0.8364 (m-30) cc_final: 0.8158 (t0)
REVERT: B  720 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8020 (mtmt)
REVERT: C  464 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7289 (mtm180)
REVERT: C  553 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8309 (p90)
REVERT: C  602 MET cc_start: 0.8450 (mtm) cc_final: 0.8217 (ttp)
REVERT: C  666 ARG cc_start: 0.8363 (mmp-170) cc_final: 0.8154 (mmm160)
REVERT: C  781 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8665 (mm-30)
REVERT: C  868 LYS cc_start: 0.9062 (mttt) cc_final: 0.8630 (mtmm)
REVERT: C  869 ASP cc_start: 0.8439 (m-30) cc_final: 0.8195 (m-30)
REVERT: C  926 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8448 (pm20)
REVERT: C  940 THR cc_start: 0.8776 (m) cc_final: 0.8491 (p)
REVERT: C  991 ASP cc_start: 0.8279 (p0) cc_final: 0.8003 (p0)
  outliers start: 29
  outliers final: 17
  residues processed: 128
  average time/residue: 0.7688
  time to fit residues: 107.0803
Evaluate side-chains
  124 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 VAL
Chi-restraints excluded: chain A residue  553 TYR
Chi-restraints excluded: chain A residue  574 ARG
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 1011 VAL
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  486 GLN
Chi-restraints excluded: chain B residue  497 ARG
Chi-restraints excluded: chain B residue  550 SER
Chi-restraints excluded: chain B residue  553 TYR
Chi-restraints excluded: chain B residue  639 VAL
Chi-restraints excluded: chain B residue  692 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  821 PHE
Chi-restraints excluded: chain B residue  951 THR
Chi-restraints excluded: chain C residue  553 TYR
Chi-restraints excluded: chain C residue  737 ILE
Chi-restraints excluded: chain C residue  862 LEU
Chi-restraints excluded: chain C residue  926 GLN
Chi-restraints excluded: chain C residue  959 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 57 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 151 optimal weight:    0.6980
   chunk 174 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 145 optimal weight:    0.0970
   chunk 152 optimal weight:    0.9980
   overall best weight:    0.3156

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

Flipped N/Q/H residues before XYZ refinement:
** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 805 ASN
C1020 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.072588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.060533 restraints weight = 27034.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.01
r_work: 0.2696 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2589 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          1.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  14865  Z= 0.169
  Angle     :  0.723  15.816  20208  Z= 0.377
  Chirality :  0.046   0.230   2121
  Planarity :  0.009   0.288   2616
  Dihedral  :  7.000 149.739   2064
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.76 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 21.29 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.19), residues: 1869
  helix: -0.71 (0.24), residues: 474
  sheet: -0.91 (0.24), residues: 480
  loop : -0.84 (0.21), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.041   0.001   ARG B 497 
 TYR   0.022   0.002   TYR A 553 
 PHE   0.025   0.002   PHE C 496 
 TRP   0.018   0.002   TRP B 654 
 HIS   0.010   0.001   HIS C 736 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (14859)
  covalent geometry    : angle       0.72314 (20202)
  SS BOND              : bond        0.00172 (    3)
  SS BOND              : angle       1.05803 (    6)
  hydrogen bonds       : bond        0.04301 (  600)
  hydrogen bonds       : angle       5.73213 ( 1764)
  Misc. bond           : bond        0.00706 (    3)

===============================================================================
Job complete
usr+sys time: 5704.23 seconds
wall clock time: 98 minutes 32.01 seconds (5912.01 seconds total)