Starting phenix.real_space_refine
on Tue Mar  3 19:09:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v0v_21003/03_2026/6v0v_21003.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v0v_21003/03_2026/6v0v_21003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2026/6v0v_21003.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2026/6v0v_21003.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2026/6v0v_21003.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2026/6v0v_21003.cif"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     P      60      5.49       5
     S      51      5.16       5
     C    5002      2.51       5
     N    1428      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8192
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4286
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 516}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 67
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2673
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "F"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 617
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "I"
      Number of atoms: 613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 613
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2016  SG  CYS A 727      70.241  55.803  61.715  1.00 82.81           S
  ATOM   2037  SG  CYS A 730      72.316  58.531  60.217  1.00 86.87           S

  Time building chain proxies: 1.61, per 1000 atoms: 0.20
  Number of scatterers: 8192
  At special positions: 0
  Unit cell: (107.06, 95.4, 118.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      51     16.00
     P      60     15.00
     O    1648      8.00
     N    1428      7.00
     C    5002      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 234.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1103 "
        pdb="ZN    ZN A1103 " - pdb=" NE2 HIS A 937 "
        pdb="ZN    ZN A1103 " - pdb=" NE2 HIS A 942 "
        pdb="ZN    ZN A1103 " - pdb=" SG  CYS A 730 "
        pdb="ZN    ZN A1103 " - pdb=" SG  CYS A 727 "
      Number of angles added : 2


  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1662

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      33.8% alpha, 25.0% beta
      28 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 463 through 474
      removed outlier: 3.849A  pdb=" N   CYS A 467 " --> pdb=" O   GLN A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 493
    Processing helix  chain 'A' and resid 499 through 511
      removed outlier: 3.670A  pdb=" N   ALA A 506 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A 508 " --> pdb=" O   ARG A 504 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   VAL A 509 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LEU A 510 " --> pdb=" O   ALA A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 570
      removed outlier: 3.603A  pdb=" N   SER A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   MET A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 581
    Processing helix  chain 'A' and resid 664 through 682
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 708 through 716
      removed outlier: 3.579A  pdb=" N   GLU A 716 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 738
    Processing helix  chain 'A' and resid 750 through 763
    Processing helix  chain 'A' and resid 768 through 776
    Processing helix  chain 'A' and resid 793 through 814
      removed outlier: 3.964A  pdb=" N   GLY A 813 " --> pdb=" O   GLN A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 841
    Processing helix  chain 'A' and resid 850 through 858
      removed outlier: 4.005A  pdb=" N   MET A 858 " --> pdb=" O   ALA A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 870
      removed outlier: 3.548A  pdb=" N   VAL A 863 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 890
      removed outlier: 3.769A  pdb=" N   GLU A 877 " --> pdb=" O   GLU A 873 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 895
    Processing helix  chain 'A' and resid 897 through 902
      removed outlier: 3.843A  pdb=" N   CYS A 902 " --> pdb=" O   PRO A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 924
      removed outlier: 5.330A  pdb=" N   SER A 910 " --> pdb=" O   LEU A 906 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   PHE A 911 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE A 916 " --> pdb=" O   ASN A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 942
      removed outlier: 3.904A  pdb=" N   HIS A 937 " --> pdb=" O   THR A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 950
      removed outlier: 3.787A  pdb=" N   GLU A 948 " --> pdb=" O   PRO A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 964
    Processing helix  chain 'A' and resid 964 through 975
      removed outlier: 3.567A  pdb=" N   PHE A 968 " --> pdb=" O   GLY A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.815A  pdb=" N   VAL A 987 " --> pdb=" O   GLU A 983 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU A 988 " --> pdb=" O   MET A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1001
    Processing helix  chain 'A' and resid 1002 through 1005
    Processing helix  chain 'B' and resid 11 through 15
      removed outlier: 4.008A  pdb=" N   LEU B  14 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520
      removed outlier: 10.087A  pdb=" N   PHE A 591 " --> pdb=" O   PHE A 700 " (cutoff:3.500A)
      removed outlier: 10.936A  pdb=" N   PHE A 702 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLY A 704 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 10.350A  pdb=" N   VAL A 595 " --> pdb=" O   GLY A 704 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY A 706 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A 631 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 621 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   PHE A 624 " --> pdb=" O   PRO A 654 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520
      removed outlier: 10.087A  pdb=" N   PHE A 591 " --> pdb=" O   PHE A 700 " (cutoff:3.500A)
      removed outlier: 10.936A  pdb=" N   PHE A 702 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLY A 704 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 10.350A  pdb=" N   VAL A 595 " --> pdb=" O   GLY A 704 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY A 706 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A 631 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 621 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ILE A 631 " --> pdb=" O   LYS A 639 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LYS A 639 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   HIS A 633 " --> pdb=" O   ASN A 637 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASN A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6
      removed outlier: 4.650A  pdb=" N   PHE B 345 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24
      removed outlier: 4.147A  pdb=" N   VAL B  28 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASP B  49 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62
      removed outlier: 7.102A  pdb=" N   ILE B  61 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   CYS B 124 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   LYS B 119 " --> pdb=" O   LYS B 115 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LYS B 115 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   THR B 121 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131
      removed outlier: 6.722A  pdb=" N   VAL B 130 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   SER B 194 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212
      removed outlier: 4.540A  pdb=" N   LEU B 233 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267
      removed outlier: 3.809A  pdb=" N   ILE B 262 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B 266 " --> pdb=" O   GLU B 270 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLU B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)

    303 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2196
        1.33 -     1.45: 2147
        1.45 -     1.58: 3960
        1.58 -     1.70: 117
        1.70 -     1.82: 78
  Bond restraints: 8498
  Sorted by residual:
  bond pdb=" O3'  DT F  29 "
       pdb=" P    DG F  30 "
    ideal  model  delta    sigma   weight residual
    1.607  1.562  0.045 1.50e-02 4.44e+03 9.15e+00
  bond pdb=" CA  LEU A 735 "
       pdb=" C   LEU A 735 "
    ideal  model  delta    sigma   weight residual
    1.522  1.484  0.038 1.37e-02 5.33e+03 7.83e+00
  bond pdb=" N   MET A 847 "
       pdb=" CA  MET A 847 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.24e-02 6.50e+03 6.22e+00
  bond pdb=" C   PRO A 654 "
       pdb=" N   LEU A 655 "
    ideal  model  delta    sigma   weight residual
    1.331  1.299  0.033 1.40e-02 5.10e+03 5.47e+00
  bond pdb=" C3'  DG I   6 "
       pdb=" O3'  DG I   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.491 -0.069 3.00e-02 1.11e+03 5.34e+00
  ... (remaining 8493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 11497
        2.76 -     5.53: 234
        5.53 -     8.29: 22
        8.29 -    11.06: 4
       11.06 -    13.82: 1
  Bond angle restraints: 11758
  Sorted by residual:
  angle pdb=" C4'  DT F  29 "
        pdb=" C3'  DT F  29 "
        pdb=" O3'  DT F  29 "
      ideal   model   delta    sigma   weight residual
     110.00   96.18   13.82 1.50e+00 4.44e-01 8.49e+01
  angle pdb=" C2'  DC F  26 "
        pdb=" C1'  DC F  26 "
        pdb=" N1   DC F  26 "
      ideal   model   delta    sigma   weight residual
     113.50  120.36   -6.86 1.50e+00 4.44e-01 2.09e+01
  angle pdb=" C   ARG B 212 "
        pdb=" N   ASN B 213 "
        pdb=" CA  ASN B 213 "
      ideal   model   delta    sigma   weight residual
     121.54  130.19   -8.65 1.91e+00 2.74e-01 2.05e+01
  angle pdb=" C4'  DT F  27 "
        pdb=" C3'  DT F  27 "
        pdb=" O3'  DT F  27 "
      ideal   model   delta    sigma   weight residual
     110.00  103.31    6.69 1.50e+00 4.44e-01 1.99e+01
  angle pdb=" C3'  DG I   6 "
        pdb=" O3'  DG I   6 "
        pdb=" P    DG I   7 "
      ideal   model   delta    sigma   weight residual
     120.20  125.96   -5.76 1.50e+00 4.44e-01 1.47e+01
  ... (remaining 11753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 4578
       35.36 -    70.72: 347
       70.72 -   106.09: 9
      106.09 -   141.45: 1
      141.45 -   176.81: 2
  Dihedral angle restraints: 4937
    sinusoidal: 2358
      harmonic: 2579
  Sorted by residual:
  dihedral pdb=" CA  ARG B 212 "
           pdb=" C   ARG B 212 "
           pdb=" N   ASN B 213 "
           pdb=" CA  ASN B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  CYS B  41 "
           pdb=" C   CYS B  41 "
           pdb=" N   PRO B  42 "
           pdb=" CA  PRO B  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.91  -22.09     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  PRO A 871 "
           pdb=" C   PRO A 871 "
           pdb=" N   SER A 872 "
           pdb=" CA  SER A 872 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.23  -21.77     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 4934 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1013
       0.065 -    0.129: 244
       0.129 -    0.194: 33
       0.194 -    0.259: 6
       0.259 -    0.323: 2
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" C1'  DC F  26 "
            pdb=" O4'  DC F  26 "
            pdb=" C2'  DC F  26 "
            pdb=" N1   DC F  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.15    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CB  VAL A 943 "
            pdb=" CA  VAL A 943 "
            pdb=" CG1 VAL A 943 "
            pdb=" CG2 VAL A 943 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL B   8 "
            pdb=" CA  VAL B   8 "
            pdb=" CG1 VAL B   8 "
            pdb=" CG2 VAL B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1295 not shown)

  Planarity restraints: 1303
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  26 "    0.095 2.00e-02 2.50e+03   4.30e-02 4.17e+01
        pdb=" N1   DC F  26 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2   DC F  26 "   -0.021 2.00e-02 2.50e+03
        pdb=" O2   DC F  26 "   -0.030 2.00e-02 2.50e+03
        pdb=" N3   DC F  26 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DC F  26 "    0.009 2.00e-02 2.50e+03
        pdb=" N4   DC F  26 "    0.044 2.00e-02 2.50e+03
        pdb=" C5   DC F  26 "   -0.018 2.00e-02 2.50e+03
        pdb=" C6   DC F  26 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 212 "    0.015 2.00e-02 2.50e+03   3.09e-02 9.57e+00
        pdb=" C   ARG B 212 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ARG B 212 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN B 213 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  98 "   -0.050 5.00e-02 4.00e+02   7.49e-02 8.98e+00
        pdb=" N   PRO B  99 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1300 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 83
        2.53 -     3.12: 5775
        3.12 -     3.71: 13865
        3.71 -     4.31: 18150
        4.31 -     4.90: 28488
  Nonbonded interactions: 66361
  Sorted by model distance:
  nonbonded pdb=" OP1  DC I  17 "
            pdb="CA    CA A1102 "
     model   vdw
     1.932 2.510
  nonbonded pdb=" OE1 GLU A 962 "
            pdb="CA    CA A1102 "
     model   vdw
     2.026 2.510
  nonbonded pdb=" OD1 ASP A 600 "
            pdb="CA    CA A1101 "
     model   vdw
     2.193 2.510
  nonbonded pdb=" OE2 GLU A 803 "
            pdb=" OH  TYR A 928 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   SER A 958 "
            pdb=" OG  SER A 958 "
     model   vdw
     2.266 3.040
  ... (remaining 66356 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.270
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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   0.156   8502  Z= 0.373
  Angle     :  1.101  46.250  11760  Z= 0.584
  Chirality :  0.057   0.323   1298
  Planarity :  0.007   0.075   1303
  Dihedral  : 21.033 176.809   3275
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.28 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.88 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.85 (0.23), residues: 879
  helix: -2.89 (0.22), residues: 271
  sheet: -1.77 (0.40), residues: 158
  loop : -2.63 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 696 
 TYR   0.016   0.002   TYR A 805 
 PHE   0.035   0.003   PHE A 804 
 TRP   0.022   0.003   TRP A 893 
 HIS   0.008   0.002   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 ( 8498)
  covalent geometry    : angle       1.00539 (11758)
  hydrogen bonds       : bond        0.14331 (  359)
  hydrogen bonds       : angle       7.42489 (  977)
  metal coordination   : bond        0.10255 (    4)
  metal coordination   : angle      34.40681 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: A  753 ASN cc_start: 0.8184 (t0) cc_final: 0.6963 (t0)
REVERT: A  857 LEU cc_start: 0.9194 (mt) cc_final: 0.8898 (tt)
REVERT: B   24 PHE cc_start: 0.6579 (m-10) cc_final: 0.6234 (m-80)
REVERT: B   80 TYR cc_start: 0.7482 (t80) cc_final: 0.6994 (t80)
REVERT: B   90 GLN cc_start: 0.8212 (pt0) cc_final: 0.7826 (pt0)
REVERT: B  281 ASN cc_start: 0.7903 (p0) cc_final: 0.7242 (p0)
REVERT: B  313 HIS cc_start: 0.8340 (t70) cc_final: 0.7988 (t-90)
  outliers start: 3
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0855
  time to fit residues: 16.3237
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 515 HIS
A 800 ASN
A 820 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 267 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.085527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.063729 restraints weight = 24906.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.065433 restraints weight = 14129.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.066560 restraints weight = 9998.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.067273 restraints weight = 8079.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.067665 restraints weight = 7085.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8502  Z= 0.157
  Angle     :  0.656  10.328  11760  Z= 0.354
  Chirality :  0.042   0.163   1298
  Planarity :  0.005   0.057   1303
  Dihedral  : 23.657 176.018   1618
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.02 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.26), residues: 879
  helix: -1.08 (0.29), residues: 272
  sheet: -0.77 (0.41), residues: 164
  loop : -2.12 (0.26), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  39 
 TYR   0.012   0.001   TYR A 757 
 PHE   0.032   0.002   PHE A 804 
 TRP   0.028   0.002   TRP B 317 
 HIS   0.004   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8498)
  covalent geometry    : angle       0.64901 (11758)
  hydrogen bonds       : bond        0.04038 (  359)
  hydrogen bonds       : angle       5.10007 (  977)
  metal coordination   : bond        0.00771 (    4)
  metal coordination   : angle       7.34503 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: A  841 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7936 (mmp)
REVERT: A  919 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8221 (tt)
REVERT: B   80 TYR cc_start: 0.7661 (t80) cc_final: 0.7405 (t80)
REVERT: B  313 HIS cc_start: 0.8422 (t70) cc_final: 0.8121 (t-90)
  outliers start: 14
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0783
  time to fit residues: 12.1839
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 GLU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue  272 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 79 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 750 HIS
A 852 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN
B  33 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.083200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061473 restraints weight = 24528.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.063168 restraints weight = 13887.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.064244 restraints weight = 9807.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.064928 restraints weight = 7941.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.065237 restraints weight = 6979.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8502  Z= 0.192
  Angle     :  0.672   8.679  11760  Z= 0.357
  Chirality :  0.043   0.165   1298
  Planarity :  0.005   0.055   1303
  Dihedral  : 23.533 174.861   1618
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.34 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.27), residues: 879
  helix: -0.31 (0.31), residues: 270
  sheet: -0.27 (0.42), residues: 163
  loop : -1.78 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  39 
 TYR   0.013   0.001   TYR A 805 
 PHE   0.033   0.002   PHE A 804 
 TRP   0.025   0.002   TRP B 317 
 HIS   0.004   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8498)
  covalent geometry    : angle       0.66873 (11758)
  hydrogen bonds       : bond        0.03987 (  359)
  hydrogen bonds       : angle       4.74952 (  977)
  metal coordination   : bond        0.00861 (    4)
  metal coordination   : angle       5.28706 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8365 (ttm) cc_final: 0.7827 (ttm)
REVERT: A  576 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: A  627 MET cc_start: 0.7660 (ttm) cc_final: 0.7458 (ttp)
REVERT: A  760 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.8711 (t-100)
REVERT: A  849 MET cc_start: 0.7613 (ttm) cc_final: 0.7377 (ttm)
REVERT: A  887 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9108 (mp)
REVERT: A  919 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8194 (tt)
REVERT: A  961 ASN cc_start: 0.7095 (t0) cc_final: 0.6797 (t0)
  outliers start: 26
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0769
  time to fit residues: 11.6839
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0030
   chunk 37 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0470
   overall best weight:    0.4688

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.086160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.064800 restraints weight = 24941.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.066630 restraints weight = 13500.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.067803 restraints weight = 9261.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.068531 restraints weight = 7360.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068879 restraints weight = 6417.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8502  Z= 0.128
  Angle     :  0.613   7.952  11760  Z= 0.328
  Chirality :  0.041   0.195   1298
  Planarity :  0.004   0.054   1303
  Dihedral  : 23.320 176.917   1618
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.05 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.28), residues: 879
  helix:  0.22 (0.33), residues: 268
  sheet: -0.05 (0.41), residues: 165
  loop : -1.55 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 212 
 TYR   0.011   0.001   TYR A 757 
 PHE   0.043   0.001   PHE A 804 
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 836 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8498)
  covalent geometry    : angle       0.61256 (11758)
  hydrogen bonds       : bond        0.03341 (  359)
  hydrogen bonds       : angle       4.44507 (  977)
  metal coordination   : bond        0.00342 (    4)
  metal coordination   : angle       2.36340 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8166 (ttm) cc_final: 0.7866 (ttm)
REVERT: A  576 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: A  658 MET cc_start: 0.8414 (ptp) cc_final: 0.8150 (ptp)
REVERT: A  760 TRP cc_start: 0.8810 (OUTLIER) cc_final: 0.8386 (t-100)
REVERT: A  812 ILE cc_start: 0.5777 (OUTLIER) cc_final: 0.5564 (tt)
REVERT: A  887 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9053 (mp)
REVERT: A  919 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8119 (tt)
REVERT: B  170 GLU cc_start: 0.8061 (mp0) cc_final: 0.7817 (mp0)
  outliers start: 19
  outliers final: 7
  residues processed: 91
  average time/residue: 0.0653
  time to fit residues: 8.9806
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  887 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 836 HIS
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.082500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.060642 restraints weight = 24883.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.062327 restraints weight = 14026.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.063414 restraints weight = 9894.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.064107 restraints weight = 7981.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.064484 restraints weight = 7024.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8502  Z= 0.185
  Angle     :  0.654  10.711  11760  Z= 0.343
  Chirality :  0.042   0.186   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.355 175.806   1618
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.39 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.28), residues: 879
  helix:  0.36 (0.33), residues: 269
  sheet:  0.39 (0.43), residues: 150
  loop : -1.41 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 734 
 TYR   0.013   0.001   TYR A 805 
 PHE   0.038   0.002   PHE A 804 
 TRP   0.019   0.002   TRP B 317 
 HIS   0.004   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8498)
  covalent geometry    : angle       0.65184 (11758)
  hydrogen bonds       : bond        0.03829 (  359)
  hydrogen bonds       : angle       4.51304 (  977)
  metal coordination   : bond        0.00819 (    4)
  metal coordination   : angle       4.04797 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  485 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8336 (t80)
REVERT: A  576 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: A  812 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5743 (tt)
REVERT: A  843 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8048 (tt)
REVERT: A  883 MET cc_start: 0.8294 (tpt) cc_final: 0.7956 (tpp)
REVERT: A  919 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8215 (tt)
REVERT: B  280 GLU cc_start: 0.7989 (pm20) cc_final: 0.7680 (pm20)
REVERT: B  322 MET cc_start: 0.8671 (mtm) cc_final: 0.7975 (mpp)
  outliers start: 24
  outliers final: 15
  residues processed: 88
  average time/residue: 0.0799
  time to fit residues: 10.2978
Evaluate side-chains
  86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0060
   chunk 41 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.084647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.062674 restraints weight = 24590.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.064457 restraints weight = 13425.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.065648 restraints weight = 9324.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.066391 restraints weight = 7437.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.066787 restraints weight = 6487.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8502  Z= 0.128
  Angle     :  0.602   8.252  11760  Z= 0.319
  Chirality :  0.041   0.182   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.205 177.555   1618
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.24 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.28), residues: 879
  helix:  0.58 (0.34), residues: 269
  sheet:  0.59 (0.43), residues: 148
  loop : -1.27 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 838 
 TYR   0.010   0.001   TYR A 757 
 PHE   0.038   0.001   PHE A 804 
 TRP   0.016   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8498)
  covalent geometry    : angle       0.60196 (11758)
  hydrogen bonds       : bond        0.03296 (  359)
  hydrogen bonds       : angle       4.30523 (  977)
  metal coordination   : bond        0.00343 (    4)
  metal coordination   : angle       1.80179 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8568 (ttm) cc_final: 0.8094 (ttm)
REVERT: A  576 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: A  597 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7384 (mm-30)
REVERT: A  658 MET cc_start: 0.8354 (ptp) cc_final: 0.8117 (ptp)
REVERT: A  812 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5671 (tt)
REVERT: A  844 LYS cc_start: 0.6782 (mmtt) cc_final: 0.5861 (tttp)
REVERT: A  883 MET cc_start: 0.8025 (tpt) cc_final: 0.7772 (tpp)
REVERT: A  919 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8255 (tt)
REVERT: B  280 GLU cc_start: 0.7883 (pm20) cc_final: 0.7650 (pm20)
REVERT: B  322 MET cc_start: 0.8623 (mtm) cc_final: 0.8001 (mpp)
  outliers start: 16
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0808
  time to fit residues: 9.9019
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
B  89 HIS
B 181 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.080920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.059095 restraints weight = 25182.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.060769 restraints weight = 14148.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.061835 restraints weight = 9981.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.062462 restraints weight = 8064.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.062908 restraints weight = 7138.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8502  Z= 0.250
  Angle     :  0.710   9.475  11760  Z= 0.372
  Chirality :  0.044   0.184   1298
  Planarity :  0.004   0.055   1303
  Dihedral  : 23.452 175.963   1618
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.63 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.28), residues: 879
  helix:  0.38 (0.33), residues: 271
  sheet:  0.52 (0.44), residues: 150
  loop : -1.31 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 734 
 TYR   0.019   0.002   TYR A 485 
 PHE   0.035   0.002   PHE A 804 
 TRP   0.020   0.002   TRP B 317 
 HIS   0.004   0.001   HIS B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 8498)
  covalent geometry    : angle       0.70779 (11758)
  hydrogen bonds       : bond        0.04314 (  359)
  hydrogen bonds       : angle       4.57338 (  977)
  metal coordination   : bond        0.01127 (    4)
  metal coordination   : angle       4.47052 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: A  812 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5773 (tt)
REVERT: A  843 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8100 (tt)
REVERT: A  844 LYS cc_start: 0.6933 (mmtt) cc_final: 0.6261 (tttp)
REVERT: A  919 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8356 (tt)
REVERT: B  280 GLU cc_start: 0.8004 (pm20) cc_final: 0.7768 (pm20)
REVERT: B  322 MET cc_start: 0.8738 (mtm) cc_final: 0.8055 (mpp)
  outliers start: 25
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0754
  time to fit residues: 9.5404
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0980
   chunk 48 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 79 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0670
   chunk 70 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.082902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.061039 restraints weight = 24844.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.062747 restraints weight = 13882.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.063853 restraints weight = 9772.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.064483 restraints weight = 7883.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.064945 restraints weight = 6961.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8502  Z= 0.155
  Angle     :  0.642  12.044  11760  Z= 0.336
  Chirality :  0.042   0.180   1298
  Planarity :  0.004   0.055   1303
  Dihedral  : 23.355 178.144   1618
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.30 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.29), residues: 879
  helix:  0.54 (0.33), residues: 271
  sheet:  0.50 (0.41), residues: 170
  loop : -1.16 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 848 
 TYR   0.020   0.001   TYR A 485 
 PHE   0.034   0.002   PHE A 804 
 TRP   0.017   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8498)
  covalent geometry    : angle       0.64091 (11758)
  hydrogen bonds       : bond        0.03607 (  359)
  hydrogen bonds       : angle       4.45480 (  977)
  metal coordination   : bond        0.00515 (    4)
  metal coordination   : angle       2.29542 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: A  627 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7358 (ttm)
REVERT: A  844 LYS cc_start: 0.6860 (mmtt) cc_final: 0.5930 (tttp)
REVERT: A  919 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8347 (tt)
REVERT: B  280 GLU cc_start: 0.7925 (pm20) cc_final: 0.7574 (pm20)
REVERT: B  322 MET cc_start: 0.8644 (mtm) cc_final: 0.8046 (mpp)
  outliers start: 19
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0674
  time to fit residues: 8.3334
Evaluate side-chains
  76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 85 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.083546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061518 restraints weight = 24964.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.063276 restraints weight = 13801.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.064412 restraints weight = 9621.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.065127 restraints weight = 7713.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.065470 restraints weight = 6752.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8502  Z= 0.147
  Angle     :  0.636  11.025  11760  Z= 0.332
  Chirality :  0.042   0.182   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.248 177.835   1618
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 21.56 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.29), residues: 879
  helix:  0.62 (0.33), residues: 266
  sheet:  0.54 (0.41), residues: 170
  loop : -1.13 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 838 
 TYR   0.020   0.001   TYR A 485 
 PHE   0.034   0.002   PHE A 804 
 TRP   0.017   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8498)
  covalent geometry    : angle       0.63577 (11758)
  hydrogen bonds       : bond        0.03536 (  359)
  hydrogen bonds       : angle       4.42321 (  977)
  metal coordination   : bond        0.00358 (    4)
  metal coordination   : angle       2.09400 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: A  627 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7379 (ttm)
REVERT: A  844 LYS cc_start: 0.6764 (mmtt) cc_final: 0.5837 (tttp)
REVERT: A  919 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8397 (tt)
REVERT: B  263 LEU cc_start: 0.8412 (tp) cc_final: 0.8085 (tp)
REVERT: B  280 GLU cc_start: 0.7999 (pm20) cc_final: 0.7634 (pm20)
REVERT: B  322 MET cc_start: 0.8652 (mtm) cc_final: 0.8028 (mpp)
  outliers start: 16
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0751
  time to fit residues: 8.8770
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 9 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.083375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.061382 restraints weight = 24753.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.063104 restraints weight = 13903.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.064211 restraints weight = 9796.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.064898 restraints weight = 7909.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.065236 restraints weight = 6973.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8502  Z= 0.153
  Angle     :  0.644  11.916  11760  Z= 0.337
  Chirality :  0.042   0.181   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.217 177.693   1618
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.96 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.29), residues: 879
  helix:  0.64 (0.33), residues: 266
  sheet:  0.59 (0.41), residues: 170
  loop : -1.10 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 734 
 TYR   0.022   0.001   TYR A 485 
 PHE   0.034   0.002   PHE A 804 
 TRP   0.017   0.001   TRP B 317 
 HIS   0.005   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8498)
  covalent geometry    : angle       0.64374 (11758)
  hydrogen bonds       : bond        0.03551 (  359)
  hydrogen bonds       : angle       4.43309 (  977)
  metal coordination   : bond        0.00397 (    4)
  metal coordination   : angle       2.42229 (    2)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: A  627 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7365 (ttm)
REVERT: A  844 LYS cc_start: 0.6758 (mmtt) cc_final: 0.5834 (tttp)
REVERT: A  919 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8399 (tt)
REVERT: B  110 MET cc_start: 0.8423 (mmm) cc_final: 0.7849 (mmp)
REVERT: B  263 LEU cc_start: 0.8392 (tp) cc_final: 0.8083 (tp)
REVERT: B  280 GLU cc_start: 0.7997 (pm20) cc_final: 0.7646 (pm20)
REVERT: B  322 MET cc_start: 0.8647 (mtm) cc_final: 0.7989 (mpp)
  outliers start: 14
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0685
  time to fit residues: 7.7054
Evaluate side-chains
  77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.083086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.061131 restraints weight = 25021.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.062849 restraints weight = 13958.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.063964 restraints weight = 9802.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.064656 restraints weight = 7903.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.064991 restraints weight = 6946.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8502  Z= 0.160
  Angle     :  0.652  11.535  11760  Z= 0.341
  Chirality :  0.042   0.181   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.190 177.977   1618
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.43 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.29), residues: 879
  helix:  0.67 (0.33), residues: 266
  sheet:  0.56 (0.41), residues: 170
  loop : -1.11 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 734 
 TYR   0.022   0.001   TYR A 485 
 PHE   0.031   0.002   PHE A 804 
 TRP   0.019   0.001   TRP B 317 
 HIS   0.005   0.001   HIS A 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8498)
  covalent geometry    : angle       0.65153 (11758)
  hydrogen bonds       : bond        0.03578 (  359)
  hydrogen bonds       : angle       4.44976 (  977)
  metal coordination   : bond        0.00462 (    4)
  metal coordination   : angle       2.41000 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1360.12 seconds
wall clock time: 24 minutes 12.12 seconds (1452.12 seconds total)