Starting phenix.real_space_refine
on Fri Jul  3 05:21:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gck_51231/07_2026/9gck_51231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gck_51231/07_2026/9gck_51231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gck_51231/07_2026/9gck_51231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gck_51231/07_2026/9gck_51231.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gck_51231/07_2026/9gck_51231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gck_51231/07_2026/9gck_51231.map"
  }
  resolution = 3.7
  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: 5
    Type Number    sf(0)   Gaussians
     P      90      5.49       5
     S      41      5.16       5
     C    7590      2.51       5
     N    2092      2.21       5
     O    2485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12298
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3491
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 13, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 2443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2443
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 6, 'TRANS': 287}
    Chain: "C"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1823
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 20, 'TRANS': 210}
    Chain: "D"
      Number of atoms: 2696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2696
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 309}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 900
          Classifications: {'DNA': 45}
          Link IDs: {'rna3p': 44}
    Chain: "F"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 945
          Classifications: {'DNA': 45}
          Link IDs: {'rna3p': 44}
  Time building chain proxies: 2.59, per 1000 atoms: 0.21
  Number of scatterers: 12298
  At special positions: 0
  Unit cell: (89.598, 116.724, 160.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P      90     15.00
     O    2485      8.00
     N    2092      7.00
     C    7590      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: 0.75
  Conformation dependent library (CDL) restraints added in 424.4 milliseconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2460

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 5 sheets defined
      50.4% alpha, 7.7% beta
      33 base pairs and 87 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 739 through 758
      removed outlier: 4.211A  pdb=" N   GLN A 744 " --> pdb=" O   LYS A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 766
    Processing helix  chain 'A' and resid 767 through 769
      No H-bonds generated for 'chain 'A' and resid 767 through 769'
    Processing helix  chain 'A' and resid 773 through 809
      removed outlier: 6.192A  pdb=" N   HIS A 790 " --> pdb=" O   VAL A 786 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   SER A 791 " --> pdb=" O   ARG A 787 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A 794 " --> pdb=" O   HIS A 790 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ALA A 795 " --> pdb=" O   SER A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 820
      removed outlier: 3.598A  pdb=" N   VAL A 818 " --> pdb=" O   SER A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 838
    Processing helix  chain 'A' and resid 847 through 855
    Processing helix  chain 'A' and resid 874 through 885
    Processing helix  chain 'A' and resid 897 through 916
      removed outlier: 4.039A  pdb=" N   SER A 903 " --> pdb=" O   SER A 899 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   TYR A 906 " --> pdb=" O   GLN A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 927
      removed outlier: 4.146A  pdb=" N   GLU A 927 " --> pdb=" O   ARG A 923 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 923 through 927'
    Processing helix  chain 'A' and resid 933 through 947
    Processing helix  chain 'A' and resid 961 through 971
    Processing helix  chain 'A' and resid 972 through 991
      removed outlier: 3.882A  pdb=" N   PHE A 976 " --> pdb=" O   ASN A 972 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   CYS A 984 " --> pdb=" O   PHE A 980 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   LEU A 989 " --> pdb=" O   LYS A 985 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLU A 991 " --> pdb=" O   ASN A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1016
      removed outlier: 4.557A  pdb=" N   ASP A1012 " --> pdb=" O   TRP A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1041 through 1046
      removed outlier: 3.660A  pdb=" N   LEU A1045 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1105
      removed outlier: 4.265A  pdb=" N   PHE A1104 " --> pdb=" O   ASN A1100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1117
      removed outlier: 3.668A  pdb=" N   LEU A1113 " --> pdb=" O   THR A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1136
      removed outlier: 4.536A  pdb=" N   GLU A1128 " --> pdb=" O   HIS A1124 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A1129 " --> pdb=" O   GLU A1125 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP A1132 " --> pdb=" O   GLU A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1145
      No H-bonds generated for 'chain 'A' and resid 1143 through 1145'
    Processing helix  chain 'B' and resid 733 through 747
    Processing helix  chain 'B' and resid 752 through 765
      removed outlier: 3.502A  pdb=" N   VAL B 758 " --> pdb=" O   ASP B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 770
    Processing helix  chain 'B' and resid 771 through 787
      removed outlier: 3.533A  pdb=" N   LEU B 787 " --> pdb=" O   LEU B 783 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 792 through 804
      removed outlier: 3.714A  pdb=" N   ASN B 804 " --> pdb=" O   ARG B 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 820
    Processing helix  chain 'B' and resid 823 through 825
      No H-bonds generated for 'chain 'B' and resid 823 through 825'
    Processing helix  chain 'B' and resid 826 through 832
      removed outlier: 3.785A  pdb=" N   LEU B 830 " --> pdb=" O   SER B 826 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 852
      removed outlier: 3.774A  pdb=" N   PHE B 838 " --> pdb=" O   ILE B 834 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 874 through 887
      removed outlier: 4.131A  pdb=" N   ILE B 880 " --> pdb=" O   TYR B 876 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 903
      removed outlier: 3.851A  pdb=" N   TYR B 897 " --> pdb=" O   SER B 893 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 908 through 924
      removed outlier: 3.774A  pdb=" N   ASN B 912 " --> pdb=" O   ASP B 908 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 930 through 953
      removed outlier: 3.507A  pdb=" N   HIS B 937 " --> pdb=" O   PHE B 933 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY B 938 " --> pdb=" O   GLN B 934 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR B 941 " --> pdb=" O   HIS B 937 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 957
    Processing helix  chain 'B' and resid 958 through 972
    Processing helix  chain 'B' and resid 974 through 988
      removed outlier: 3.749A  pdb=" N   TYR B 981 " --> pdb=" O   ILE B 977 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 992 through 1009
      removed outlier: 3.915A  pdb=" N   HIS B 997 " --> pdb=" O   LYS B 993 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ILE B1005 " --> pdb=" O   ASN B1001 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B1008 " --> pdb=" O   ILE B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1011 through 1023
    Processing helix  chain 'C' and resid 48 through 59
      removed outlier: 4.066A  pdb=" N   LYS C  54 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS C  59 " --> pdb=" O   ALA C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 71
      removed outlier: 4.176A  pdb=" N   LYS C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LYS C  66 " --> pdb=" O   ILE C  62 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   PHE C  69 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS C  70 " --> pdb=" O   LYS C  66 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU C  71 " --> pdb=" O   GLU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 129
    Processing helix  chain 'C' and resid 132 through 139
    Processing helix  chain 'C' and resid 173 through 183
    Processing helix  chain 'C' and resid 187 through 196
      removed outlier: 5.185A  pdb=" N   SER C 193 " --> pdb=" O   ASN C 189 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE C 194 " --> pdb=" O   ASN C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 213
    Processing helix  chain 'D' and resid 14 through 18
    Processing helix  chain 'D' and resid 37 through 54
      removed outlier: 3.562A  pdb=" N   LEU D  54 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 81
      removed outlier: 3.597A  pdb=" N   LEU D  70 " --> pdb=" O   PHE D  66 " (cutoff:3.500A)
      Proline residue:  D  75  - end of helix
      removed outlier: 3.813A  pdb=" N   LYS D  78 " --> pdb=" O   GLN D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 91
    Processing helix  chain 'D' and resid 107 through 115
      removed outlier: 4.435A  pdb=" N   LYS D 113 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE D 114 " --> pdb=" O   ILE D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 158
      Proline residue:  D 148  - end of helix
      removed outlier: 3.520A  pdb=" N   LYS D 156 " --> pdb=" O   GLU D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 182
      removed outlier: 3.603A  pdb=" N   LEU D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 351 through 354
    Processing sheet with id=AA1, first strand: chain 'A' and resid 858 through 860
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 858 through 860
    current: chain 'C' and resid 103 through 107
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 103 through 107
    current: chain 'C' and resid 147 through 162
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 147 through 162
    current: chain 'D' and resid 328 through 331
      removed outlier: 4.396A  pdb=" N   LEU D 335 " --> pdb=" O   VAL D 432 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU D 337 " --> pdb=" O   SER D 430 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   LYS D 424 " --> pdb=" O   LEU D 343 " (cutoff:3.500A)
      removed outlier: 10.844A  pdb=" N   GLY D 345 " --> pdb=" O   ARG D 422 " (cutoff:3.500A)
      removed outlier: 9.997A  pdb=" N   ARG D 422 " --> pdb=" O   GLY D 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 920 through 922
    Processing sheet with id=AA3, first strand: chain 'A' and resid 997 through 998
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1141
    Processing sheet with id=AA5, first strand: chain 'D' and resid 119 through 120
      removed outlier: 6.326A  pdb=" N   VAL D  84 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ALA D  61 " --> pdb=" O   TYR D  85 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   LYS D 206 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   ASN D 241 " --> pdb=" O   LYS D 206 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   GLU D 208 " --> pdb=" O   THR D 239 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   THR D 239 " --> pdb=" O   GLU D 208 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      66 hydrogen bonds
      132 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      87 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1985
        1.32 -     1.46: 3902
        1.46 -     1.61: 6685
        1.61 -     1.75: 105
        1.75 -     1.89: 72
  Bond restraints: 12749
  Sorted by residual:
  bond pdb=" CA  SER A1076 "
       pdb=" CB  SER A1076 "
    ideal  model  delta    sigma   weight residual
    1.530  1.443  0.086 1.69e-02 3.50e+03 2.61e+01
  bond pdb=" C   VAL A1080 "
       pdb=" O   VAL A1080 "
    ideal  model  delta    sigma   weight residual
    1.238  1.182  0.056 1.10e-02 8.26e+03 2.59e+01
  bond pdb=" C   TYR B1000 "
       pdb=" O   TYR B1000 "
    ideal  model  delta    sigma   weight residual
    1.236  1.178  0.058 1.15e-02 7.56e+03 2.55e+01
  bond pdb=" N   VAL D 104 "
       pdb=" CA  VAL D 104 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 7.70e-03 1.69e+04 2.54e+01
  bond pdb=" C   ASN B 964 "
       pdb=" O   ASN B 964 "
    ideal  model  delta    sigma   weight residual
    1.237  1.180  0.057 1.16e-02 7.43e+03 2.40e+01
  ... (remaining 12744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 13945
        2.31 -     4.62: 3285
        4.62 -     6.93: 374
        6.93 -     9.24: 22
        9.24 -    11.55: 6
  Bond angle restraints: 17632
  Sorted by residual:
  angle pdb=" CA  PHE B 933 "
        pdb=" CB  PHE B 933 "
        pdb=" CG  PHE B 933 "
      ideal   model   delta    sigma   weight residual
     113.80  124.03  -10.23 1.00e+00 1.00e+00 1.05e+02
  angle pdb=" C3'  DA F  11 "
        pdb=" C2'  DA F  11 "
        pdb=" C1'  DA F  11 "
      ideal   model   delta    sigma   weight residual
     102.50   94.34    8.16 1.20e+00 6.94e-01 4.63e+01
  angle pdb=" CA  ASN B 964 "
        pdb=" CB  ASN B 964 "
        pdb=" CG  ASN B 964 "
      ideal   model   delta    sigma   weight residual
     112.60  105.87    6.73 1.00e+00 1.00e+00 4.53e+01
  angle pdb=" C   LEU C 140 "
        pdb=" N   LYS C 141 "
        pdb=" CA  LYS C 141 "
      ideal   model   delta    sigma   weight residual
     120.38  129.13   -8.75 1.37e+00 5.33e-01 4.08e+01
  angle pdb=" C   ASN C  44 "
        pdb=" CA  ASN C  44 "
        pdb=" CB  ASN C  44 "
      ideal   model   delta    sigma   weight residual
     112.07  121.26   -9.19 1.48e+00 4.57e-01 3.85e+01
  ... (remaining 17627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 6066
       17.93 -    35.86: 963
       35.86 -    53.79: 355
       53.79 -    71.72: 198
       71.72 -    89.65: 10
  Dihedral angle restraints: 7592
    sinusoidal: 3794
      harmonic: 3798
  Sorted by residual:
  dihedral pdb=" CA  LEU D 343 "
           pdb=" C   LEU D 343 "
           pdb=" N   VAL D 344 "
           pdb=" CA  VAL D 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.73   32.27     0      5.00e+00 4.00e-02 4.17e+01
  dihedral pdb=" CA  ARG C  35 "
           pdb=" C   ARG C  35 "
           pdb=" N   ILE C  36 "
           pdb=" CA  ILE C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.21  -31.79     0      5.00e+00 4.00e-02 4.04e+01
  dihedral pdb=" CA  TYR C 242 "
           pdb=" C   TYR C 242 "
           pdb=" N   LYS C 243 "
           pdb=" CA  LYS C 243 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.55   31.45     0      5.00e+00 4.00e-02 3.96e+01
  ... (remaining 7589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.130: 1627
       0.130 -    0.259: 235
       0.259 -    0.389: 38
       0.389 -    0.518: 55
       0.518 -    0.648: 2
  Chirality restraints: 1957
  Sorted by residual:
  chirality pdb=" P    DA F   1 "
            pdb=" OP1  DA F   1 "
            pdb=" OP2  DA F   1 "
            pdb=" O5'  DA F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.98   -0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" P    DT E   1 "
            pdb=" OP1  DT E   1 "
            pdb=" OP2  DT E   1 "
            pdb=" O5'  DT E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.97   -0.63 2.00e-01 2.50e+01 9.99e+00
  chirality pdb=" P    DT E  28 "
            pdb=" OP1  DT E  28 "
            pdb=" OP2  DT E  28 "
            pdb=" O5'  DT E  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.85   -0.51 2.00e-01 2.50e+01 6.55e+00
  ... (remaining 1954 not shown)

  Planarity restraints: 1931
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 943 "    0.126 2.00e-02 2.50e+03   7.04e-02 9.91e+01
        pdb=" CG  TYR B 943 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 943 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 943 "   -0.056 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 943 "   -0.048 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 943 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 943 "   -0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR B 943 "    0.114 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 886 "    0.095 2.00e-02 2.50e+03   4.88e-02 4.76e+01
        pdb=" CG  TYR B 886 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 886 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 886 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 886 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 886 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 886 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR B 886 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 963 "   -0.094 2.00e-02 2.50e+03   4.85e-02 4.70e+01
        pdb=" CG  TYR B 963 "    0.076 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 963 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 963 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 963 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 963 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 963 "   -0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR B 963 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 1928 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 33
        2.54 -     3.13: 9360
        3.13 -     3.72: 20085
        3.72 -     4.31: 30106
        4.31 -     4.90: 45890
  Nonbonded interactions: 105474
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 811 "
            pdb=" O   SER C 197 "
     model   vdw
     1.954 3.120
  nonbonded pdb=" OG  SER C  38 "
            pdb=" OE2 GLU D 347 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR B 879 "
            pdb=" O   PRO C 228 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NE2 GLN B 814 "
            pdb=" O   GLN C 226 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OD1 ASN A1054 "
            pdb=" NZ  LYS B 947 "
     model   vdw
     2.286 3.120
  ... (remaining 105469 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:             2.110
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.900
  Find NCS groups from input model:        0.060
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
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      :  0.015   0.091  12749  Z= 1.083
  Angle     :  1.892  11.545  17632  Z= 1.301
  Chirality :  0.122   0.648   1957
  Planarity :  0.010   0.153   1931
  Dihedral  : 21.024  89.645   5132
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.03 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  3.33 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -2.69 (0.21), residues: 1273
  helix: -2.43 (0.16), residues: 547
  sheet: -0.46 (0.56), residues: 64
  loop : -1.23 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.002   ARG A 923 
 TYR   0.126   0.014   TYR B 943 
 PHE   0.055   0.009   PHE D 350 
 TRP   0.062   0.012   TRP A1153 
 HIS   0.027   0.005   HIS A1151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01485 /  1.08 (12749)
  covalent geometry    : angle       1.89168 /  1.30 (17632)
  hydrogen bonds       : bond        0.19361 / 12.54 (  497)
  hydrogen bonds       : angle       8.39377 /  5.92 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 203
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6572 (mtm) cc_final: 0.5435 (ttp)
REVERT: A  872 MET cc_start: 0.5620 (mtm) cc_final: 0.4170 (mtm)
REVERT: A 1033 LEU cc_start: 0.8015 (mp) cc_final: 0.7517 (tp)
REVERT: A 1040 PHE cc_start: 0.6134 (t80) cc_final: 0.5764 (t80)
REVERT: A 1045 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6536 (tt)
REVERT: A 1068 LYS cc_start: 0.9081 (mptt) cc_final: 0.8727 (tmtt)
REVERT: A 1069 VAL cc_start: 0.7888 (t) cc_final: 0.7630 (t)
REVERT: A 1097 MET cc_start: 0.9627 (ttp) cc_final: 0.9303 (tmm)
REVERT: B  740 MET cc_start: 0.6936 (mmp) cc_final: 0.6432 (mmt)
REVERT: B  777 MET cc_start: 0.5755 (ttm) cc_final: 0.5470 (ttt)
REVERT: B  793 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8652 (tm-30)
REVERT: B  870 ASN cc_start: 0.9605 (m-40) cc_final: 0.9337 (t0)
REVERT: B  871 LYS cc_start: 0.8782 (mttt) cc_final: 0.8354 (ptmm)
REVERT: B  910 MET cc_start: 0.7625 (mmm) cc_final: 0.7205 (mmm)
REVERT: C   79 HIS cc_start: 0.8358 (m-70) cc_final: 0.7978 (m90)
REVERT: C  116 ILE cc_start: 0.8724 (mt) cc_final: 0.8512 (mm)
REVERT: C  204 GLN cc_start: 0.9396 (mt0) cc_final: 0.9108 (mm-40)
REVERT: C  233 LEU cc_start: 0.8461 (mt) cc_final: 0.8168 (mt)
REVERT: D   55 ASP cc_start: 0.8666 (m-30) cc_final: 0.8384 (m-30)
REVERT: D  141 MET cc_start: 0.8862 (mmm) cc_final: 0.8579 (mtt)
REVERT: D  204 LEU cc_start: 0.6800 (tp) cc_final: 0.6393 (tp)
REVERT: D  239 THR cc_start: 0.2250 (p) cc_final: 0.1807 (p)
REVERT: D  311 ILE cc_start: 0.8154 (mt) cc_final: 0.7935 (mm)
REVERT: D  323 GLU cc_start: 0.8586 (pm20) cc_final: 0.8254 (mp0)
  outliers start: 9
  outliers final: 1
  residues processed: 211
  average time/residue: 0.1301
  time to fit residues: 37.2881
Evaluate side-chains
  127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain B residue  836 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 946 HIS
D  57 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.125626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.103383 restraints weight = 57355.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.105924 restraints weight = 33098.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.107213 restraints weight = 18745.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.107291 restraints weight = 14812.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.107350 restraints weight = 13112.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.4522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5930
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  12749  Z= 0.223
  Angle     :  0.908  10.576  17632  Z= 0.493
  Chirality :  0.057   0.252   1957
  Planarity :  0.006   0.072   1931
  Dihedral  : 23.833  84.250   2487
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.22 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  9.13 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.49 (0.22), residues: 1273
  helix: -1.04 (0.20), residues: 570
  sheet: -0.70 (0.51), residues: 79
  loop : -0.83 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 748 
 TYR   0.035   0.003   TYR B1000 
 PHE   0.031   0.003   PHE B 839 
 TRP   0.029   0.003   TRP A 800 
 HIS   0.016   0.002   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00489 /  0.22 (12749)
  covalent geometry    : angle       0.90754 /  0.49 (17632)
  hydrogen bonds       : bond        0.07019 /  4.70 (  497)
  hydrogen bonds       : angle       5.86316 /  4.12 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6302 (mtm) cc_final: 0.5454 (ttp)
REVERT: A  826 LEU cc_start: 0.8627 (mm) cc_final: 0.8237 (pp)
REVERT: A  830 TRP cc_start: 0.7332 (t60) cc_final: 0.7078 (t60)
REVERT: A  833 PHE cc_start: 0.8519 (m-80) cc_final: 0.7842 (m-80)
REVERT: A 1033 LEU cc_start: 0.7116 (mp) cc_final: 0.6732 (mp)
REVERT: B  774 ARG cc_start: 0.7955 (mmp-170) cc_final: 0.7629 (mmp-170)
REVERT: B  871 LYS cc_start: 0.8083 (mttt) cc_final: 0.7818 (ptmm)
REVERT: B  958 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6856 (ptpp)
REVERT: C  204 GLN cc_start: 0.8462 (mt0) cc_final: 0.8085 (mp10)
REVERT: D  141 MET cc_start: 0.8208 (mmm) cc_final: 0.7922 (mtt)
REVERT: D  158 TYR cc_start: 0.5578 (m-80) cc_final: 0.4739 (m-80)
REVERT: D  233 ASP cc_start: 0.4530 (t0) cc_final: 0.4245 (t0)
  outliers start: 31
  outliers final: 11
  residues processed: 156
  average time/residue: 0.1186
  time to fit residues: 25.8930
Evaluate side-chains
  122 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  781 TRP
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain B residue  836 GLN
Chi-restraints excluded: chain B residue  958 LYS
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  258 ASP
Chi-restraints excluded: chain D residue  297 SER
Chi-restraints excluded: chain D residue  355 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 121 optimal weight:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   chunk 78 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.121887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.097167 restraints weight = 57995.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.099697 restraints weight = 32540.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.101484 restraints weight = 21356.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.102675 restraints weight = 16069.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 64)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.103495 restraints weight = 13281.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5981
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12749  Z= 0.179
  Angle     :  0.805  12.471  17632  Z= 0.433
  Chirality :  0.050   0.241   1957
  Planarity :  0.005   0.043   1931
  Dihedral  : 23.351  76.557   2485
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.46 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.43 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.00 (0.23), residues: 1273
  helix: -0.52 (0.20), residues: 560
  sheet: -0.41 (0.53), residues: 81
  loop : -0.71 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 177 
 TYR   0.044   0.002   TYR B 818 
 PHE   0.027   0.002   PHE B 839 
 TRP   0.019   0.002   TRP A 800 
 HIS   0.011   0.001   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 (12749)
  covalent geometry    : angle       0.80504 /  0.43 (17632)
  hydrogen bonds       : bond        0.05843 /  3.99 (  497)
  hydrogen bonds       : angle       5.37554 /  3.75 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6150 (mtm) cc_final: 0.5272 (ttp)
REVERT: A  826 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8127 (pp)
REVERT: A  830 TRP cc_start: 0.7666 (t60) cc_final: 0.7369 (t60)
REVERT: A  833 PHE cc_start: 0.8775 (m-80) cc_final: 0.8087 (m-80)
REVERT: A 1104 PHE cc_start: 0.7145 (m-80) cc_final: 0.6596 (m-80)
REVERT: B  871 LYS cc_start: 0.8493 (mttt) cc_final: 0.8005 (pttp)
REVERT: C   58 MET cc_start: 0.6935 (mtp) cc_final: 0.6646 (ttm)
REVERT: C  204 GLN cc_start: 0.8534 (mt0) cc_final: 0.8033 (mp10)
REVERT: D  139 MET cc_start: -0.1043 (ppp) cc_final: -0.1369 (ppp)
REVERT: D  141 MET cc_start: 0.8227 (mmm) cc_final: 0.7976 (mtt)
REVERT: D  158 TYR cc_start: 0.6528 (m-80) cc_final: 0.6120 (m-80)
REVERT: D  188 MET cc_start: 0.0071 (mmm) cc_final: -0.1649 (tpt)
REVERT: D  252 GLU cc_start: 0.7864 (tt0) cc_final: 0.7618 (pt0)
  outliers start: 27
  outliers final: 15
  residues processed: 138
  average time/residue: 0.1056
  time to fit residues: 21.4017
Evaluate side-chains
  123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  836 GLN
Chi-restraints excluded: chain B residue  901 LEU
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  204 LEU
Chi-restraints excluded: chain D residue  297 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0000
   chunk 73 optimal weight:    0.7980
   chunk 106 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 836 GLN
** C  86 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 = 0.4693 r_free = 0.4693 target = 0.120957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.095826 restraints weight = 57058.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.098631 restraints weight = 31230.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.100325 restraints weight = 20693.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.101565 restraints weight = 15754.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.101946 restraints weight = 13094.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12749  Z= 0.184
  Angle     :  0.740  10.107  17632  Z= 0.401
  Chirality :  0.048   0.271   1957
  Planarity :  0.005   0.053   1931
  Dihedral  : 23.316  70.869   2485
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.38 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.46 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.81 (0.23), residues: 1273
  helix: -0.29 (0.21), residues: 557
  sheet: -0.30 (0.55), residues: 84
  loop : -0.68 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 983 
 TYR   0.030   0.002   TYR B1000 
 PHE   0.027   0.002   PHE B 839 
 TRP   0.017   0.002   TRP A 800 
 HIS   0.011   0.001   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.18 (12749)
  covalent geometry    : angle       0.73986 /  0.40 (17632)
  hydrogen bonds       : bond        0.05451 /  3.70 (  497)
  hydrogen bonds       : angle       5.28907 /  3.67 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6228 (mtm) cc_final: 0.5313 (ttt)
REVERT: A  826 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8200 (pp)
REVERT: A  830 TRP cc_start: 0.7701 (t60) cc_final: 0.7452 (t60)
REVERT: A  833 PHE cc_start: 0.8784 (m-80) cc_final: 0.7940 (m-80)
REVERT: A 1104 PHE cc_start: 0.6992 (m-80) cc_final: 0.6500 (m-80)
REVERT: B  740 MET cc_start: 0.4708 (mmm) cc_final: 0.4458 (mmt)
REVERT: B  871 LYS cc_start: 0.8424 (mttt) cc_final: 0.8007 (pttp)
REVERT: C   58 MET cc_start: 0.7026 (mtp) cc_final: 0.6825 (ttm)
REVERT: C  204 GLN cc_start: 0.8596 (mt0) cc_final: 0.8103 (mp10)
REVERT: D  158 TYR cc_start: 0.6456 (m-80) cc_final: 0.5935 (m-80)
REVERT: D  188 MET cc_start: 0.0217 (mmm) cc_final: -0.1347 (tpt)
  outliers start: 32
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1045
  time to fit residues: 20.5509
Evaluate side-chains
  116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  204 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 129 optimal weight:   40.0000
   chunk 54 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   chunk 100 optimal weight:   20.0000
   chunk 120 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 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 = 0.4664 r_free = 0.4664 target = 0.119173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.094761 restraints weight = 56787.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.098277 restraints weight = 32721.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.098662 restraints weight = 17280.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.098937 restraints weight = 16472.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.099168 restraints weight = 15322.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6173
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  12749  Z= 0.230
  Angle     :  0.774  10.642  17632  Z= 0.413
  Chirality :  0.048   0.263   1957
  Planarity :  0.005   0.063   1931
  Dihedral  : 23.444  68.137   2482
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.16 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.99 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.03 (0.23), residues: 1273
  helix: -0.55 (0.20), residues: 569
  sheet: -0.31 (0.59), residues: 78
  loop : -0.73 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 784 
 TYR   0.051   0.002   TYR B 818 
 PHE   0.027   0.002   PHE B 839 
 TRP   0.017   0.002   TRP A 800 
 HIS   0.012   0.002   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00513 /  0.23 (12749)
  covalent geometry    : angle       0.77351 /  0.41 (17632)
  hydrogen bonds       : bond        0.05693 /  3.90 (  497)
  hydrogen bonds       : angle       5.36148 /  3.74 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6145 (mtm) cc_final: 0.5364 (ttt)
REVERT: A  826 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8232 (pp)
REVERT: A  830 TRP cc_start: 0.7808 (t60) cc_final: 0.7565 (t60)
REVERT: A  833 PHE cc_start: 0.8854 (m-10) cc_final: 0.8031 (m-80)
REVERT: A 1104 PHE cc_start: 0.7035 (m-80) cc_final: 0.6561 (m-80)
REVERT: B  774 ARG cc_start: 0.8000 (mmp-170) cc_final: 0.7355 (mmp80)
REVERT: B  871 LYS cc_start: 0.8556 (mttt) cc_final: 0.8126 (pttp)
REVERT: C   58 MET cc_start: 0.7213 (mtp) cc_final: 0.6998 (ttm)
REVERT: C  204 GLN cc_start: 0.8787 (mt0) cc_final: 0.8263 (mp10)
REVERT: D  141 MET cc_start: 0.8235 (mtt) cc_final: 0.7813 (mpp)
REVERT: D  158 TYR cc_start: 0.6098 (m-80) cc_final: 0.5472 (m-80)
REVERT: D  188 MET cc_start: 0.0574 (mmm) cc_final: -0.0034 (mmm)
  outliers start: 29
  outliers final: 17
  residues processed: 124
  average time/residue: 0.1033
  time to fit residues: 19.1764
Evaluate side-chains
  116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1012 ASP
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 131 optimal weight:   50.0000
   chunk 64 optimal weight:    0.9980
   chunk 118 optimal weight:    0.0980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 959 GLN
** C  86 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 = 0.4713 r_free = 0.4713 target = 0.121633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.097082 restraints weight = 56605.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.099676 restraints weight = 30422.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.101256 restraints weight = 19915.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.102514 restraints weight = 15054.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.102891 restraints weight = 12529.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6027
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12749  Z= 0.155
  Angle     :  0.697   8.875  17632  Z= 0.377
  Chirality :  0.045   0.226   1957
  Planarity :  0.004   0.061   1931
  Dihedral  : 23.314  69.395   2482
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.69 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.76 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.71 (0.23), residues: 1273
  helix: -0.23 (0.21), residues: 569
  sheet: -0.26 (0.59), residues: 81
  loop : -0.61 (0.26), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 784 
 TYR   0.032   0.002   TYR B 818 
 PHE   0.018   0.002   PHE B 839 
 TRP   0.043   0.002   TRP D  93 
 HIS   0.009   0.001   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 (12749)
  covalent geometry    : angle       0.69734 /  0.38 (17632)
  hydrogen bonds       : bond        0.04872 /  3.32 (  497)
  hydrogen bonds       : angle       5.10535 /  3.53 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6189 (mtm) cc_final: 0.5406 (ttt)
REVERT: A  826 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8174 (pp)
REVERT: A  830 TRP cc_start: 0.7688 (t60) cc_final: 0.7434 (t60)
REVERT: A  833 PHE cc_start: 0.8835 (m-10) cc_final: 0.8072 (m-80)
REVERT: A 1104 PHE cc_start: 0.6898 (m-80) cc_final: 0.6471 (m-80)
REVERT: B  871 LYS cc_start: 0.8458 (mttt) cc_final: 0.8039 (pttp)
REVERT: C  186 LEU cc_start: 0.7834 (mt) cc_final: 0.7631 (pp)
REVERT: C  204 GLN cc_start: 0.8563 (mt0) cc_final: 0.7988 (mp10)
REVERT: D  141 MET cc_start: 0.8171 (mtt) cc_final: 0.7773 (mpp)
REVERT: D  158 TYR cc_start: 0.6547 (m-80) cc_final: 0.5839 (m-80)
REVERT: D  188 MET cc_start: 0.0289 (mmm) cc_final: -0.0376 (mmm)
  outliers start: 26
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0946
  time to fit residues: 17.7393
Evaluate side-chains
  115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0980
   chunk 116 optimal weight:   10.0000
   chunk 119 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 959 GLN
** B1017 HIS ** 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 = 0.4656 r_free = 0.4656 target = 0.118791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.093892 restraints weight = 56931.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.096357 restraints weight = 31764.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.097973 restraints weight = 21458.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.098631 restraints weight = 16500.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.099514 restraints weight = 14330.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6176
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  12749  Z= 0.226
  Angle     :  0.746  10.596  17632  Z= 0.398
  Chirality :  0.046   0.246   1957
  Planarity :  0.005   0.065   1931
  Dihedral  : 23.399  69.948   2482
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.24 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.70 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.86 (0.23), residues: 1273
  helix: -0.35 (0.21), residues: 572
  sheet: -0.40 (0.60), residues: 78
  loop : -0.69 (0.26), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 784 
 TYR   0.043   0.003   TYR B 818 
 PHE   0.023   0.002   PHE C 166 
 TRP   0.050   0.003   TRP D  93 
 HIS   0.008   0.001   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.23 (12749)
  covalent geometry    : angle       0.74619 /  0.40 (17632)
  hydrogen bonds       : bond        0.05483 /  3.79 (  497)
  hydrogen bonds       : angle       5.23749 /  3.64 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6130 (mtm) cc_final: 0.5118 (ttt)
REVERT: A  826 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8270 (pp)
REVERT: A  833 PHE cc_start: 0.8960 (m-10) cc_final: 0.8190 (m-80)
REVERT: A 1104 PHE cc_start: 0.7026 (m-80) cc_final: 0.6556 (m-80)
REVERT: B  774 ARG cc_start: 0.8031 (mmp-170) cc_final: 0.7361 (mmp80)
REVERT: B  871 LYS cc_start: 0.8579 (mttt) cc_final: 0.8106 (ptmm)
REVERT: B  927 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5271 (mt)
REVERT: C  186 LEU cc_start: 0.7946 (mt) cc_final: 0.7725 (pp)
REVERT: C  204 GLN cc_start: 0.8806 (mt0) cc_final: 0.8214 (mp10)
REVERT: D  141 MET cc_start: 0.8227 (mtt) cc_final: 0.7845 (mpp)
REVERT: D  158 TYR cc_start: 0.6535 (m-80) cc_final: 0.5719 (m-80)
REVERT: D  178 MET cc_start: 0.7238 (mmm) cc_final: 0.6320 (mmt)
REVERT: D  188 MET cc_start: 0.0417 (mmm) cc_final: 0.0101 (mmm)
  outliers start: 29
  outliers final: 21
  residues processed: 121
  average time/residue: 0.1037
  time to fit residues: 18.6752
Evaluate side-chains
  120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  940 VAL
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1012 ASP
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  970 HIS
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 119 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 122 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 120 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 959 GLN
** C  86 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 = 0.4698 r_free = 0.4698 target = 0.120921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.096429 restraints weight = 56476.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.098972 restraints weight = 31425.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.100695 restraints weight = 20805.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.101804 restraints weight = 15786.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.102348 restraints weight = 13178.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6058
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12749  Z= 0.154
  Angle     :  0.694  10.599  17632  Z= 0.373
  Chirality :  0.044   0.276   1957
  Planarity :  0.005   0.060   1931
  Dihedral  : 23.316  70.695   2482
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.93 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.30 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.62 (0.24), residues: 1273
  helix: -0.15 (0.21), residues: 570
  sheet: -0.35 (0.63), residues: 71
  loop : -0.55 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 784 
 TYR   0.033   0.002   TYR B 818 
 PHE   0.020   0.002   PHE C 166 
 TRP   0.041   0.002   TRP D  93 
 HIS   0.008   0.001   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 (12749)
  covalent geometry    : angle       0.69396 /  0.37 (17632)
  hydrogen bonds       : bond        0.04649 /  3.17 (  497)
  hydrogen bonds       : angle       5.06386 /  3.51 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6073 (mtm) cc_final: 0.5170 (ttt)
REVERT: A  826 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8236 (pp)
REVERT: A  833 PHE cc_start: 0.8884 (m-10) cc_final: 0.8141 (m-80)
REVERT: A 1104 PHE cc_start: 0.6936 (m-80) cc_final: 0.6525 (m-80)
REVERT: B  774 ARG cc_start: 0.8007 (mmp-170) cc_final: 0.7350 (mmp80)
REVERT: B  871 LYS cc_start: 0.8556 (mttt) cc_final: 0.8128 (pttp)
REVERT: B  927 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5152 (mt)
REVERT: C  186 LEU cc_start: 0.7850 (mt) cc_final: 0.7593 (pp)
REVERT: C  204 GLN cc_start: 0.8666 (mt0) cc_final: 0.8057 (mp10)
REVERT: C  233 LEU cc_start: 0.7319 (mt) cc_final: 0.6658 (mp)
REVERT: D  141 MET cc_start: 0.8277 (mtt) cc_final: 0.7923 (mmt)
REVERT: D  158 TYR cc_start: 0.6538 (m-80) cc_final: 0.5655 (m-80)
REVERT: D  178 MET cc_start: 0.7344 (mmm) cc_final: 0.6253 (mmt)
REVERT: D  188 MET cc_start: 0.0484 (mmm) cc_final: 0.0244 (mmm)
REVERT: D  343 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4768 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0947
  time to fit residues: 17.4592
Evaluate side-chains
  120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  940 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  343 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 78 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 132 optimal weight:   50.0000
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1114 GLN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 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 = 0.4712 r_free = 0.4712 target = 0.121591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.096976 restraints weight = 56279.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.099644 restraints weight = 30717.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.101304 restraints weight = 20462.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.102488 restraints weight = 15563.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.103241 restraints weight = 13022.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12749  Z= 0.148
  Angle     :  0.686  12.983  17632  Z= 0.369
  Chirality :  0.044   0.202   1957
  Planarity :  0.004   0.063   1931
  Dihedral  : 23.213  70.560   2482
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.01 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.04 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.56 (0.24), residues: 1273
  helix: -0.08 (0.21), residues: 575
  sheet: -0.39 (0.63), residues: 71
  loop : -0.52 (0.26), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 784 
 TYR   0.057   0.002   TYR B1000 
 PHE   0.024   0.002   PHE C 166 
 TRP   0.033   0.002   TRP D  93 
 HIS   0.012   0.001   HIS B 970 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.15 (12749)
  covalent geometry    : angle       0.68616 /  0.37 (17632)
  hydrogen bonds       : bond        0.04445 /  3.02 (  497)
  hydrogen bonds       : angle       5.00556 /  3.48 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6024 (mtm) cc_final: 0.5362 (ttt)
REVERT: A  826 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8236 (pp)
REVERT: A  830 TRP cc_start: 0.7719 (t60) cc_final: 0.7494 (t60)
REVERT: A  833 PHE cc_start: 0.8893 (m-10) cc_final: 0.8155 (m-80)
REVERT: A 1104 PHE cc_start: 0.6864 (m-80) cc_final: 0.6526 (m-80)
REVERT: B  871 LYS cc_start: 0.8509 (mttt) cc_final: 0.8102 (pttp)
REVERT: B  927 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5150 (mt)
REVERT: C  186 LEU cc_start: 0.7736 (mt) cc_final: 0.7463 (pp)
REVERT: C  204 GLN cc_start: 0.8565 (mt0) cc_final: 0.7999 (mp10)
REVERT: D    1 MET cc_start: 0.4862 (ppp) cc_final: 0.4634 (tpp)
REVERT: D  141 MET cc_start: 0.8304 (mtt) cc_final: 0.7961 (mmt)
REVERT: D  158 TYR cc_start: 0.6448 (m-80) cc_final: 0.5487 (m-80)
REVERT: D  178 MET cc_start: 0.7432 (mmm) cc_final: 0.6358 (mmt)
REVERT: D  188 MET cc_start: 0.0657 (mmm) cc_final: 0.0440 (mmm)
REVERT: D  343 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4399 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1058
  time to fit residues: 19.2705
Evaluate side-chains
  117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  940 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  343 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 127 optimal weight:   50.0000
   chunk 49 optimal weight:    0.2980
   chunk 122 optimal weight:    0.8980
   chunk 117 optimal weight:    0.0870
   chunk 99 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 126 optimal weight:    0.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 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 = 0.4726 r_free = 0.4726 target = 0.122457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.098116 restraints weight = 56370.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.100749 restraints weight = 30139.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.102459 restraints weight = 19776.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.103595 restraints weight = 15031.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.104409 restraints weight = 12573.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5950
moved from start:          0.4978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  12749  Z= 0.153
  Angle     :  0.710  13.281  17632  Z= 0.380
  Chirality :  0.045   0.255   1957
  Planarity :  0.005   0.119   1931
  Dihedral  : 23.157  70.198   2482
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.85 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.15 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.57 (0.24), residues: 1273
  helix: -0.08 (0.21), residues: 574
  sheet: -0.54 (0.61), residues: 72
  loop : -0.52 (0.26), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG D 426 
 TYR   0.036   0.002   TYR B1000 
 PHE   0.040   0.002   PHE C 166 
 TRP   0.041   0.002   TRP D  93 
 HIS   0.007   0.001   HIS B 919 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (12749)
  covalent geometry    : angle       0.71033 /  0.38 (17632)
  hydrogen bonds       : bond        0.04450 /  2.98 (  497)
  hydrogen bonds       : angle       5.01499 /  3.48 ( 1383)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6005 (mtm) cc_final: 0.5369 (ttt)
REVERT: A  826 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8230 (pp)
REVERT: A  833 PHE cc_start: 0.8881 (m-10) cc_final: 0.8145 (m-80)
REVERT: A 1104 PHE cc_start: 0.6781 (m-80) cc_final: 0.6477 (m-80)
REVERT: A 1135 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7592 (mt-10)
REVERT: A 1154 TYR cc_start: 0.7238 (p90) cc_final: 0.6971 (p90)
REVERT: B  871 LYS cc_start: 0.8497 (mttt) cc_final: 0.8075 (pttp)
REVERT: B  927 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5165 (mt)
REVERT: C  173 VAL cc_start: 0.7327 (t) cc_final: 0.7101 (t)
REVERT: C  186 LEU cc_start: 0.7681 (mt) cc_final: 0.7397 (pp)
REVERT: C  204 GLN cc_start: 0.8525 (mt0) cc_final: 0.8008 (mp10)
REVERT: D  141 MET cc_start: 0.8347 (mtt) cc_final: 0.7948 (mpp)
REVERT: D  158 TYR cc_start: 0.6401 (m-80) cc_final: 0.5339 (m-80)
REVERT: D  188 MET cc_start: 0.0697 (mmm) cc_final: -0.0266 (tpt)
  outliers start: 19
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0918
  time to fit residues: 16.0774
Evaluate side-chains
  115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  940 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  818 TYR
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1005 ILE
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 25 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 116 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 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 = 0.4724 r_free = 0.4724 target = 0.122384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.097775 restraints weight = 56045.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.100356 restraints weight = 31034.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.101882 restraints weight = 20460.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.103164 restraints weight = 15554.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.103982 restraints weight = 12936.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5974
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12749  Z= 0.156
  Angle     :  0.740  17.578  17632  Z= 0.387
  Chirality :  0.045   0.269   1957
  Planarity :  0.005   0.065   1931
  Dihedral  : 23.088  69.739   2482
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.93 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.83 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.55 (0.24), residues: 1273
  helix: -0.11 (0.21), residues: 576
  sheet: -0.53 (0.67), residues: 66
  loop : -0.46 (0.26), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 426 
 TYR   0.056   0.002   TYR B1000 
 PHE   0.032   0.002   PHE C 166 
 TRP   0.081   0.004   TRP D  93 
 HIS   0.009   0.001   HIS B 970 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 (12749)
  covalent geometry    : angle       0.74030 /  0.39 (17632)
  hydrogen bonds       : bond        0.04479 /  3.02 (  497)
  hydrogen bonds       : angle       5.03391 /  3.51 ( 1383)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2644.48 seconds
wall clock time: 46 minutes 15.28 seconds (2775.28 seconds total)