Starting phenix.real_space_refine
on Wed Aug  5 19:12:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q63_18183/08_2026/8q63_18183.cif"
  }
  resolution = 3.68
  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=   0.001 sd=   0.010
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      70      5.49       5
     S      35      5.16       5
     C    7041      2.51       5
     N    1971      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11346
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2698
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 7200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 915, 7200
          Classifications: {'peptide': 915}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 44, 'TRANS': 870}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "N"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 642
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "T"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 630
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "C"
      Number of atoms: 152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 152
          Classifications: {'RNAv2': 7}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 6}
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 2.58, per 1000 atoms: 0.23
  Number of scatterers: 11346
  At special positions: 0
  Unit cell: (103.79, 116.4, 118.34, 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      35     16.00
     P      70     15.00
     O    2229      8.00
     N    1971      7.00
     C    7041      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 486.4 milliseconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2354

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 11 sheets defined
      59.8% alpha, 7.3% beta
      26 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 3.890A  pdb=" N   LEU B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 38 through 41
    Processing helix  chain 'B' and resid 44 through 47
      removed outlier: 3.762A  pdb=" N   GLU B  47 " --> pdb=" O   HIS B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 44 through 47'
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 79 through 90
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 3.834A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 157
      removed outlier: 3.960A  pdb=" N   MET B 148 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE B 154 " --> pdb=" O   TRP B 150 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLY B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.729A  pdb=" N   GLY B 164 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 182
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 209 through 215
      removed outlier: 3.521A  pdb=" N   GLU B 212 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS B 214 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 4.297A  pdb=" N   ILE B 234 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 267
    Processing helix  chain 'B' and resid 268 through 270
      No H-bonds generated for 'chain 'B' and resid 268 through 270'
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 4.141A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 295 through 301
      removed outlier: 3.573A  pdb=" N   LEU B 299 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 321
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 4.247A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 442
    Processing helix  chain 'A' and resid 448 through 476
      removed outlier: 4.518A  pdb=" N   VAL A 452 " --> pdb=" O   LYS A 448 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 490 through 497
      removed outlier: 3.764A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 515
      removed outlier: 4.529A  pdb=" N   GLY A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 552
      removed outlier: 3.855A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 549 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 611
      removed outlier: 3.747A  pdb=" N   VAL A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 663
      removed outlier: 3.628A  pdb=" N   GLU A 662 " --> pdb=" O   GLN A 658 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
      removed outlier: 3.884A  pdb=" N   VAL A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 731
    Processing helix  chain 'A' and resid 737 through 751
    Processing helix  chain 'A' and resid 777 through 813
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 857 through 873
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 906 through 911
    Processing helix  chain 'A' and resid 913 through 930
    Processing helix  chain 'A' and resid 932 through 935
    Processing helix  chain 'A' and resid 948 through 959
      removed outlier: 3.703A  pdb=" N   ALA A 956 " --> pdb=" O   GLN A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 977 through 997
    Processing helix  chain 'A' and resid 998 through 1004
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 3.729A  pdb=" N   VAL A1021 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1038
    Processing helix  chain 'A' and resid 1046 through 1066
      removed outlier: 4.435A  pdb=" N   PHE A1050 " --> pdb=" O   GLU A1046 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR A1053 " --> pdb=" O   ASP A1049 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS A1057 " --> pdb=" O   TYR A1053 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER A1060 " --> pdb=" O   LYS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1085
    Processing helix  chain 'A' and resid 1089 through 1094
      removed outlier: 4.066A  pdb=" N   LYS A1094 " --> pdb=" O   ASP A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1181
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1197 through 1213
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1244
      No H-bonds generated for 'chain 'A' and resid 1242 through 1244'
    Processing helix  chain 'A' and resid 1245 through 1260
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.647A  pdb=" N   LEU A1279 " --> pdb=" O   ARG A1275 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   SER A1281 " --> pdb=" O   GLU A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1293
    Processing helix  chain 'A' and resid 1295 through 1301
      removed outlier: 3.774A  pdb=" N   LEU A1299 " --> pdb=" O   THR A1295 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE A1300 " --> pdb=" O   THR A1296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1310
    Processing helix  chain 'A' and resid 1339 through 1344
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99
      removed outlier: 3.704A  pdb=" N   VAL B 135 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   MET B 247 " --> pdb=" O   MET B 168 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 207
      removed outlier: 3.953A  pdb=" N   ILE B 207 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530
      removed outlier: 3.547A  pdb=" N   ALA A 635 " --> pdb=" O   LYS A 650 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 613 through 619
    Processing sheet with id=AA5, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856
      removed outlier: 3.997A  pdb=" N   LYS A 855 " --> pdb=" O   SER A 938 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER A 938 " --> pdb=" O   LYS A 855 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 944
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1087
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111
      removed outlier: 3.739A  pdb=" N   TRP A1110 " --> pdb=" O   ILE A1118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131
      removed outlier: 3.610A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1524 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      59 hydrogen bonds
      118 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1999
        1.33 -     1.45: 3277
        1.45 -     1.57: 6274
        1.57 -     1.69: 146
        1.69 -     1.82: 60
  Bond restraints: 11756
  Sorted by residual:
  bond pdb=" C3'  DC N 137 "
       pdb=" C2'  DC N 137 "
    ideal  model  delta    sigma   weight residual
    1.516  1.696 -0.180 8.00e-03 1.56e+04 5.04e+02
  bond pdb=" C3'  DT N 111 "
       pdb=" C2'  DT N 111 "
    ideal  model  delta    sigma   weight residual
    1.516  1.632 -0.116 8.00e-03 1.56e+04 2.09e+02
  bond pdb=" O3'  DG N 136 "
       pdb=" P    DC N 137 "
    ideal  model  delta    sigma   weight residual
    1.607  1.449  0.158 1.20e-02 6.94e+03 1.73e+02
  bond pdb=" C2'  DC N 137 "
       pdb=" C1'  DC N 137 "
    ideal  model  delta    sigma   weight residual
    1.518  1.409  0.109 1.00e-02 1.00e+04 1.18e+02
  bond pdb=" C3'  DA T  30 "
       pdb=" C2'  DA T  30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.597 -0.081 8.00e-03 1.56e+04 1.03e+02
  ... (remaining 11751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.16: 16024
        4.16 -     8.32: 177
        8.32 -    12.48: 18
       12.48 -    16.64: 6
       16.64 -    20.80: 2
  Bond angle restraints: 16227
  Sorted by residual:
  angle pdb=" C3'  DC T  18 "
        pdb=" O3'  DC T  18 "
        pdb=" P    DA T  19 "
      ideal   model   delta    sigma   weight residual
     119.70  104.85   14.85 1.20e+00 6.94e-01 1.53e+02
  angle pdb=" C3'  DT T  20 "
        pdb=" O3'  DT T  20 "
        pdb=" P    DT T  21 "
      ideal   model   delta    sigma   weight residual
     119.70  105.74   13.96 1.20e+00 6.94e-01 1.35e+02
  angle pdb=" C3'  DA N 131 "
        pdb=" O3'  DA N 131 "
        pdb=" P    DA N 132 "
      ideal   model   delta    sigma   weight residual
     119.70  132.94  -13.24 1.20e+00 6.94e-01 1.22e+02
  angle pdb=" O3'  DG N 136 "
        pdb=" P    DC N 137 "
        pdb=" O5'  DC N 137 "
      ideal   model   delta    sigma   weight residual
     104.00  124.80  -20.80 1.90e+00 2.77e-01 1.20e+02
  angle pdb=" C2'  DC N 137 "
        pdb=" C1'  DC N 137 "
        pdb=" N1   DC N 137 "
      ideal   model   delta    sigma   weight residual
     114.30  100.28   14.02 1.40e+00 5.10e-01 1.00e+02
  ... (remaining 16222 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.16: 6532
       34.16 -    68.31: 360
       68.31 -   102.47: 16
      102.47 -   136.62: 1
      136.62 -   170.78: 2
  Dihedral angle restraints: 6911
    sinusoidal: 3280
      harmonic: 3631
  Sorted by residual:
  dihedral pdb=" C4'   G C 108 "
           pdb=" C3'   G C 108 "
           pdb=" C2'   G C 108 "
           pdb=" C1'   G C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -12.01   48.35     1      3.10e+00 1.04e-01 3.35e+02
  dihedral pdb=" O4'   G C 108 "
           pdb=" C2'   G C 108 "
           pdb=" C1'   G C 108 "
           pdb=" C3'   G C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.60  -27.95   53.54     3      3.80e+00 6.93e-02 1.44e+02
  dihedral pdb=" O4'   G C 108 "
           pdb=" C4'   G C 108 "
           pdb=" C3'   G C 108 "
           pdb=" C2'   G C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.15   -7.29  -27.86     1      4.00e+00 6.25e-02 6.96e+01
  ... (remaining 6908 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1720
       0.139 -    0.278: 32
       0.278 -    0.418: 4
       0.418 -    0.557: 31
       0.557 -    0.696: 13
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" P     A C 105 "
            pdb=" OP1   A C 105 "
            pdb=" OP2   A C 105 "
            pdb=" O5'   A C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.87   -0.70 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" P     G C 108 "
            pdb=" OP1   G C 108 "
            pdb=" OP2   G C 108 "
            pdb=" O5'   G C 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.86   -0.68 2.00e-01 2.50e+01 1.17e+01
  chirality pdb=" P     U C 107 "
            pdb=" OP1   U C 107 "
            pdb=" OP2   U C 107 "
            pdb=" O5'   U C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.84   -0.67 2.00e-01 2.50e+01 1.11e+01
  ... (remaining 1797 not shown)

  Planarity restraints: 1825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT N 135 "    0.034 2.00e-02 2.50e+03   1.68e-02 7.09e+00
        pdb=" N1   DT N 135 "   -0.037 2.00e-02 2.50e+03
        pdb=" C2   DT N 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DT N 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DT N 135 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DT N 135 "    0.012 2.00e-02 2.50e+03
        pdb=" O4   DT N 135 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DT N 135 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT N 135 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT N 135 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 159 "    0.017 2.00e-02 2.50e+03   1.60e-02 6.42e+00
        pdb=" CG  TRP B 159 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 159 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 159 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 159 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 159 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 159 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 159 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 159 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 159 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 320 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.63e+00
        pdb=" C   GLU B 320 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLU B 320 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP B 321 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1822 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 285
        2.68 -     3.23: 11044
        3.23 -     3.79: 18562
        3.79 -     4.34: 24480
        4.34 -     4.90: 38376
  Nonbonded interactions: 92747
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OD1 ASP A 843 "
            pdb=" NE2 GLN A 916 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   SER B 190 "
            pdb=" OG  SER B 193 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" N   LYS B  49 "
            pdb=" O   LYS B 131 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OD1 ASP A 876 "
            pdb=" NH1 ARG A 883 "
     model   vdw
     2.264 3.120
  ... (remaining 92742 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:             0.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.330
  Find NCS groups from input model:        0.050
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
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      :  0.007   0.180  11757  Z= 0.587
  Angle     :  1.050  20.795  16227  Z= 0.604
  Chirality :  0.100   0.696   1800
  Planarity :  0.004   0.042   1825
  Dihedral  : 18.380 170.778   4557
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.66 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.60 (0.25), residues: 1232
  helix:  1.59 (0.21), residues: 666
  sheet: -1.19 (0.56), residues: 80
  loop : -1.01 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 989 
 TYR   0.020   0.002   TYR A 954 
 PHE   0.028   0.002   PHE A 936 
 TRP   0.043   0.002   TRP B 159 
 HIS   0.013   0.001   HIS A 943 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00718 /  0.59 (11756)
  covalent geometry    : angle       1.04984 /  0.60 (16227)
  hydrogen bonds       : bond        0.15627 / 10.42 (  586)
  hydrogen bonds       : angle       6.37006 /  4.41 ( 1642)
  Misc. bond           : bond        0.01190 /  0.63 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  727 ASN cc_start: 0.7988 (m-40) cc_final: 0.7540 (m110)
REVERT: A  796 ASP cc_start: 0.8051 (m-30) cc_final: 0.7791 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0977
  time to fit residues: 25.8226
Evaluate side-chains
  128 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:   40.0000
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 550 GLN
A 642 ASN
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.148811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.115301 restraints weight = 20617.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.119194 restraints weight = 11030.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.121753 restraints weight = 7608.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.123443 restraints weight = 6096.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.124418 restraints weight = 5304.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  11757  Z= 0.243
  Angle     :  0.728   9.187  16227  Z= 0.386
  Chirality :  0.048   0.307   1800
  Planarity :  0.005   0.101   1825
  Dihedral  : 19.289 178.031   2142
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.11 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.34 (0.25), residues: 1232
  helix:  1.30 (0.20), residues: 679
  sheet: -1.05 (0.58), residues: 74
  loop : -1.09 (0.30), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 883 
 TYR   0.026   0.002   TYR A 496 
 PHE   0.032   0.002   PHE A 754 
 TRP   0.026   0.002   TRP B 159 
 HIS   0.008   0.001   HIS A1188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00537 /  0.24 (11756)
  covalent geometry    : angle       0.72795 /  0.39 (16227)
  hydrogen bonds       : bond        0.06325 /  4.30 (  586)
  hydrogen bonds       : angle       4.99135 /  3.51 ( 1642)
  Misc. bond           : bond        0.00106 /  0.06 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  533 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7143 (ptm160)
REVERT: A  796 ASP cc_start: 0.8086 (m-30) cc_final: 0.7801 (m-30)
REVERT: A  856 LYS cc_start: 0.7231 (mmmt) cc_final: 0.7002 (mmmt)
  outliers start: 17
  outliers final: 10
  residues processed: 154
  average time/residue: 0.0993
  time to fit residues: 22.8316
Evaluate side-chains
  150 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  909 THR
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 67 optimal weight:   50.0000
   chunk 58 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 63 optimal weight:    0.2980
   chunk 83 optimal weight:    6.9990
   chunk 38 optimal weight:    0.3980
   chunk 22 optimal weight:   10.0000
   overall best weight:    3.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 925 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 = 0.4119 r_free = 0.4119 target = 0.151444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.117915 restraints weight = 20620.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.121970 restraints weight = 10881.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.124661 restraints weight = 7467.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.126367 restraints weight = 5901.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.127272 restraints weight = 5131.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  11757  Z= 0.153
  Angle     :  0.641   8.034  16227  Z= 0.337
  Chirality :  0.044   0.309   1800
  Planarity :  0.004   0.054   1825
  Dihedral  : 19.105 175.694   2142
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.64 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1232
  helix:  1.53 (0.20), residues: 670
  sheet: -0.84 (0.59), residues: 74
  loop : -1.07 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 530 
 TYR   0.030   0.002   TYR A 496 
 PHE   0.026   0.002   PHE A 936 
 TRP   0.026   0.001   TRP B 159 
 HIS   0.006   0.001   HIS A1188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 (11756)
  covalent geometry    : angle       0.64076 /  0.34 (16227)
  hydrogen bonds       : bond        0.05093 /  3.51 (  586)
  hydrogen bonds       : angle       4.58838 /  3.23 ( 1642)
  Misc. bond           : bond        0.00086 /  0.05 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: B  228 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7979 (tt)
REVERT: B  321 TRP cc_start: 0.8100 (t60) cc_final: 0.7508 (t60)
REVERT: A  727 ASN cc_start: 0.7889 (m-40) cc_final: 0.7394 (m110)
REVERT: A  796 ASP cc_start: 0.8057 (m-30) cc_final: 0.7806 (m-30)
REVERT: A  856 LYS cc_start: 0.7297 (mmmt) cc_final: 0.6818 (mmmt)
REVERT: A 1160 ASN cc_start: 0.8917 (m-40) cc_final: 0.8692 (m-40)
  outliers start: 23
  outliers final: 14
  residues processed: 170
  average time/residue: 0.0977
  time to fit residues: 25.1792
Evaluate side-chains
  163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  172 MET
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 18 optimal weight:   50.0000
   chunk 69 optimal weight:   20.0000
   chunk 82 optimal weight:   10.0000
   chunk 114 optimal weight:   10.0000
   chunk 90 optimal weight:   20.0000
   chunk 65 optimal weight:    0.0870
   chunk 24 optimal weight:   10.0000
   overall best weight:    7.2168

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 459 ASN
A 628 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.147616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.113951 restraints weight = 20716.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.117814 restraints weight = 11134.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.120370 restraints weight = 7696.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.122010 restraints weight = 6163.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.122989 restraints weight = 5368.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  11757  Z= 0.235
  Angle     :  0.692   8.741  16227  Z= 0.363
  Chirality :  0.045   0.280   1800
  Planarity :  0.005   0.056   1825
  Dihedral  : 19.118 172.783   2142
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.27 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.31 (0.25), residues: 1232
  helix:  1.35 (0.20), residues: 675
  sheet: -1.26 (0.53), residues: 84
  loop : -1.18 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 533 
 TYR   0.027   0.002   TYR A 496 
 PHE   0.024   0.002   PHE B 132 
 TRP   0.031   0.002   TRP B 159 
 HIS   0.008   0.001   HIS A1188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00528 /  0.23 (11756)
  covalent geometry    : angle       0.69160 /  0.36 (16227)
  hydrogen bonds       : bond        0.05416 /  3.67 (  586)
  hydrogen bonds       : angle       4.75163 /  3.34 ( 1642)
  Misc. bond           : bond        0.00070 /  0.04 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: B  228 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8028 (tt)
REVERT: B  299 LEU cc_start: 0.8276 (tt) cc_final: 0.7735 (tp)
REVERT: B  321 TRP cc_start: 0.8157 (t60) cc_final: 0.7572 (t60)
REVERT: A  656 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9076 (tt)
REVERT: A  796 ASP cc_start: 0.8088 (m-30) cc_final: 0.7847 (m-30)
REVERT: A 1128 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7525 (ptmm)
REVERT: A 1160 ASN cc_start: 0.8962 (m-40) cc_final: 0.8545 (m110)
REVERT: A 1201 MET cc_start: 0.7668 (ttp) cc_final: 0.7371 (ttp)
  outliers start: 33
  outliers final: 22
  residues processed: 165
  average time/residue: 0.0944
  time to fit residues: 23.5985
Evaluate side-chains
  161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  400 GLU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 113 optimal weight:   40.0000
   chunk 104 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0010
   chunk 76 optimal weight:    6.9990
   chunk 94 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    4.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 925 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 = 0.4100 r_free = 0.4100 target = 0.149530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.115849 restraints weight = 20475.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119848 restraints weight = 11006.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.122457 restraints weight = 7571.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.124110 restraints weight = 6041.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.125039 restraints weight = 5266.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  11757  Z= 0.171
  Angle     :  0.659   9.433  16227  Z= 0.342
  Chirality :  0.044   0.288   1800
  Planarity :  0.004   0.043   1825
  Dihedral  : 19.008 170.740   2142
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.15 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.47 (0.25), residues: 1232
  helix:  1.49 (0.20), residues: 672
  sheet: -1.29 (0.51), residues: 84
  loop : -1.09 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.027   0.002   TYR A 496 
 PHE   0.025   0.002   PHE B 132 
 TRP   0.032   0.002   TRP B 159 
 HIS   0.006   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.17 (11756)
  covalent geometry    : angle       0.65938 /  0.34 (16227)
  hydrogen bonds       : bond        0.04993 /  3.44 (  586)
  hydrogen bonds       : angle       4.61463 /  3.24 ( 1642)
  Misc. bond           : bond        0.00070 /  0.04 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7999 (tt)
REVERT: B  299 LEU cc_start: 0.8223 (tt) cc_final: 0.7664 (tp)
REVERT: A  796 ASP cc_start: 0.8071 (m-30) cc_final: 0.7831 (m-30)
REVERT: A 1160 ASN cc_start: 0.8932 (m-40) cc_final: 0.8498 (m110)
REVERT: A 1201 MET cc_start: 0.7712 (ttp) cc_final: 0.7219 (ttp)
  outliers start: 29
  outliers final: 18
  residues processed: 168
  average time/residue: 0.0899
  time to fit residues: 23.3680
Evaluate side-chains
  155 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 74 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 98 optimal weight:    5.9990
   chunk 117 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0070
   overall best weight:    3.2004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  44 HIS
A 691 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.150388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.116740 restraints weight = 20651.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.120769 restraints weight = 11111.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.123417 restraints weight = 7656.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.125078 restraints weight = 6097.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.126001 restraints weight = 5303.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  11757  Z= 0.151
  Angle     :  0.651  10.221  16227  Z= 0.337
  Chirality :  0.044   0.292   1800
  Planarity :  0.004   0.047   1825
  Dihedral  : 18.981 168.556   2142
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.46 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.60 (0.25), residues: 1232
  helix:  1.53 (0.21), residues: 673
  sheet: -0.92 (0.57), residues: 74
  loop : -1.00 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 800 
 TYR   0.045   0.002   TYR B  29 
 PHE   0.024   0.001   PHE B 132 
 TRP   0.034   0.002   TRP B 159 
 HIS   0.012   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.15 (11756)
  covalent geometry    : angle       0.65134 /  0.34 (16227)
  hydrogen bonds       : bond        0.04749 /  3.25 (  586)
  hydrogen bonds       : angle       4.53858 /  3.19 ( 1642)
  Misc. bond           : bond        0.00067 /  0.04 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 HIS cc_start: 0.6644 (t70) cc_final: 0.6340 (t-90)
REVERT: B  228 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8004 (tt)
REVERT: A  656 ILE cc_start: 0.9284 (tp) cc_final: 0.9050 (tt)
REVERT: A  796 ASP cc_start: 0.8037 (m-30) cc_final: 0.7814 (m-30)
REVERT: A 1160 ASN cc_start: 0.8944 (m-40) cc_final: 0.8505 (m110)
REVERT: A 1201 MET cc_start: 0.7704 (ttp) cc_final: 0.7150 (ttp)
  outliers start: 25
  outliers final: 18
  residues processed: 168
  average time/residue: 0.0935
  time to fit residues: 23.9957
Evaluate side-chains
  162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 125 optimal weight:   50.0000
   chunk 111 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 112 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9990
   chunk 118 optimal weight:   40.0000
   chunk 109 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0570
   overall best weight:    3.2106

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 925 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 = 0.4118 r_free = 0.4118 target = 0.150954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.117376 restraints weight = 20502.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.121423 restraints weight = 11030.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.124071 restraints weight = 7588.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.125677 restraints weight = 6040.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.126558 restraints weight = 5267.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.101  11757  Z= 0.153
  Angle     :  0.656  14.994  16227  Z= 0.338
  Chirality :  0.044   0.299   1800
  Planarity :  0.004   0.042   1825
  Dihedral  : 18.941 168.342   2142
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.31 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.64 (0.25), residues: 1232
  helix:  1.54 (0.21), residues: 674
  sheet: -0.87 (0.57), residues: 74
  loop : -0.95 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1082 
 TYR   0.039   0.002   TYR B  29 
 PHE   0.035   0.002   PHE A 936 
 TRP   0.041   0.002   TRP B 159 
 HIS   0.007   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 (11756)
  covalent geometry    : angle       0.65599 /  0.34 (16227)
  hydrogen bonds       : bond        0.04629 /  3.16 (  586)
  hydrogen bonds       : angle       4.51925 /  3.18 ( 1642)
  Misc. bond           : bond        0.00061 /  0.03 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7974 (tt)
REVERT: B  296 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7498 (mmmt)
REVERT: A  656 ILE cc_start: 0.9271 (tp) cc_final: 0.9045 (tt)
REVERT: A  796 ASP cc_start: 0.8033 (m-30) cc_final: 0.7818 (m-30)
REVERT: A  926 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7762 (tm-30)
REVERT: A  936 PHE cc_start: 0.7439 (t80) cc_final: 0.7106 (t80)
REVERT: A 1160 ASN cc_start: 0.8954 (m-40) cc_final: 0.8514 (m110)
REVERT: A 1201 MET cc_start: 0.7736 (ttp) cc_final: 0.7161 (ttp)
  outliers start: 26
  outliers final: 22
  residues processed: 164
  average time/residue: 0.0975
  time to fit residues: 24.2780
Evaluate side-chains
  163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 126 optimal weight:   50.0000
   chunk 76 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 925 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 = 0.4163 r_free = 0.4163 target = 0.155295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.123787 restraints weight = 20447.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.127930 restraints weight = 11012.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.130509 restraints weight = 7480.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.132271 restraints weight = 5917.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.133328 restraints weight = 5100.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092  11757  Z= 0.132
  Angle     :  0.656  16.497  16227  Z= 0.335
  Chirality :  0.043   0.304   1800
  Planarity :  0.004   0.040   1825
  Dihedral  : 18.775 170.573   2142
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.78 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.80 (0.25), residues: 1232
  helix:  1.62 (0.20), residues: 669
  sheet: -0.81 (0.54), residues: 86
  loop : -0.74 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 292 
 TYR   0.032   0.002   TYR B  29 
 PHE   0.029   0.002   PHE B 132 
 TRP   0.049   0.002   TRP B 159 
 HIS   0.005   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 (11756)
  covalent geometry    : angle       0.65565 /  0.33 (16227)
  hydrogen bonds       : bond        0.04293 /  2.94 (  586)
  hydrogen bonds       : angle       4.42049 /  3.10 ( 1642)
  Misc. bond           : bond        0.00058 /  0.03 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.6793 (mpp80) cc_final: 0.6342 (mmt-90)
REVERT: B  292 ARG cc_start: 0.7462 (mmm-85) cc_final: 0.7251 (mmm-85)
REVERT: B  296 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7530 (mmmt)
REVERT: B  321 TRP cc_start: 0.7870 (t60) cc_final: 0.7366 (t60)
REVERT: A  926 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  936 PHE cc_start: 0.7416 (t80) cc_final: 0.7197 (t80)
REVERT: A 1201 MET cc_start: 0.7852 (ttp) cc_final: 0.7220 (ttp)
  outliers start: 24
  outliers final: 19
  residues processed: 169
  average time/residue: 0.0958
  time to fit residues: 24.2446
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1350 PHE
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 123 optimal weight:   50.0000
   chunk 81 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0270
   chunk 60 optimal weight:    8.9990
   chunk 109 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 36 optimal weight:    9.9990
   chunk 100 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    5.6046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.150051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.116588 restraints weight = 20286.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.120520 restraints weight = 10986.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.123133 restraints weight = 7596.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.124559 restraints weight = 6062.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.125705 restraints weight = 5341.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093  11757  Z= 0.197
  Angle     :  0.694  14.642  16227  Z= 0.355
  Chirality :  0.044   0.288   1800
  Planarity :  0.004   0.040   1825
  Dihedral  : 18.854 171.121   2142
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.81 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.64 (0.25), residues: 1232
  helix:  1.44 (0.20), residues: 675
  sheet: -0.85 (0.58), residues: 74
  loop : -0.79 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 906 
 TYR   0.030   0.002   TYR A 954 
 PHE   0.034   0.002   PHE B 132 
 TRP   0.043   0.002   TRP B 159 
 HIS   0.007   0.001   HIS A1163 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.20 (11756)
  covalent geometry    : angle       0.69379 /  0.35 (16227)
  hydrogen bonds       : bond        0.04794 /  3.22 (  586)
  hydrogen bonds       : angle       4.60481 /  3.23 ( 1642)
  Misc. bond           : bond        0.00046 /  0.02 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6670 (t-170)
REVERT: B  228 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8074 (tt)
REVERT: B  296 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7551 (mmmt)
REVERT: B  321 TRP cc_start: 0.7915 (t60) cc_final: 0.7457 (t60)
REVERT: A  461 MET cc_start: 0.6558 (mmm) cc_final: 0.6121 (mmm)
REVERT: A 1160 ASN cc_start: 0.8906 (m110) cc_final: 0.8513 (m110)
REVERT: A 1201 MET cc_start: 0.7923 (ttp) cc_final: 0.7214 (ttp)
  outliers start: 24
  outliers final: 19
  residues processed: 153
  average time/residue: 0.0963
  time to fit residues: 22.1067
Evaluate side-chains
  164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   44 HIS
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 125 optimal weight:   50.0000
   chunk 124 optimal weight:   50.0000
   chunk 117 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 94 optimal weight:   10.0000
   chunk 115 optimal weight:    0.2980
   chunk 80 optimal weight:    0.1980
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 925 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 = 0.4155 r_free = 0.4155 target = 0.154075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.120879 restraints weight = 20239.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.125044 restraints weight = 10703.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.127712 restraints weight = 7279.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.129522 restraints weight = 5759.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.130601 restraints weight = 4980.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  11757  Z= 0.131
  Angle     :  0.669  16.248  16227  Z= 0.337
  Chirality :  0.043   0.298   1800
  Planarity :  0.004   0.040   1825
  Dihedral  : 18.721 171.592   2142
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.09 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.80 (0.25), residues: 1232
  helix:  1.58 (0.20), residues: 670
  sheet: -0.68 (0.55), residues: 86
  loop : -0.72 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 292 
 TYR   0.025   0.002   TYR A 496 
 PHE   0.030   0.002   PHE B 132 
 TRP   0.040   0.002   TRP B 159 
 HIS   0.003   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 (11756)
  covalent geometry    : angle       0.66938 /  0.34 (16227)
  hydrogen bonds       : bond        0.04290 /  2.94 (  586)
  hydrogen bonds       : angle       4.43994 /  3.10 ( 1642)
  Misc. bond           : bond        0.00048 /  0.03 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.6816 (mpp80) cc_final: 0.6336 (mmt180)
REVERT: B  296 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7495 (mmmt)
REVERT: B  321 TRP cc_start: 0.7849 (t60) cc_final: 0.7431 (t60)
REVERT: A 1160 ASN cc_start: 0.8876 (m110) cc_final: 0.8665 (m-40)
REVERT: A 1201 MET cc_start: 0.7854 (ttp) cc_final: 0.7063 (ttp)
  outliers start: 20
  outliers final: 17
  residues processed: 159
  average time/residue: 0.1003
  time to fit residues: 23.7142
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   77 GLU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.0870
   chunk 79 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 85 optimal weight:    0.3980
   chunk 113 optimal weight:   40.0000
   chunk 119 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 86 optimal weight:    0.1980
   chunk 102 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.7362

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 925 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 = 0.4156 r_free = 0.4156 target = 0.154184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.120910 restraints weight = 20275.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.125065 restraints weight = 10675.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.127752 restraints weight = 7235.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.129577 restraints weight = 5727.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.130502 restraints weight = 4925.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11757  Z= 0.131
  Angle     :  0.660  15.916  16227  Z= 0.333
  Chirality :  0.043   0.295   1800
  Planarity :  0.004   0.049   1825
  Dihedral  : 18.690 171.185   2142
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.28 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.85 (0.25), residues: 1232
  helix:  1.64 (0.20), residues: 670
  sheet: -0.68 (0.55), residues: 86
  loop : -0.72 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 657 
 TYR   0.025   0.002   TYR A 496 
 PHE   0.030   0.001   PHE B 132 
 TRP   0.048   0.002   TRP B 259 
 HIS   0.013   0.001   HIS B  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 (11756)
  covalent geometry    : angle       0.65981 /  0.33 (16227)
  hydrogen bonds       : bond        0.04233 /  2.87 (  586)
  hydrogen bonds       : angle       4.39839 /  3.07 ( 1642)
  Misc. bond           : bond        0.00047 /  0.02 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1949.26 seconds
wall clock time: 34 minutes 38.58 seconds (2078.58 seconds total)