Starting phenix.real_space_refine
on Thu Sep 18 05:01:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ko9_62471/09_2025/9ko9_62471.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ko9_62471/09_2025/9ko9_62471.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ko9_62471/09_2025/9ko9_62471.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ko9_62471/09_2025/9ko9_62471.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ko9_62471/09_2025/9ko9_62471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ko9_62471/09_2025/9ko9_62471.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.050
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     114      5.49       5
     S      38      5.16       5
     C    8314      2.51       5
     N    2456      2.21       5
     O    2929      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13851
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1409, 11424
          Classifications: {'peptide': 1409}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 1370}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 2427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 2427
          Classifications: {'RNA': 114}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 12, 'rna3p_pur': 54, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 19, 'rna3p': 94}
  Time building chain proxies: 3.25, per 1000 atoms: 0.23
  Number of scatterers: 13851
  At special positions: 0
  Unit cell: (92.07, 105.09, 146.01, 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      38     16.00
     P     114     15.00
     O    2929      8.00
     N    2456      7.00
     C    8314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 534.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2690

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 9 sheets defined
      54.5% alpha, 13.1% beta
      30 base pairs and 62 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 82
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 113 through 117
      removed outlier: 4.059A  pdb=" N   GLY A 116 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 124
      removed outlier: 3.599A  pdb=" N   PHE A 121 " --> pdb=" O   GLU A 118 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A 123 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   CYS A 124 " --> pdb=" O   PHE A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 148
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.676A  pdb=" N   GLN A 158 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.952A  pdb=" N   PHE A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
    Processing helix  chain 'A' and resid 186 through 188
      No H-bonds generated for 'chain 'A' and resid 186 through 188'
    Processing helix  chain 'A' and resid 190 through 202
      removed outlier: 4.026A  pdb=" N   SER A 202 " --> pdb=" O   MET A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 205
      No H-bonds generated for 'chain 'A' and resid 203 through 205'
    Processing helix  chain 'A' and resid 207 through 218
      removed outlier: 4.033A  pdb=" N   LEU A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 233
    Processing helix  chain 'A' and resid 235 through 248
    Processing helix  chain 'A' and resid 250 through 259
      removed outlier: 3.502A  pdb=" N   LEU A 254 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 3.506A  pdb=" N   LYS A 264 " --> pdb=" O   PRO A 261 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASN A 265 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 280
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 314
    Processing helix  chain 'A' and resid 340 through 349
    Processing helix  chain 'A' and resid 350 through 361
      removed outlier: 3.562A  pdb=" N   ILE A 354 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.540A  pdb=" N   LYS A 366 " --> pdb=" O   PRO A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 376
      removed outlier: 3.748A  pdb=" N   LEU A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
    Processing helix  chain 'A' and resid 397 through 412
    Processing helix  chain 'A' and resid 433 through 443
    Processing helix  chain 'A' and resid 448 through 450
      No H-bonds generated for 'chain 'A' and resid 448 through 450'
    Processing helix  chain 'A' and resid 451 through 472
    Processing helix  chain 'A' and resid 473 through 478
      removed outlier: 3.536A  pdb=" N   ILE A 476 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLU A 478 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 505
    Processing helix  chain 'A' and resid 513 through 518
    Processing helix  chain 'A' and resid 525 through 541
    Processing helix  chain 'A' and resid 543 through 557
      removed outlier: 3.512A  pdb=" N   LEU A 547 " --> pdb=" O   SER A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 587
      removed outlier: 4.046A  pdb=" N   ASP A 567 " --> pdb=" O   ALA A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 597
      removed outlier: 4.175A  pdb=" N   PHE A 596 " --> pdb=" O   GLN A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 610
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 652 through 676
      removed outlier: 3.626A  pdb=" N   THR A 676 " --> pdb=" O   GLU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 704
      removed outlier: 4.180A  pdb=" N   SER A 697 " --> pdb=" O   GLN A 693 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLU A 702 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS A 704 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 728
      removed outlier: 3.656A  pdb=" N   LYS A 718 " --> pdb=" O   GLN A 714 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 719 " --> pdb=" O   LYS A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 790
      removed outlier: 3.894A  pdb=" N   LEU A 790 " --> pdb=" O   ASN A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 800 through 808
    Processing helix  chain 'A' and resid 812 through 826
    Processing helix  chain 'A' and resid 828 through 834
    Processing helix  chain 'A' and resid 835 through 838
    Processing helix  chain 'A' and resid 839 through 849
    Processing helix  chain 'A' and resid 850 through 852
      No H-bonds generated for 'chain 'A' and resid 850 through 852'
    Processing helix  chain 'A' and resid 856 through 867
    Processing helix  chain 'A' and resid 875 through 893
    Processing helix  chain 'A' and resid 893 through 899
    Processing helix  chain 'A' and resid 912 through 929
      removed outlier: 3.945A  pdb=" N   ARG A 921 " --> pdb=" O   SER A 917 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   LYS A 922 " --> pdb=" O   GLN A 918 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 923 " --> pdb=" O   ASP A 919 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 924 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 941 through 954
      removed outlier: 4.033A  pdb=" N   ALA A 945 " --> pdb=" O   ILE A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 957
      No H-bonds generated for 'chain 'A' and resid 955 through 957'
    Processing helix  chain 'A' and resid 972 through 984
      removed outlier: 3.826A  pdb=" N   GLN A 982 " --> pdb=" O   LYS A 978 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   MET A 984 " --> pdb=" O   ILE A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1007
    Processing helix  chain 'A' and resid 1045 through 1053
      removed outlier: 3.957A  pdb=" N   LEU A1049 " --> pdb=" O   ASP A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1088
      removed outlier: 3.527A  pdb=" N   PHE A1086 " --> pdb=" O   LEU A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1104
    Processing helix  chain 'A' and resid 1126 through 1131
    Processing helix  chain 'A' and resid 1132 through 1135
    Processing helix  chain 'A' and resid 1143 through 1147
      removed outlier: 3.606A  pdb=" N   GLY A1147 " --> pdb=" O   ASN A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1166
      removed outlier: 4.009A  pdb=" N   GLU A1160 " --> pdb=" O   PRO A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1167 through 1172
      removed outlier: 4.716A  pdb=" N   ASN A1172 " --> pdb=" O   SER A1168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1181
    Processing helix  chain 'A' and resid 1188 through 1198
      removed outlier: 3.821A  pdb=" N   LEU A1192 " --> pdb=" O   ASP A1188 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE A1197 " --> pdb=" O   ILE A1193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1269 through 1272
    Processing helix  chain 'A' and resid 1325 through 1332
    Processing helix  chain 'A' and resid 1338 through 1342
    Processing helix  chain 'A' and resid 1349 through 1361
      removed outlier: 3.771A  pdb=" N   GLN A1361 " --> pdb=" O   VAL A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1362 through 1366
    Processing helix  chain 'A' and resid 1368 through 1370
      No H-bonds generated for 'chain 'A' and resid 1368 through 1370'
    Processing helix  chain 'A' and resid 1392 through 1409
      removed outlier: 3.987A  pdb=" N   GLN A1409 " --> pdb=" O   VAL A1405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 904 through 910
      removed outlier: 6.785A  pdb=" N   ALA A  35 " --> pdb=" O   ASN A 989 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   VAL A  37 " --> pdb=" O   ILE A 991 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   ILE A1376 " --> pdb=" O   LEU A 990 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   GLN A1372 " --> pdb=" O   CYS A1387 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   CYS A1387 " --> pdb=" O   GLN A1372 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LYS A1383 " --> pdb=" O   ILE A1376 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   LEU A1378 " --> pdb=" O   THR A1381 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   THR A1381 " --> pdb=" O   LEU A1378 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 904 through 910
      removed outlier: 6.785A  pdb=" N   ALA A  35 " --> pdb=" O   ASN A 989 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   VAL A  37 " --> pdb=" O   ILE A 991 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   ILE A1376 " --> pdb=" O   LEU A 990 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339
    Processing sheet with id=AA4, first strand: chain 'A' and resid 754 through 757
      removed outlier: 3.527A  pdb=" N   ASP A 756 " --> pdb=" O   ILE A 779 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1215 through 1218
      removed outlier: 6.201A  pdb=" N   ASN A1110 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
      removed outlier: 8.612A  pdb=" N   ILE A1014 " --> pdb=" O   ASN A1110 " (cutoff:3.500A)
      removed outlier: 13.287A  pdb=" N   SER A1112 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
      removed outlier: 18.457A  pdb=" N   GLU A1012 " --> pdb=" O   SER A1112 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   MET A1243 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY A1013 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   LEU A1241 " --> pdb=" O   GLY A1013 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   PHE A1015 " --> pdb=" O   TYR A1239 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   TYR A1239 " --> pdb=" O   PHE A1015 " (cutoff:3.500A)
      removed outlier: 13.185A  pdb=" N   GLU A1017 " --> pdb=" O   ASP A1237 " (cutoff:3.500A)
      removed outlier: 15.055A  pdb=" N   ASP A1237 " --> pdb=" O   GLU A1017 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1040 through 1043
      removed outlier: 4.631A  pdb=" N   CYS A1029 " --> pdb=" O   VAL A1043 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1118
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1137 through 1142
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1260 through 1267
      removed outlier: 4.053A  pdb=" N   VAL A1253 " --> pdb=" O   ASP A1261 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   SER A1263 " --> pdb=" O   GLY A1251 " (cutoff:3.500A)
      removed outlier: 10.982A  pdb=" N   GLY A1251 " --> pdb=" O   SER A1263 " (cutoff:3.500A)
      removed outlier: 9.501A  pdb=" N   ASP A1265 " --> pdb=" O   CYS A1249 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   CYS A1249 " --> pdb=" O   ASP A1265 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1620 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      73 hydrogen bonds
      126 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      62 stacking parallelities
  Total time for adding SS restraints: 3.78

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3546
        1.33 -     1.46: 3460
        1.46 -     1.58: 7051
        1.58 -     1.70: 227
        1.70 -     1.82: 59
  Bond restraints: 14343
  Sorted by residual:
  bond pdb=" N   ALA A 972 "
       pdb=" CA  ALA A 972 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.016 1.29e-02 6.01e+03 1.57e+00
  bond pdb=" CB  GLU A 677 "
       pdb=" CG  GLU A 677 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.39e+00
  bond pdb=" CA  GLN A 292 "
       pdb=" CB  GLN A 292 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.28e+00
  bond pdb=" C3'   U B 122 "
       pdb=" O3'   U B 122 "
    ideal  model  delta    sigma   weight residual
    1.427  1.444 -0.017 1.50e-02 4.44e+03 1.26e+00
  bond pdb=" CB  LYS A 453 "
       pdb=" CG  LYS A 453 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.21e+00
  ... (remaining 14338 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 19751
        2.81 -     5.62: 126
        5.62 -     8.43: 16
        8.43 -    11.24: 1
       11.24 -    14.06: 2
  Bond angle restraints: 19896
  Sorted by residual:
  angle pdb=" CB  MET A 984 "
        pdb=" CG  MET A 984 "
        pdb=" SD  MET A 984 "
      ideal   model   delta    sigma   weight residual
     112.70  126.76  -14.06 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" CA  GLN A 292 "
        pdb=" CB  GLN A 292 "
        pdb=" CG  GLN A 292 "
      ideal   model   delta    sigma   weight residual
     114.10  122.22   -8.12 2.00e+00 2.50e-01 1.65e+01
  angle pdb=" CA  GLU A 677 "
        pdb=" CB  GLU A 677 "
        pdb=" CG  GLU A 677 "
      ideal   model   delta    sigma   weight residual
     114.10  121.25   -7.15 2.00e+00 2.50e-01 1.28e+01
  angle pdb=" N   GLN A 901 "
        pdb=" CA  GLN A 901 "
        pdb=" CB  GLN A 901 "
      ideal   model   delta    sigma   weight residual
     113.65  108.41    5.24 1.47e+00 4.63e-01 1.27e+01
  angle pdb=" C3'   U B 122 "
        pdb=" O3'   U B 122 "
        pdb=" P     U B 123 "
      ideal   model   delta    sigma   weight residual
     120.20  125.47   -5.27 1.50e+00 4.44e-01 1.23e+01
  ... (remaining 19891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 8414
       35.91 -    71.81: 409
       71.81 -   107.72: 38
      107.72 -   143.63: 4
      143.63 -   179.53: 5
  Dihedral angle restraints: 8870
    sinusoidal: 4721
      harmonic: 4149
  Sorted by residual:
  dihedral pdb=" O4'   U B  34 "
           pdb=" C1'   U B  34 "
           pdb=" N1    U B  34 "
           pdb=" C2    U B  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   20.47  179.53     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U B  58 "
           pdb=" C1'   U B  58 "
           pdb=" N1    U B  58 "
           pdb=" C2    U B  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   13.17 -173.17     1      1.50e+01 4.44e-03 8.50e+01
  dihedral pdb=" O4'   U B 112 "
           pdb=" C1'   U B 112 "
           pdb=" N1    U B 112 "
           pdb=" C2    U B 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    4.87 -164.87     1      1.50e+01 4.44e-03 8.39e+01
  ... (remaining 8867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1821
       0.041 -    0.082: 376
       0.082 -    0.124: 93
       0.124 -    0.165: 11
       0.165 -    0.206: 2
  Chirality restraints: 2303
  Sorted by residual:
  chirality pdb=" C1'   A B  42 "
            pdb=" O4'   A B  42 "
            pdb=" C2'   A B  42 "
            pdb=" N9    A B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.23    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C3'   C B  43 "
            pdb=" C4'   C B  43 "
            pdb=" O3'   C B  43 "
            pdb=" C2'   C B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.18 2.00e-01 2.50e+01 7.78e-01
  chirality pdb=" C3'   U B 122 "
            pdb=" C4'   U B 122 "
            pdb=" O3'   U B 122 "
            pdb=" C2'   U B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.59   -0.15 2.00e-01 2.50e+01 6.00e-01
  ... (remaining 2300 not shown)

  Planarity restraints: 2127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  99 "    0.032 2.00e-02 2.50e+03   1.38e-02 5.74e+00
        pdb=" N9    G B  99 "   -0.032 2.00e-02 2.50e+03
        pdb=" C8    G B  99 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G B  99 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G B  99 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  99 "    0.013 2.00e-02 2.50e+03
        pdb=" N1    G B  99 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B  99 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2    G B  99 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G B  99 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B  99 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 939 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 940 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 940 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 940 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 494 "    0.011 2.00e-02 2.50e+03   2.12e-02 4.47e+00
        pdb=" C   ASP A 494 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ASP A 494 "    0.014 2.00e-02 2.50e+03
        pdb=" N   SER A 495 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2124 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 489
        2.69 -     3.25: 13708
        3.25 -     3.80: 24332
        3.80 -     4.35: 32428
        4.35 -     4.90: 49260
  Nonbonded interactions: 120217
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 939 "
            pdb=" OG  SER A 943 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   ASN A 777 "
            pdb=" ND2 ASN A 777 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" OG  SER A1215 "
            pdb=" OP1   U B  24 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O2    C B  57 "
            pdb=" N6    A B  61 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OD1 ASN A 875 "
            pdb=" N   GLY A 876 "
     model   vdw
     2.205 3.120
  ... (remaining 120212 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.220
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.810
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
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      :  0.003   0.035  14343  Z= 0.123
  Angle     :  0.599  14.055  19896  Z= 0.305
  Chirality :  0.037   0.206   2303
  Planarity :  0.004   0.055   2127
  Dihedral  : 18.875 179.535   6180
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.54 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 16.15 %
    Favored  : 83.29 %
  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 aren not related in a simple way.
  whole:  0.36 (0.23), residues: 1407
  helix:  0.93 (0.20), residues: 662
  sheet:  0.47 (0.46), residues: 132
  loop : -0.51 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 361 
 TYR   0.014   0.001   TYR A 744 
 PHE   0.029   0.002   PHE A1068 
 TRP   0.017   0.001   TRP A 139 
 HIS   0.005   0.001   HIS A 944 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (14343)
  covalent geometry    : angle       0.59946 (19896)
  hydrogen bonds       : bond        0.14675 (  619)
  hydrogen bonds       : angle       5.81333 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.563 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3125 (tpp) cc_final: 0.2034 (tmm)
REVERT: A   40 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8106 (tpp)
REVERT: A   50 MET cc_start: 0.8574 (mmm) cc_final: 0.7954 (mmt)
REVERT: A  464 ASP cc_start: 0.7013 (t70) cc_final: 0.6717 (t0)
REVERT: A  491 MET cc_start: 0.7891 (mtm) cc_final: 0.7449 (mtt)
REVERT: A  494 ASP cc_start: 0.5893 (t0) cc_final: 0.5624 (t0)
REVERT: A  535 LYS cc_start: 0.6103 (ttpt) cc_final: 0.5596 (tptt)
REVERT: A  765 MET cc_start: 0.5524 (tpt) cc_final: 0.4774 (mmp)
REVERT: A  768 MET cc_start: 0.2295 (ttt) cc_final: 0.1823 (tmm)
REVERT: A  987 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6356 (mm-30)
REVERT: A 1012 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6838 (mt-10)
REVERT: A 1017 GLU cc_start: 0.7559 (pt0) cc_final: 0.7062 (pt0)
REVERT: A 1129 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5965 (mt-10)
REVERT: A 1394 MET cc_start: 0.6252 (pmm) cc_final: 0.6021 (ptt)
  outliers start: 7
  outliers final: 3
  residues processed: 117
  average time/residue: 0.7151
  time to fit residues: 90.9162
Evaluate side-chains
  101 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 MET
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue 1012 GLU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0040
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.0796

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

Flipped N/Q/H residues before XYZ refinement:
A1351 GLN
A1359 ASN
A1392 ASN
A1406 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.221702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.204983 restraints weight = 11221.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 0.46
r_work: 0.3805 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3569 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work: 0.3443 rms_B_bonded: 4.67 restraints_weight: 0.1250
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14343  Z= 0.172
  Angle     :  0.619  10.050  19896  Z= 0.321
  Chirality :  0.040   0.215   2303
  Planarity :  0.005   0.047   2127
  Dihedral  : 19.149 179.651   3294
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.97 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.08 %
    Favored  : 83.13 %
  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 aren not related in a simple way.
  whole:  0.36 (0.22), residues: 1407
  helix:  0.88 (0.20), residues: 670
  sheet:  0.44 (0.44), residues: 129
  loop : -0.44 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 361 
 TYR   0.015   0.002   TYR A1399 
 PHE   0.020   0.002   PHE A 160 
 TRP   0.016   0.001   TRP A 727 
 HIS   0.006   0.002   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (14343)
  covalent geometry    : angle       0.61934 (19896)
  hydrogen bonds       : bond        0.04131 (  619)
  hydrogen bonds       : angle       4.56559 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 100
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3540 (tpp) cc_final: 0.2207 (tmm)
REVERT: A  189 LYS cc_start: 0.1924 (OUTLIER) cc_final: 0.0711 (tmtt)
REVERT: A  238 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8364 (mttt)
REVERT: A  270 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7764 (mmtm)
REVERT: A  381 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8427 (mtt-85)
REVERT: A  464 ASP cc_start: 0.7432 (t70) cc_final: 0.7023 (t0)
REVERT: A  491 MET cc_start: 0.8242 (mtm) cc_final: 0.7846 (mtt)
REVERT: A  535 LYS cc_start: 0.5800 (ttpt) cc_final: 0.4998 (ttpp)
REVERT: A  671 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7257 (mt-10)
REVERT: A  693 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5768 (tt0)
REVERT: A  765 MET cc_start: 0.5329 (tpt) cc_final: 0.4224 (mmp)
REVERT: A  768 MET cc_start: 0.2427 (ttt) cc_final: 0.1752 (tmm)
REVERT: A  987 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6906 (mm-30)
REVERT: A 1017 GLU cc_start: 0.7948 (pt0) cc_final: 0.7433 (pt0)
REVERT: A 1129 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6587 (mt-10)
REVERT: A 1133 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6743 (m-30)
REVERT: A 1154 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7906 (m)
REVERT: A 1330 ASP cc_start: 0.6586 (m-30) cc_final: 0.6265 (m-30)
  outliers start: 35
  outliers final: 7
  residues processed: 125
  average time/residue: 0.6257
  time to fit residues: 86.0129
Evaluate side-chains
  106 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue 1133 ASP
Chi-restraints excluded: chain A residue 1154 THR
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 121 optimal weight:    0.4980
   chunk 130 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 134 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 106 optimal weight:   20.0000
   chunk 131 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 144 optimal weight:    5.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A1406 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.223952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.206679 restraints weight = 11292.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 0.46
r_work: 0.3835 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14343  Z= 0.130
  Angle     :  0.561   9.350  19896  Z= 0.292
  Chirality :  0.038   0.222   2303
  Planarity :  0.004   0.045   2127
  Dihedral  : 19.025 179.976   3288
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.76 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.92 %
    Favored  : 82.82 %
  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 aren not related in a simple way.
  whole:  0.45 (0.23), residues: 1407
  helix:  1.04 (0.20), residues: 664
  sheet:  0.07 (0.44), residues: 132
  loop : -0.39 (0.26), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 361 
 TYR   0.015   0.001   TYR A 184 
 PHE   0.014   0.001   PHE A 160 
 TRP   0.015   0.001   TRP A 727 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (14343)
  covalent geometry    : angle       0.56106 (19896)
  hydrogen bonds       : bond        0.03690 (  619)
  hydrogen bonds       : angle       4.29971 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 98
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3567 (tpp) cc_final: 0.2256 (tmm)
REVERT: A  157 ILE cc_start: 0.4122 (OUTLIER) cc_final: 0.3860 (mm)
REVERT: A  189 LYS cc_start: 0.1718 (OUTLIER) cc_final: 0.0755 (tmtt)
REVERT: A  238 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (mttt)
REVERT: A  270 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7807 (mmtm)
REVERT: A  368 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5136 (tp)
REVERT: A  381 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8236 (mtt-85)
REVERT: A  464 ASP cc_start: 0.7256 (t70) cc_final: 0.6919 (t0)
REVERT: A  491 MET cc_start: 0.8083 (mtp) cc_final: 0.7854 (mtt)
REVERT: A  535 LYS cc_start: 0.5821 (ttpt) cc_final: 0.4847 (tptm)
REVERT: A  671 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7198 (mt-10)
REVERT: A  765 MET cc_start: 0.5269 (tpt) cc_final: 0.4265 (mmp)
REVERT: A  768 MET cc_start: 0.2450 (ttt) cc_final: 0.1922 (tmm)
REVERT: A  907 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6730 (t70)
REVERT: A  987 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6801 (mm-30)
REVERT: A 1012 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7394 (mt-10)
REVERT: A 1017 GLU cc_start: 0.7744 (pt0) cc_final: 0.7183 (mt-10)
REVERT: A 1154 THR cc_start: 0.7834 (t) cc_final: 0.7550 (m)
REVERT: A 1184 GLU cc_start: 0.2142 (OUTLIER) cc_final: 0.1827 (tp30)
REVERT: A 1288 GLN cc_start: 0.7684 (mt0) cc_final: 0.7284 (tt0)
REVERT: A 1330 ASP cc_start: 0.6552 (m-30) cc_final: 0.6182 (m-30)
  outliers start: 41
  outliers final: 7
  residues processed: 130
  average time/residue: 0.6558
  time to fit residues: 93.2862
Evaluate side-chains
  106 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue 1012 GLU
Chi-restraints excluded: chain A residue 1184 GLU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 112 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1018 HIS
A1359 ASN
A1406 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.215698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.201032 restraints weight = 11234.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 0.44
r_work: 0.3776 rms_B_bonded: 1.20 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 2.20 restraints_weight: 0.2500
r_work: 0.3509 rms_B_bonded: 3.33 restraints_weight: 0.1250
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.079  14343  Z= 0.362
  Angle     :  0.772  13.102  19896  Z= 0.392
  Chirality :  0.049   0.222   2303
  Planarity :  0.006   0.057   2127
  Dihedral  : 19.387 179.162   3288
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.61 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 14.16 %
    Favored  : 81.70 %
  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 aren not related in a simple way.
  whole: -0.25 (0.22), residues: 1407
  helix:  0.31 (0.19), residues: 666
  sheet:  0.13 (0.44), residues: 123
  loop : -0.63 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 100 
 TYR   0.018   0.003   TYR A1399 
 PHE   0.023   0.003   PHE A  66 
 TRP   0.019   0.003   TRP A 727 
 HIS   0.008   0.003   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00785 (14343)
  covalent geometry    : angle       0.77194 (19896)
  hydrogen bonds       : bond        0.05039 (  619)
  hydrogen bonds       : angle       4.84470 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 99
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3583 (tpp) cc_final: 0.2380 (tmm)
REVERT: A   14 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.7145 (ttp-170)
REVERT: A  157 ILE cc_start: 0.4043 (OUTLIER) cc_final: 0.3778 (mm)
REVERT: A  189 LYS cc_start: 0.1726 (OUTLIER) cc_final: 0.0604 (tptp)
REVERT: A  270 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8051 (mttm)
REVERT: A  368 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5532 (pp)
REVERT: A  491 MET cc_start: 0.8340 (mtp) cc_final: 0.8037 (mtm)
REVERT: A  535 LYS cc_start: 0.6098 (ttpt) cc_final: 0.5071 (tptt)
REVERT: A  671 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7082 (mt-10)
REVERT: A  693 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5997 (tt0)
REVERT: A  700 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.6963 (mp)
REVERT: A  765 MET cc_start: 0.5867 (tpt) cc_final: 0.4480 (mmp)
REVERT: A  768 MET cc_start: 0.3311 (ttt) cc_final: 0.2744 (tmm)
REVERT: A  907 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7022 (t70)
REVERT: A  987 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6881 (mm-30)
REVERT: A 1012 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7319 (mt-10)
REVERT: A 1362 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6524 (mtt)
  outliers start: 52
  outliers final: 14
  residues processed: 139
  average time/residue: 0.6559
  time to fit residues: 99.7134
Evaluate side-chains
  119 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  484 ARG
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue 1012 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1362 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 144 optimal weight:    4.9990
   chunk 76 optimal weight:    9.9990
   chunk 134 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 142 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 139 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.221071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.208152 restraints weight = 11320.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 0.40
r_work: 0.3856 rms_B_bonded: 1.27 restraints_weight: 0.5000
r_work: 0.3658 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work: 0.3562 rms_B_bonded: 4.89 restraints_weight: 0.1250
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14343  Z= 0.147
  Angle     :  0.587   9.357  19896  Z= 0.304
  Chirality :  0.039   0.224   2303
  Planarity :  0.004   0.054   2127
  Dihedral  : 19.145 179.634   3288
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.11 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.27 %
    Favored  : 81.70 %
  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 aren not related in a simple way.
  whole:  0.03 (0.22), residues: 1407
  helix:  0.63 (0.20), residues: 675
  sheet: -0.05 (0.44), residues: 129
  loop : -0.56 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 279 
 TYR   0.013   0.002   TYR A 257 
 PHE   0.014   0.001   PHE A 952 
 TRP   0.017   0.001   TRP A 727 
 HIS   0.005   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (14343)
  covalent geometry    : angle       0.58739 (19896)
  hydrogen bonds       : bond        0.03799 (  619)
  hydrogen bonds       : angle       4.38137 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3645 (tpp) cc_final: 0.2423 (tmm)
REVERT: A  157 ILE cc_start: 0.4160 (OUTLIER) cc_final: 0.3931 (mm)
REVERT: A  189 LYS cc_start: 0.1624 (OUTLIER) cc_final: 0.0687 (tptp)
REVERT: A  270 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7945 (mttm)
REVERT: A  381 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8376 (mtt-85)
REVERT: A  384 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8067 (ttm170)
REVERT: A  464 ASP cc_start: 0.7138 (t70) cc_final: 0.6830 (t0)
REVERT: A  535 LYS cc_start: 0.6077 (ttpt) cc_final: 0.5067 (tptt)
REVERT: A  671 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7113 (mt-10)
REVERT: A  765 MET cc_start: 0.5598 (tpt) cc_final: 0.4512 (mmp)
REVERT: A  768 MET cc_start: 0.3589 (ttt) cc_final: 0.3176 (tmm)
REVERT: A  903 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7995 (m)
REVERT: A  907 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6876 (t70)
REVERT: A  908 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8352 (tt)
REVERT: A  987 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6928 (mm-30)
REVERT: A 1017 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7623 (pt0)
REVERT: A 1133 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6668 (m-30)
REVERT: A 1154 THR cc_start: 0.8038 (t) cc_final: 0.7735 (m)
REVERT: A 1330 ASP cc_start: 0.6739 (m-30) cc_final: 0.5677 (t0)
  outliers start: 38
  outliers final: 9
  residues processed: 125
  average time/residue: 0.6516
  time to fit residues: 89.0850
Evaluate side-chains
  112 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  384 ARG
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1017 GLU
Chi-restraints excluded: chain A residue 1133 ASP
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1300 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0030
   chunk 139 optimal weight:    4.9990
   chunk 140 optimal weight:    2.9990
   chunk 11 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    2.7998

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1359 ASN
A1406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.215820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.201209 restraints weight = 11231.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 0.46
r_work: 0.3859 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3807 rms_B_bonded: 2.25 restraints_weight: 0.2500
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076  14343  Z= 0.345
  Angle     :  0.749  14.309  19896  Z= 0.379
  Chirality :  0.048   0.221   2303
  Planarity :  0.006   0.058   2127
  Dihedral  : 19.343 179.702   3288
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.89 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 15.67 %
    Favored  : 80.83 %
  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 aren not related in a simple way.
  whole: -0.34 (0.22), residues: 1407
  helix:  0.25 (0.19), residues: 670
  sheet:  0.10 (0.45), residues: 122
  loop : -0.72 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  61 
 TYR   0.017   0.003   TYR A1399 
 PHE   0.019   0.003   PHE A  66 
 TRP   0.020   0.003   TRP A 727 
 HIS   0.009   0.002   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 (14343)
  covalent geometry    : angle       0.74864 (19896)
  hydrogen bonds       : bond        0.04778 (  619)
  hydrogen bonds       : angle       4.74417 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3848 (tpp) cc_final: 0.2472 (tmm)
REVERT: A  157 ILE cc_start: 0.3847 (OUTLIER) cc_final: 0.3633 (mm)
REVERT: A  189 LYS cc_start: 0.1735 (OUTLIER) cc_final: 0.0799 (tptp)
REVERT: A  270 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8094 (mttm)
REVERT: A  473 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (mt)
REVERT: A  535 LYS cc_start: 0.6228 (ttpt) cc_final: 0.5471 (tptt)
REVERT: A  671 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6862 (mt-10)
REVERT: A  693 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6089 (tt0)
REVERT: A  765 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.4864 (mmp)
REVERT: A  768 MET cc_start: 0.3669 (ttt) cc_final: 0.3326 (tmm)
REVERT: A  907 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6808 (t70)
REVERT: A  987 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6861 (mm-30)
REVERT: A 1133 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6350 (m-30)
REVERT: A 1369 ARG cc_start: 0.8015 (ttt180) cc_final: 0.7804 (ttp80)
REVERT: A 1394 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7140 (mmp)
  outliers start: 44
  outliers final: 17
  residues processed: 126
  average time/residue: 0.6443
  time to fit residues: 88.9214
Evaluate side-chains
  124 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  392 ARG
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1133 ASP
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1300 CYS
Chi-restraints excluded: chain A residue 1394 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 36 optimal weight:    0.0670
   chunk 112 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 130 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 131 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 135 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 GLN
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.222897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.205714 restraints weight = 11275.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 0.45
r_work: 0.3821 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work: 0.3490 rms_B_bonded: 4.34 restraints_weight: 0.1250
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14343  Z= 0.121
  Angle     :  0.585  13.550  19896  Z= 0.302
  Chirality :  0.038   0.225   2303
  Planarity :  0.004   0.055   2127
  Dihedral  : 19.076 179.287   3288
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.04 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.02 %
    Favored  : 80.51 %
  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 aren not related in a simple way.
  whole:  0.07 (0.22), residues: 1407
  helix:  0.69 (0.20), residues: 676
  sheet:  0.10 (0.45), residues: 115
  loop : -0.61 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 347 
 TYR   0.012   0.001   TYR A 184 
 PHE   0.013   0.001   PHE A 952 
 TRP   0.017   0.001   TRP A 727 
 HIS   0.003   0.001   HIS A 944 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (14343)
  covalent geometry    : angle       0.58512 (19896)
  hydrogen bonds       : bond        0.03626 (  619)
  hydrogen bonds       : angle       4.25140 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3711 (tpp) cc_final: 0.2281 (tmm)
REVERT: A  157 ILE cc_start: 0.4167 (OUTLIER) cc_final: 0.3937 (mm)
REVERT: A  189 LYS cc_start: 0.1358 (OUTLIER) cc_final: 0.0596 (tptp)
REVERT: A  270 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7892 (mttm)
REVERT: A  381 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8394 (mtt-85)
REVERT: A  464 ASP cc_start: 0.7182 (t70) cc_final: 0.6860 (t0)
REVERT: A  535 LYS cc_start: 0.5904 (ttpt) cc_final: 0.4759 (tptt)
REVERT: A  572 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6489 (tp-100)
REVERT: A  765 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.4069 (mmp)
REVERT: A  768 MET cc_start: 0.3641 (ttt) cc_final: 0.3127 (tmm)
REVERT: A  903 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8082 (m)
REVERT: A  907 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6932 (t70)
REVERT: A  987 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6937 (mm-30)
REVERT: A 1017 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7677 (pt0)
REVERT: A 1031 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7889 (mp)
REVERT: A 1154 THR cc_start: 0.8002 (t) cc_final: 0.7736 (m)
REVERT: A 1330 ASP cc_start: 0.6602 (m-30) cc_final: 0.5542 (t0)
REVERT: A 1369 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7766 (ttp80)
  outliers start: 31
  outliers final: 10
  residues processed: 117
  average time/residue: 0.6598
  time to fit residues: 84.5388
Evaluate side-chains
  112 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1017 GLU
Chi-restraints excluded: chain A residue 1031 ILE
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1300 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 143 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 ASN
A1406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.217066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.200445 restraints weight = 11147.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 0.48
r_work: 0.3764 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work: 0.3425 rms_B_bonded: 4.97 restraints_weight: 0.1250
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  14343  Z= 0.275
  Angle     :  0.695  13.271  19896  Z= 0.352
  Chirality :  0.044   0.223   2303
  Planarity :  0.005   0.058   2127
  Dihedral  : 19.196 179.984   3288
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.75 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.18 %
    Favored  : 80.03 %
  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 aren not related in a simple way.
  whole: -0.15 (0.22), residues: 1407
  helix:  0.48 (0.20), residues: 670
  sheet:  0.14 (0.46), residues: 111
  loop : -0.70 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  61 
 TYR   0.016   0.002   TYR A 257 
 PHE   0.018   0.002   PHE A  66 
 TRP   0.019   0.002   TRP A 727 
 HIS   0.007   0.002   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (14343)
  covalent geometry    : angle       0.69465 (19896)
  hydrogen bonds       : bond        0.04326 (  619)
  hydrogen bonds       : angle       4.52551 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 98
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3777 (tpp) cc_final: 0.2356 (tmm)
REVERT: A  157 ILE cc_start: 0.4057 (OUTLIER) cc_final: 0.3802 (mm)
REVERT: A  189 LYS cc_start: 0.1430 (OUTLIER) cc_final: 0.0636 (tmtm)
REVERT: A  270 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8074 (mttm)
REVERT: A  535 LYS cc_start: 0.6071 (ttpt) cc_final: 0.4942 (tptt)
REVERT: A  671 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7310 (mt-10)
REVERT: A  693 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.6095 (tt0)
REVERT: A  765 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.4405 (mmp)
REVERT: A  768 MET cc_start: 0.3860 (ttt) cc_final: 0.3391 (tmm)
REVERT: A  903 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8110 (m)
REVERT: A  907 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7142 (t70)
REVERT: A  968 PHE cc_start: 0.3182 (OUTLIER) cc_final: 0.2044 (m-80)
REVERT: A  987 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7112 (mm-30)
REVERT: A 1017 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7800 (pt0)
REVERT: A 1154 THR cc_start: 0.8150 (t) cc_final: 0.7850 (m)
REVERT: A 1369 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7927 (ttp80)
  outliers start: 35
  outliers final: 14
  residues processed: 122
  average time/residue: 0.6767
  time to fit residues: 90.3598
Evaluate side-chains
  117 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  392 ARG
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue  968 PHE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1017 GLU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1300 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 145 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 119 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 126 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 572 GLN
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.220812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.201124 restraints weight = 11280.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 0.50
r_work: 0.3779 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14343  Z= 0.153
  Angle     :  0.604  12.894  19896  Z= 0.310
  Chirality :  0.039   0.224   2303
  Planarity :  0.004   0.057   2127
  Dihedral  : 19.077 179.630   3288
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.75 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.38 %
    Favored  : 79.63 %
  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 aren not related in a simple way.
  whole:  0.03 (0.22), residues: 1407
  helix:  0.66 (0.20), residues: 675
  sheet:  0.03 (0.45), residues: 117
  loop : -0.62 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1088 
 TYR   0.019   0.002   TYR A 348 
 PHE   0.014   0.001   PHE A  66 
 TRP   0.018   0.001   TRP A 727 
 HIS   0.004   0.001   HIS A 944 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (14343)
  covalent geometry    : angle       0.60411 (19896)
  hydrogen bonds       : bond        0.03708 (  619)
  hydrogen bonds       : angle       4.29573 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3733 (tpp) cc_final: 0.2333 (tmm)
REVERT: A  157 ILE cc_start: 0.3902 (OUTLIER) cc_final: 0.3660 (mm)
REVERT: A  189 LYS cc_start: 0.1697 (OUTLIER) cc_final: 0.0854 (tmtm)
REVERT: A  270 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7969 (mttm)
REVERT: A  334 ASP cc_start: 0.8113 (t0) cc_final: 0.7861 (t0)
REVERT: A  470 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7485 (mmpt)
REVERT: A  535 LYS cc_start: 0.6002 (ttpt) cc_final: 0.4886 (tptt)
REVERT: A  572 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6504 (tp-100)
REVERT: A  765 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.4268 (mmp)
REVERT: A  768 MET cc_start: 0.3618 (ttt) cc_final: 0.3224 (tmm)
REVERT: A  907 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6973 (t70)
REVERT: A  968 PHE cc_start: 0.3085 (OUTLIER) cc_final: 0.2012 (m-80)
REVERT: A  987 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7066 (mm-30)
REVERT: A 1017 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7509 (pt0)
REVERT: A 1154 THR cc_start: 0.7958 (t) cc_final: 0.7691 (m)
REVERT: A 1330 ASP cc_start: 0.6609 (m-30) cc_final: 0.5568 (t0)
REVERT: A 1369 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7783 (ttp80)
  outliers start: 25
  outliers final: 10
  residues processed: 109
  average time/residue: 0.6818
  time to fit residues: 81.2063
Evaluate side-chains
  106 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue  968 PHE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1017 GLU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1300 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 149 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 105 optimal weight:    0.0970
   chunk 102 optimal weight:    1.9990
   chunk 125 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 GLN
A1406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.216504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.199672 restraints weight = 11201.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 0.47
r_work: 0.3900 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3850 rms_B_bonded: 2.33 restraints_weight: 0.2500
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069  14343  Z= 0.302
  Angle     :  0.719  12.550  19896  Z= 0.364
  Chirality :  0.046   0.222   2303
  Planarity :  0.005   0.058   2127
  Dihedral  : 19.234 179.975   3288
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.11 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.30 %
    Favored  : 79.55 %
  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 aren not related in a simple way.
  whole: -0.26 (0.22), residues: 1407
  helix:  0.39 (0.20), residues: 670
  sheet:  0.13 (0.45), residues: 122
  loop : -0.77 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  61 
 TYR   0.021   0.003   TYR A 348 
 PHE   0.020   0.003   PHE A  66 
 TRP   0.020   0.002   TRP A 727 
 HIS   0.008   0.002   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 (14343)
  covalent geometry    : angle       0.71906 (19896)
  hydrogen bonds       : bond        0.04530 (  619)
  hydrogen bonds       : angle       4.59669 ( 1746)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3900 (tpp) cc_final: 0.2526 (tmm)
REVERT: A  157 ILE cc_start: 0.3573 (OUTLIER) cc_final: 0.3354 (mm)
REVERT: A  189 LYS cc_start: 0.2023 (OUTLIER) cc_final: 0.1060 (tmtm)
REVERT: A  270 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7991 (mttm)
REVERT: A  470 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7583 (mmtt)
REVERT: A  535 LYS cc_start: 0.6279 (ttpt) cc_final: 0.5525 (tptt)
REVERT: A  572 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6425 (tp-100)
REVERT: A  671 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6890 (mt-10)
REVERT: A  693 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6072 (tt0)
REVERT: A  765 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.4776 (mmp)
REVERT: A  768 MET cc_start: 0.3637 (ttt) cc_final: 0.3386 (tmm)
REVERT: A  907 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6760 (t70)
REVERT: A  968 PHE cc_start: 0.3282 (OUTLIER) cc_final: 0.2221 (m-80)
REVERT: A  987 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6825 (mm-30)
REVERT: A 1154 THR cc_start: 0.7933 (t) cc_final: 0.7658 (m)
REVERT: A 1394 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6874 (tpt)
  outliers start: 27
  outliers final: 12
  residues processed: 109
  average time/residue: 0.6597
  time to fit residues: 78.7290
Evaluate side-chains
  112 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  452 ILE
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  646 THR
Chi-restraints excluded: chain A residue  671 GLU
Chi-restraints excluded: chain A residue  693 GLN
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue  907 ASP
Chi-restraints excluded: chain A residue  968 PHE
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1246 ASP
Chi-restraints excluded: chain A residue 1270 LEU
Chi-restraints excluded: chain A residue 1300 CYS
Chi-restraints excluded: chain A residue 1364 LEU
Chi-restraints excluded: chain A residue 1394 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   chunk 120 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1294 GLN
A1406 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.220081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.199439 restraints weight = 11302.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 0.56
r_work: 0.3919 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3870 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14343  Z= 0.160
  Angle     :  0.613  12.056  19896  Z= 0.314
  Chirality :  0.040   0.224   2303
  Planarity :  0.004   0.058   2127
  Dihedral  : 19.127 179.703   3288
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.61 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.62 %
    Favored  : 79.71 %
  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 aren not related in a simple way.
  whole: -0.09 (0.22), residues: 1407
  helix:  0.57 (0.20), residues: 672
  sheet: -0.02 (0.44), residues: 128
  loop : -0.70 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1088 
 TYR   0.024   0.002   TYR A 348 
 PHE   0.014   0.002   PHE A  66 
 TRP   0.018   0.002   TRP A 727 
 HIS   0.004   0.001   HIS A1105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (14343)
  covalent geometry    : angle       0.61301 (19896)
  hydrogen bonds       : bond        0.03778 (  619)
  hydrogen bonds       : angle       4.35267 ( 1746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4734.55 seconds
wall clock time: 81 minutes 44.75 seconds (4904.75 seconds total)