Starting phenix.real_space_refine
on Sat Sep 12 06:14:27 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ync_33958/09_2026/7ync_33958.cif"
  }
  resolution = 3.14
  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=   0.004
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      66      5.49       5
     S      57      5.16       5
     C    8497      2.51       5
     N    2467      2.21       5
     O    2761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13848
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1536, 12447
          Classifications: {'peptide': 1536}
          Link IDs: {'PTRANS': 84, 'TRANS': 1451}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 810
          Classifications: {'RNAv2': 38}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 19, 'rna3p': 18}
    Chain: "C"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 591
          Classifications: {'RNAv2': 28}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 3, 'rna3p': 24}
  Time building chain proxies: 2.69, per 1000 atoms: 0.19
  Number of scatterers: 13848
  At special positions: 0
  Unit cell: (94.16, 169.06, 133.75, 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      57     16.00
     P      66     15.00
     O    2761      8.00
     N    2467      7.00
     C    8497      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: 1.03
  Conformation dependent library (CDL) restraints added in 551.6 milliseconds
  

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2858

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 19 sheets defined
      21.4% alpha, 19.6% beta
      16 base pairs and 23 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 74
      removed outlier: 4.187A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 261 through 276
      removed outlier: 3.537A  pdb=" N   ASN A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 290
    Processing helix  chain 'A' and resid 291 through 294
      removed outlier: 4.078A  pdb=" N   ARG A 294 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 291 through 294'
    Processing helix  chain 'A' and resid 295 through 302
      removed outlier: 3.983A  pdb=" N   LEU A 298 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 296 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ALA A 300 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 301 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 295 through 302'
    Processing helix  chain 'A' and resid 328 through 336
    Processing helix  chain 'A' and resid 344 through 365
      removed outlier: 4.125A  pdb=" N   ASP A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.573A  pdb=" N   VAL A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 562 through 566
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.114A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 607
    Processing helix  chain 'A' and resid 642 through 649
    Processing helix  chain 'A' and resid 675 through 689
      removed outlier: 3.570A  pdb=" N   PHE A 679 " --> pdb=" O   LYS A 675 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 689 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 784
      removed outlier: 3.755A  pdb=" N   GLU A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 780 through 784'
    Processing helix  chain 'A' and resid 787 through 801
      removed outlier: 3.727A  pdb=" N   ALA A 791 " --> pdb=" O   GLU A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 813
      removed outlier: 3.582A  pdb=" N   ILE A 812 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY A 813 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 809 through 813'
    Processing helix  chain 'A' and resid 946 through 962
      removed outlier: 4.205A  pdb=" N   LEU A 950 " --> pdb=" O   PRO A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1105
      removed outlier: 3.552A  pdb=" N   ASP A1104 " --> pdb=" O   ASP A1101 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN A1105 " --> pdb=" O   ASN A1102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1101 through 1105'
    Processing helix  chain 'A' and resid 1231 through 1247
      removed outlier: 3.901A  pdb=" N   ARG A1235 " --> pdb=" O   PRO A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1264
      removed outlier: 3.526A  pdb=" N   GLU A1264 " --> pdb=" O   ARG A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1300 through 1305
      removed outlier: 3.608A  pdb=" N   LYS A1303 " --> pdb=" O   MET A1300 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A1304 " --> pdb=" O   ILE A1301 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   MET A1305 " --> pdb=" O   GLY A1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1300 through 1305'
    Processing helix  chain 'A' and resid 1343 through 1348
      removed outlier: 4.192A  pdb=" N   LEU A1347 " --> pdb=" O   PRO A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1427
      removed outlier: 3.856A  pdb=" N   ILE A1424 " --> pdb=" O   ALA A1420 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASP A1426 " --> pdb=" O   LYS A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1466 through 1476
    Processing helix  chain 'A' and resid 1515 through 1517
      No H-bonds generated for 'chain 'A' and resid 1515 through 1517'
    Processing helix  chain 'A' and resid 1518 through 1534
      removed outlier: 3.713A  pdb=" N   GLY A1524 " --> pdb=" O   PRO A1520 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE A1534 " --> pdb=" O   LEU A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1538 through 1548
    Processing helix  chain 'A' and resid 1575 through 1580
      removed outlier: 3.572A  pdb=" N   LYS A1580 " --> pdb=" O   TYR A1576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1588 through 1595
      removed outlier: 3.528A  pdb=" N   THR A1595 " --> pdb=" O   LYS A1591 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
      removed outlier: 3.746A  pdb=" N   PHE A 187 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER A 169 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44
    Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484
      removed outlier: 3.705A  pdb=" N   GLU A 403 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 576 " --> pdb=" O   CYS A 407 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   GLU A 409 " --> pdb=" O   ASN A 574 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   ASN A 574 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL A 411 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   MET A 572 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 504
      removed outlier: 3.770A  pdb=" N   GLU A 497 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ARG A 503 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 723 through 724
      removed outlier: 6.803A  pdb=" N   ASN A 629 " --> pdb=" O   ILE A 822 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ILE A 822 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   SER A 631 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU A 820 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLU A 633 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 659 through 663
    Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 744
      removed outlier: 3.646A  pdb=" N   PHE A 757 " --> pdb=" O   HIS A 741 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA A 743 " --> pdb=" O   LYS A 755 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LYS A 755 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 861 through 862
    Processing sheet with id=AB1, first strand: chain 'A' and resid 944 through 945
      removed outlier: 5.463A  pdb=" N   LEU A 891 " --> pdb=" O   ASN A1462 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945
    Processing sheet with id=AB3, first strand: chain 'A' and resid 908 through 909
      removed outlier: 4.459A  pdb=" N   ALA A 935 " --> pdb=" O   ASP A 909 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1001 through 1012
      removed outlier: 41.983A  pdb=" N   VAL A1121 " --> pdb=" O   ILE A1002 " (cutoff:3.500A)
      removed outlier: 35.885A  pdb=" N   LYS A1004 " --> pdb=" O   VAL A1121 " (cutoff:3.500A)
      removed outlier: 29.703A  pdb=" N   ASP A1123 " --> pdb=" O   LYS A1004 " (cutoff:3.500A)
      removed outlier: 23.731A  pdb=" N   SER A1006 " --> pdb=" O   ASP A1123 " (cutoff:3.500A)
      removed outlier: 17.731A  pdb=" N   ARG A1125 " --> pdb=" O   SER A1006 " (cutoff:3.500A)
      removed outlier: 14.195A  pdb=" N   THR A1008 " --> pdb=" O   ARG A1125 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   GLN A1127 " --> pdb=" O   THR A1008 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A1010 " --> pdb=" O   GLN A1127 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A1129 " --> pdb=" O   ARG A1010 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TRP A1120 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A1047 " --> pdb=" O   TRP A1120 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG A1122 " --> pdb=" O   ARG A1045 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG A1041 " --> pdb=" O   TYR A1126 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LYS A1128 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   VAL A1039 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   PHE A1130 " --> pdb=" O   MET A1037 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   MET A1037 " --> pdb=" O   PHE A1130 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   MET A1037 " --> pdb=" O   LYS A1144 " (cutoff:3.500A)
      removed outlier: 19.244A  pdb=" N   CYS A1143 " --> pdb=" O   LYS A1223 " (cutoff:3.500A)
      removed outlier: 14.148A  pdb=" N   LYS A1223 " --> pdb=" O   CYS A1143 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   GLU A1145 " --> pdb=" O   ASP A1221 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A1220 " --> pdb=" O   GLU A1007 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLU A1007 " --> pdb=" O   PHE A1220 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU A1222 " --> pdb=" O   PHE A1005 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   PHE A1005 " --> pdb=" O   LEU A1222 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   GLU A1224 " --> pdb=" O   GLN A1003 " (cutoff:3.500A)
      removed outlier: 8.641A  pdb=" N   GLN A1003 " --> pdb=" O   GLU A1224 " (cutoff:3.500A)
      removed outlier: 10.428A  pdb=" N   GLU A1226 " --> pdb=" O   HIS A1001 " (cutoff:3.500A)
      removed outlier: 9.592A  pdb=" N   HIS A1001 " --> pdb=" O   GLU A1226 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL A1275 " --> pdb=" O   GLY A 993 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   TYR A1276 " --> pdb=" O   ILE A1287 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE A1287 " --> pdb=" O   TYR A1276 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LYS A1278 " --> pdb=" O   GLU A1285 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A1283 " --> pdb=" O   ASN A1280 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL A1284 " --> pdb=" O   GLU A1227 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   GLU A1229 " --> pdb=" O   VAL A1284 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   ASP A1286 " --> pdb=" O   GLU A1229 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1070 through 1071
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1086
      removed outlier: 3.623A  pdb=" N   PHE A1083 " --> pdb=" O   LEU A1096 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1083 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A1085 " --> pdb=" O   PHE A1094 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A1094 " --> pdb=" O   VAL A1085 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1187 through 1188
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1200 through 1202
      removed outlier: 3.519A  pdb=" N   TYR A1209 " --> pdb=" O   CYS A1201 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1385 through 1387

    302 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      39 hydrogen bonds
      78 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      23 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4227
        1.34 -     1.45: 2635
        1.45 -     1.57: 7235
        1.57 -     1.69: 130
        1.69 -     1.81: 82
  Bond restraints: 14309
  Sorted by residual:
  bond pdb=" N   CYS A 965 "
       pdb=" CA  CYS A 965 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.22e-02 6.72e+03 7.79e+00
  bond pdb=" N   CYS A  86 "
       pdb=" CA  CYS A  86 "
    ideal  model  delta    sigma   weight residual
    1.452  1.491 -0.038 1.41e-02 5.03e+03 7.42e+00
  bond pdb=" N   CYS A1342 "
       pdb=" CA  CYS A1342 "
    ideal  model  delta    sigma   weight residual
    1.452  1.489 -0.037 1.41e-02 5.03e+03 6.98e+00
  bond pdb=" N   CYS A 711 "
       pdb=" CA  CYS A 711 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.31e-02 5.83e+03 6.08e+00
  bond pdb=" N   CYS A 708 "
       pdb=" CA  CYS A 708 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 1.37e-02 5.33e+03 5.87e+00
  ... (remaining 14304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 18551
        1.48 -     2.95: 804
        2.95 -     4.43: 175
        4.43 -     5.90: 57
        5.90 -     7.38: 9
  Bond angle restraints: 19596
  Sorted by residual:
  angle pdb=" N   ARG A1346 "
        pdb=" CA  ARG A1346 "
        pdb=" C   ARG A1346 "
      ideal   model   delta    sigma   weight residual
     114.04  108.63    5.41 1.24e+00 6.50e-01 1.91e+01
  angle pdb=" N   TYR A 866 "
        pdb=" CA  TYR A 866 "
        pdb=" C   TYR A 866 "
      ideal   model   delta    sigma   weight residual
     111.02  115.93   -4.91 1.25e+00 6.40e-01 1.54e+01
  angle pdb=" N   CYS A 123 "
        pdb=" CA  CYS A 123 "
        pdb=" C   CYS A 123 "
      ideal   model   delta    sigma   weight residual
     110.39  105.74    4.65 1.30e+00 5.92e-01 1.28e+01
  angle pdb=" CA  CYS A1312 "
        pdb=" C   CYS A1312 "
        pdb=" O   CYS A1312 "
      ideal   model   delta    sigma   weight residual
     122.64  118.52    4.12 1.25e+00 6.40e-01 1.09e+01
  angle pdb=" C   ALA A 919 "
        pdb=" N   ASP A 920 "
        pdb=" CA  ASP A 920 "
      ideal   model   delta    sigma   weight residual
     122.46  126.98   -4.52 1.41e+00 5.03e-01 1.03e+01
  ... (remaining 19591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.39: 8039
       31.39 -    62.79: 452
       62.79 -    94.18: 45
       94.18 -   125.58: 0
      125.58 -   156.97: 1
  Dihedral angle restraints: 8537
    sinusoidal: 4106
      harmonic: 4431
  Sorted by residual:
  dihedral pdb=" C4'   U C   7 "
           pdb=" C3'   U C   7 "
           pdb=" C2'   U C   7 "
           pdb=" C1'   U C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.70   74.04     1      3.10e+00 1.04e-01 7.24e+02
  dihedral pdb=" C4'   C B  15 "
           pdb=" C3'   C B  15 "
           pdb=" C2'   C B  15 "
           pdb=" C1'   C B  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.33   73.67     1      3.10e+00 1.04e-01 7.18e+02
  dihedral pdb=" C4'   A B  14 "
           pdb=" C3'   A B  14 "
           pdb=" C2'   A B  14 "
           pdb=" C1'   A B  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.29   73.63     1      3.10e+00 1.04e-01 7.17e+02
  ... (remaining 8534 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1716
       0.063 -    0.126: 245
       0.126 -    0.189: 27
       0.189 -    0.251: 74
       0.251 -    0.314: 37
  Chirality restraints: 2099
  Sorted by residual:
  chirality pdb=" P     G B -13 "
            pdb=" OP1   G B -13 "
            pdb=" OP2   G B -13 "
            pdb=" O5'   G B -13 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.49   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" C3'   A B   5 "
            pdb=" C4'   A B   5 "
            pdb=" O3'   A B   5 "
            pdb=" C2'   A B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.81    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" C3'   U C   7 "
            pdb=" C4'   U C   7 "
            pdb=" O3'   U C   7 "
            pdb=" C2'   U C   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.80    0.30 2.00e-01 2.50e+01 2.20e+00
  ... (remaining 2096 not shown)

  Planarity restraints: 2318
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 435 "    0.051 5.00e-02 4.00e+02   7.74e-02 9.59e+00
        pdb=" N   PRO A 436 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 436 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 436 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 863 "   -0.040 5.00e-02 4.00e+02   6.04e-02 5.83e+00
        pdb=" N   PRO A 864 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 636 "   -0.039 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO A 637 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 637 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 637 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 2315 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 408
        2.68 -     3.24: 11818
        3.24 -     3.79: 20054
        3.79 -     4.35: 27001
        4.35 -     4.90: 45936
  Nonbonded interactions: 105217
  Sorted by model distance:
  nonbonded pdb=" O2'   A B  11 "
            pdb=" O4'   C B  12 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OE1 GLU A  70 "
            pdb=" NH2 ARG A 104 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   ARG A 330 "
            pdb=" OG1 THR A 334 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER A 180 "
            pdb=" OG  SER A 180 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NH2 ARG A 917 "
            pdb=" O   GLU A 922 "
     model   vdw
     2.308 3.120
  ... (remaining 105212 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:             2.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.380
  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:             0.010
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
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   0.040  14309  Z= 0.166
  Angle     :  0.753   7.377  19596  Z= 0.410
  Chirality :  0.070   0.314   2099
  Planarity :  0.006   0.077   2318
  Dihedral  : 18.254 156.972   5679
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.55 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.94 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.51 (0.17), residues: 1526
  helix: -2.16 (0.24), residues: 293
  sheet: -1.75 (0.29), residues: 267
  loop : -3.90 (0.14), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 967 
 TYR   0.010   0.001   TYR A 313 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.035   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A 691 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.17 (14309)
  covalent geometry    : angle       0.75344 /  0.41 (19596)
  hydrogen bonds       : bond        0.19880 / 12.45 (  335)
  hydrogen bonds       : angle       7.10924 /  4.99 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A  393 ARG cc_start: 0.7549 (mpp80) cc_final: 0.7202 (ptt-90)
REVERT: A  437 ASP cc_start: 0.7376 (p0) cc_final: 0.7173 (t0)
REVERT: A  577 TYR cc_start: 0.8005 (p90) cc_final: 0.7725 (p90)
REVERT: A  621 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7647 (mmt-90)
REVERT: A  634 MET cc_start: 0.8421 (mtt) cc_final: 0.8206 (mtm)
  outliers start: 14
  outliers final: 9
  residues processed: 145
  average time/residue: 0.1510
  time to fit residues: 29.7681
Evaluate side-chains
  98 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  621 ARG
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  965 CYS
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1590 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    0.0670
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.9560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 HIS
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 ASN
A 306 HIS
A 456 GLN
A 464 ASN
A 531 GLN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 ASN
A1098 HIS
A1113 ASN
A1127 GLN
A1313 HIS
A1483 HIS
A1590 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.133786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.099858 restraints weight = 19357.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.30
r_work: 0.3086 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14309  Z= 0.171
  Angle     :  0.943  13.872  19596  Z= 0.429
  Chirality :  0.090   1.069   2099
  Planarity :  0.006   0.070   2318
  Dihedral  : 14.394 151.365   2485
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.24 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.56 (0.18), residues: 1526
  helix: -0.48 (0.30), residues: 296
  sheet: -1.26 (0.31), residues: 263
  loop : -3.56 (0.15), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1356 
 TYR   0.008   0.001   TYR A1276 
 PHE   0.013   0.001   PHE A 187 
 TRP   0.026   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.17 (14309)
  covalent geometry    : angle       0.94292 /  0.43 (19596)
  hydrogen bonds       : bond        0.04827 /  3.21 (  335)
  hydrogen bonds       : angle       4.81775 /  3.36 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   86 CYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7450 (p)
REVERT: A  314 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8453 (pt)
REVERT: A  393 ARG cc_start: 0.7788 (mpp80) cc_final: 0.6987 (ptt-90)
REVERT: A  437 ASP cc_start: 0.7578 (p0) cc_final: 0.7281 (t0)
REVERT: A  634 MET cc_start: 0.8709 (mtt) cc_final: 0.8484 (mtt)
REVERT: A 1211 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6543 (tmm)
  outliers start: 27
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1179
  time to fit residues: 19.7226
Evaluate side-chains
  109 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 121 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 134 optimal weight:    0.3980
   chunk 54 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 156 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 ASN
A 587 GLN
A1113 ASN
A1313 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.132845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.099224 restraints weight = 19552.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.50
r_work: 0.3063 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14309  Z= 0.159
  Angle     :  0.812  11.050  19596  Z= 0.381
  Chirality :  0.076   0.864   2099
  Planarity :  0.005   0.067   2318
  Dihedral  : 14.610 174.920   2473
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.43 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.19), residues: 1526
  helix:  0.35 (0.31), residues: 303
  sheet: -0.94 (0.31), residues: 263
  loop : -3.37 (0.16), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.010   0.001   TYR A1276 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.025   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 (14309)
  covalent geometry    : angle       0.81190 /  0.38 (19596)
  hydrogen bonds       : bond        0.04257 /  2.81 (  335)
  hydrogen bonds       : angle       4.36325 /  3.05 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8569 (pt)
REVERT: A  393 ARG cc_start: 0.7842 (mpp80) cc_final: 0.6997 (ptt-90)
REVERT: A  634 MET cc_start: 0.8730 (mtt) cc_final: 0.8491 (mtp)
REVERT: A 1082 TYR cc_start: 0.7247 (t80) cc_final: 0.6850 (m-80)
REVERT: A 1211 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6675 (tmm)
  outliers start: 36
  outliers final: 22
  residues processed: 121
  average time/residue: 0.1121
  time to fit residues: 19.9559
Evaluate side-chains
  111 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 112 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN
A1113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.133579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.099904 restraints weight = 19478.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.49
r_work: 0.3074 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14309  Z= 0.146
  Angle     :  0.793  14.905  19596  Z= 0.366
  Chirality :  0.073   0.798   2099
  Planarity :  0.005   0.070   2318
  Dihedral  : 14.287 173.551   2472
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.62 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.20), residues: 1526
  helix:  0.87 (0.32), residues: 303
  sheet: -0.85 (0.31), residues: 268
  loop : -3.18 (0.16), residues: 955

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A1276 
 PHE   0.012   0.001   PHE A 747 
 TRP   0.022   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 (14309)
  covalent geometry    : angle       0.79344 /  0.37 (19596)
  hydrogen bonds       : bond        0.03755 /  2.47 (  335)
  hydrogen bonds       : angle       4.19377 /  2.93 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 87
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8577 (pt)
REVERT: A  634 MET cc_start: 0.8708 (mtt) cc_final: 0.8465 (mtp)
REVERT: A 1211 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.6486 (tmm)
REVERT: A 1260 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.7754 (ttt-90)
  outliers start: 32
  outliers final: 23
  residues processed: 111
  average time/residue: 0.1239
  time to fit residues: 20.3341
Evaluate side-chains
  109 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue   43 HIS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 143 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 90 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN
A1113 ASN
A1337 HIS
A1428 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.127513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.094768 restraints weight = 19820.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.18
r_work: 0.2963 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  14309  Z= 0.255
  Angle     :  0.917  15.199  19596  Z= 0.431
  Chirality :  0.088   1.231   2099
  Planarity :  0.006   0.070   2318
  Dihedral  : 14.344 160.758   2472
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.30 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.62 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.20), residues: 1526
  helix:  0.74 (0.32), residues: 311
  sheet: -0.81 (0.31), residues: 286
  loop : -3.21 (0.17), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 444 
 TYR   0.012   0.002   TYR A1276 
 PHE   0.017   0.002   PHE A1584 
 TRP   0.026   0.002   TRP A1600 
 HIS   0.008   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00613 /  0.25 (14309)
  covalent geometry    : angle       0.91712 /  0.43 (19596)
  hydrogen bonds       : bond        0.05251 /  3.45 (  335)
  hydrogen bonds       : angle       4.40164 /  3.09 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 79
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8772 (pt)
REVERT: A  393 ARG cc_start: 0.7772 (mpp80) cc_final: 0.7015 (ptt-90)
REVERT: A  634 MET cc_start: 0.8805 (mtt) cc_final: 0.8546 (mtp)
REVERT: A 1211 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7137 (tmm)
REVERT: A 1260 ARG cc_start: 0.8442 (ttp-170) cc_final: 0.7774 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.8078 (mttm) cc_final: 0.7663 (mtmm)
REVERT: A 1300 MET cc_start: 0.8737 (mtm) cc_final: 0.8490 (mtp)
REVERT: A 1485 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8935 (pt)
  outliers start: 43
  outliers final: 31
  residues processed: 114
  average time/residue: 0.1263
  time to fit residues: 21.2640
Evaluate side-chains
  112 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 139 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 141 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 121 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 ASN
A 587 GLN
A1113 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.132794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.100500 restraints weight = 19460.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.16
r_work: 0.3052 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14309  Z= 0.137
  Angle     :  0.778  14.232  19596  Z= 0.361
  Chirality :  0.072   0.813   2099
  Planarity :  0.005   0.067   2318
  Dihedral  : 14.364 171.421   2472
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.07 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.21), residues: 1526
  helix:  1.08 (0.32), residues: 305
  sheet: -0.67 (0.31), residues: 278
  loop : -3.02 (0.17), residues: 943

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A1276 
 PHE   0.012   0.001   PHE A 747 
 TRP   0.023   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 (14309)
  covalent geometry    : angle       0.77840 /  0.36 (19596)
  hydrogen bonds       : bond        0.03675 /  2.43 (  335)
  hydrogen bonds       : angle       4.18896 /  2.92 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 85
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8676 (pt)
REVERT: A  393 ARG cc_start: 0.7785 (mpp80) cc_final: 0.7028 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7108 (tp30)
REVERT: A  634 MET cc_start: 0.8690 (mtt) cc_final: 0.8456 (mtp)
REVERT: A 1113 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5730 (t0)
REVERT: A 1211 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.6669 (tmm)
REVERT: A 1260 ARG cc_start: 0.8412 (ttp-170) cc_final: 0.7734 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.7928 (mttm) cc_final: 0.7504 (mtmm)
REVERT: A 1300 MET cc_start: 0.8688 (mtm) cc_final: 0.8460 (mtp)
  outliers start: 39
  outliers final: 29
  residues processed: 116
  average time/residue: 0.1270
  time to fit residues: 21.8253
Evaluate side-chains
  110 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1113 ASN
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 127 optimal weight:    5.9990
   chunk 118 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 112 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN
A 691 HIS
A1279 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.127276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.094626 restraints weight = 19642.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.17
r_work: 0.2960 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  14309  Z= 0.254
  Angle     :  0.907  14.200  19596  Z= 0.427
  Chirality :  0.086   1.198   2099
  Planarity :  0.006   0.073   2318
  Dihedral  : 14.329 162.374   2472
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.44 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.21), residues: 1526
  helix:  0.96 (0.32), residues: 306
  sheet: -0.40 (0.32), residues: 274
  loop : -3.12 (0.17), residues: 946

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 108 
 TYR   0.014   0.002   TYR A1276 
 PHE   0.017   0.002   PHE A 528 
 TRP   0.024   0.002   TRP A1600 
 HIS   0.010   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00611 /  0.25 (14309)
  covalent geometry    : angle       0.90695 /  0.43 (19596)
  hydrogen bonds       : bond        0.05224 /  3.43 (  335)
  hydrogen bonds       : angle       4.32557 /  3.04 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 78
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8769 (pt)
REVERT: A  382 PHE cc_start: 0.8026 (t80) cc_final: 0.7802 (t80)
REVERT: A  393 ARG cc_start: 0.7770 (mpp80) cc_final: 0.7054 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7120 (tp30)
REVERT: A  634 MET cc_start: 0.8798 (mtt) cc_final: 0.8536 (mtp)
REVERT: A 1211 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7135 (tmm)
REVERT: A 1260 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7744 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.8150 (mttm) cc_final: 0.7715 (mtmm)
REVERT: A 1300 MET cc_start: 0.8761 (mtm) cc_final: 0.8522 (mtp)
REVERT: A 1485 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8945 (pt)
  outliers start: 43
  outliers final: 36
  residues processed: 113
  average time/residue: 0.1296
  time to fit residues: 21.6868
Evaluate side-chains
  114 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 75
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 146 optimal weight:    0.8980
   chunk 127 optimal weight:    5.9990
   chunk 157 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 141 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.131472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.099059 restraints weight = 19470.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.18
r_work: 0.3027 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14309  Z= 0.154
  Angle     :  0.794  13.442  19596  Z= 0.369
  Chirality :  0.074   0.883   2099
  Planarity :  0.005   0.069   2318
  Dihedral  : 14.388 169.382   2472
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.81 %
    Favored  : 89.19 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.59 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.21), residues: 1526
  helix:  1.10 (0.32), residues: 306
  sheet: -0.33 (0.32), residues: 267
  loop : -3.00 (0.17), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 108 
 TYR   0.010   0.001   TYR A 591 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.025   0.001   TRP A1600 
 HIS   0.006   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 (14309)
  covalent geometry    : angle       0.79381 /  0.37 (19596)
  hydrogen bonds       : bond        0.03879 /  2.57 (  335)
  hydrogen bonds       : angle       4.17447 /  2.92 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 87
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8725 (pt)
REVERT: A  393 ARG cc_start: 0.7754 (mpp80) cc_final: 0.7046 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7135 (tp30)
REVERT: A  634 MET cc_start: 0.8713 (mtt) cc_final: 0.8463 (mtp)
REVERT: A 1211 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.6747 (tmm)
REVERT: A 1260 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.7756 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.8054 (mttm) cc_final: 0.7635 (mtmm)
REVERT: A 1300 MET cc_start: 0.8711 (mtm) cc_final: 0.8479 (mtp)
  outliers start: 42
  outliers final: 34
  residues processed: 122
  average time/residue: 0.1181
  time to fit residues: 21.6210
Evaluate side-chains
  117 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 81
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 155 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 156 optimal weight:    6.9990
   chunk 149 optimal weight:    2.9990
   chunk 130 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.131280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.100087 restraints weight = 19505.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.29
r_work: 0.3057 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14309  Z= 0.208
  Angle     :  0.855  18.043  19596  Z= 0.398
  Chirality :  0.080   1.043   2099
  Planarity :  0.005   0.076   2318
  Dihedral  : 14.335 166.649   2472
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.91 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.34 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.21), residues: 1526
  helix:  1.05 (0.32), residues: 306
  sheet: -0.29 (0.32), residues: 274
  loop : -3.01 (0.17), residues: 946

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 108 
 TYR   0.011   0.001   TYR A1276 
 PHE   0.014   0.002   PHE A 776 
 TRP   0.024   0.001   TRP A1600 
 HIS   0.007   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.21 (14309)
  covalent geometry    : angle       0.85458 /  0.40 (19596)
  hydrogen bonds       : bond        0.04571 /  3.01 (  335)
  hydrogen bonds       : angle       4.20441 /  2.95 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 84
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8901 (pt)
REVERT: A  382 PHE cc_start: 0.7984 (t80) cc_final: 0.7753 (t80)
REVERT: A  393 ARG cc_start: 0.7764 (mpp80) cc_final: 0.7137 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7077 (tp30)
REVERT: A  634 MET cc_start: 0.8716 (mtt) cc_final: 0.8447 (mtp)
REVERT: A 1211 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6835 (tmm)
REVERT: A 1260 ARG cc_start: 0.8416 (ttp-170) cc_final: 0.7846 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.8073 (mttm) cc_final: 0.7665 (mtmm)
REVERT: A 1300 MET cc_start: 0.8747 (mtm) cc_final: 0.8537 (mtp)
  outliers start: 39
  outliers final: 35
  residues processed: 115
  average time/residue: 0.1237
  time to fit residues: 21.0526
Evaluate side-chains
  122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 85
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0670
   chunk 19 optimal weight:    0.6980
   chunk 96 optimal weight:    0.1980
   chunk 107 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.7920

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.133816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.100971 restraints weight = 19402.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.41
r_work: 0.3081 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14309  Z= 0.136
  Angle     :  0.764  17.813  19596  Z= 0.352
  Chirality :  0.069   0.777   2099
  Planarity :  0.005   0.077   2318
  Dihedral  : 14.311 173.882   2472
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.26 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.21), residues: 1526
  helix:  1.24 (0.32), residues: 307
  sheet: -0.35 (0.32), residues: 269
  loop : -2.89 (0.17), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 108 
 TYR   0.009   0.001   TYR A1276 
 PHE   0.012   0.001   PHE A 776 
 TRP   0.024   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 (14309)
  covalent geometry    : angle       0.76436 /  0.35 (19596)
  hydrogen bonds       : bond        0.03486 /  2.30 (  335)
  hydrogen bonds       : angle       4.02395 /  2.81 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 93
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8623 (pt)
REVERT: A  340 LYS cc_start: 0.8110 (mptt) cc_final: 0.7656 (tptp)
REVERT: A  393 ARG cc_start: 0.7719 (mpp80) cc_final: 0.7059 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7100 (tp30)
REVERT: A  634 MET cc_start: 0.8665 (mtt) cc_final: 0.8404 (mtp)
REVERT: A  692 MET cc_start: 0.8726 (tpp) cc_final: 0.8185 (tpt)
REVERT: A 1120 TRP cc_start: 0.7069 (m100) cc_final: 0.6374 (m100)
REVERT: A 1211 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6530 (tmm)
REVERT: A 1260 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7669 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.7995 (mttm) cc_final: 0.7559 (mtmm)
REVERT: A 1300 MET cc_start: 0.8666 (mtm) cc_final: 0.8431 (mtp)
  outliers start: 38
  outliers final: 31
  residues processed: 123
  average time/residue: 0.1265
  time to fit residues: 22.8132
Evaluate side-chains
  119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 86
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  708 CYS
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1082 TYR
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0980
   chunk 103 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 115 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.132028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.099658 restraints weight = 19402.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.17
r_work: 0.3037 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14309  Z= 0.157
  Angle     :  0.792  17.802  19596  Z= 0.367
  Chirality :  0.072   0.792   2099
  Planarity :  0.005   0.075   2318
  Dihedral  : 14.260 170.572   2472
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.34 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.71 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.21), residues: 1526
  helix:  1.20 (0.32), residues: 313
  sheet: -0.28 (0.32), residues: 270
  loop : -2.92 (0.17), residues: 943

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 108 
 TYR   0.009   0.001   TYR A1276 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.024   0.001   TRP A1600 
 HIS   0.006   0.001   HIS A1149 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.16 (14309)
  covalent geometry    : angle       0.79246 /  0.37 (19596)
  hydrogen bonds       : bond        0.03885 /  2.56 (  335)
  hydrogen bonds       : angle       4.04026 /  2.82 (  936)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3621.34 seconds
wall clock time: 62 minutes 46.37 seconds (3766.37 seconds total)