Starting phenix.real_space_refine
on Fri Mar  6 16:10:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pgq_13392/03_2026/7pgq_13392_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pgq_13392/03_2026/7pgq_13392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pgq_13392/03_2026/7pgq_13392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pgq_13392/03_2026/7pgq_13392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pgq_13392/03_2026/7pgq_13392_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pgq_13392/03_2026/7pgq_13392_trim.cif"
  }
  resolution = 3.5
  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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       1      5.49       5
     S      99      5.16       5
     C   10056      2.51       5
     N    2647      2.21       5
     O    2897      1.98       5
     H   15807      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 31508
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "F"
      Number of atoms: 21053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1320, 21053
          Classifications: {'peptide': 1320}
          Link IDs: {'PTRANS': 53, 'TRANS': 1266}
          Chain breaks: 5
    Chain: "N"
      Number of atoms: 10405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 650, 10405
          Classifications: {'peptide': 650}
          Link IDs: {'PTRANS': 27, 'TRANS': 622}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 50
          Unusual residues: {' ZN': 1, 'PEV': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6857  SG  CYS F1032      32.721  57.243  84.664  1.00118.24           S

  Time building chain proxies: 5.58, per 1000 atoms: 0.18
  Number of scatterers: 31508
  At special positions: 0
  Unit cell: (135.88, 115.24, 154.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      99     16.00
     P       1     15.00
     O    2897      8.00
     N    2647      7.00
     C   10056      6.00
     H   15807      1.00
    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: 2.92
  Conformation dependent library (CDL) restraints added in 941.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN F2902 "
        pdb="ZN    ZN F2902 " - pdb=" NE2 HIS F1558 "
        pdb="ZN    ZN F2902 " - pdb=" NE2 HIS F1576 "
        pdb="ZN    ZN F2902 " - pdb=" SG  CYS F1032 "


  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3788

  Finding SS restraints...
    Secondary structure from input PDB file:
      110 helices and 4 sheets defined
      72.1% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'F' and resid 483 through 503
      removed outlier: 3.586A  pdb=" N   ARG F 487 " --> pdb=" O   ASP F 483 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR F 489 " --> pdb=" O   GLU F 485 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LYS F 490 " --> pdb=" O   THR F 486 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 504 through 509
      removed outlier: 3.555A  pdb=" N   LEU F 508 " --> pdb=" O   PRO F 504 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 521 through 531
    Processing helix  chain 'F' and resid 538 through 552
      removed outlier: 3.764A  pdb=" N   GLU F 547 " --> pdb=" O   GLN F 543 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 554 through 559
      removed outlier: 4.267A  pdb=" N   ASP F 559 " --> pdb=" O   LEU F 555 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 560 through 562
      No H-bonds generated for 'chain 'F' and resid 560 through 562'
    Processing helix  chain 'F' and resid 568 through 588
      removed outlier: 3.872A  pdb=" N   GLU F 572 " --> pdb=" O   GLU F 568 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN F 576 " --> pdb=" O   GLU F 572 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS F 584 " --> pdb=" O   TYR F 580 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS F 588 " --> pdb=" O   LYS F 584 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 592 through 618
      removed outlier: 3.696A  pdb=" N   LEU F 597 " --> pdb=" O   SER F 593 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LYS F 598 " --> pdb=" O   THR F 594 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP F 599 " --> pdb=" O   GLU F 595 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU F 602 " --> pdb=" O   LYS F 598 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 677 through 693
      removed outlier: 4.018A  pdb=" N   LYS F 686 " --> pdb=" O   GLN F 682 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   MET F 693 " --> pdb=" O   VAL F 689 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 699 through 709
    Processing helix  chain 'F' and resid 709 through 721
      removed outlier: 3.773A  pdb=" N   LEU F 713 " --> pdb=" O   CYS F 709 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU F 716 " --> pdb=" O   HIS F 712 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA F 717 " --> pdb=" O   LEU F 713 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP F 718 " --> pdb=" O   CYS F 714 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE F 719 " --> pdb=" O   GLU F 715 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 723 through 728
      removed outlier: 3.709A  pdb=" N   SER F 727 " --> pdb=" O   VAL F 723 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 734 through 746
      removed outlier: 3.607A  pdb=" N   PHE F 738 " --> pdb=" O   ASN F 734 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   MET F 739 " --> pdb=" O   TYR F 735 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLU F 740 " --> pdb=" O   ASN F 736 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE F 741 " --> pdb=" O   THR F 737 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA F 742 " --> pdb=" O   PHE F 738 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   SER F 743 " --> pdb=" O   MET F 739 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 751 through 764
      removed outlier: 3.854A  pdb=" N   ARG F 758 " --> pdb=" O   ALA F 754 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 770 through 794
      removed outlier: 4.202A  pdb=" N   GLU F 778 " --> pdb=" O   THR F 774 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS F 783 " --> pdb=" O   ASP F 779 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS F 789 " --> pdb=" O   GLU F 785 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU F 790 " --> pdb=" O   GLN F 786 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 832 through 847
      removed outlier: 3.561A  pdb=" N   LEU F 847 " --> pdb=" O   PHE F 843 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 847 through 852
      removed outlier: 4.521A  pdb=" N   CYS F 851 " --> pdb=" O   LEU F 847 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU F 852 " --> pdb=" O   GLY F 848 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 847 through 852'
    Processing helix  chain 'F' and resid 889 through 903
      removed outlier: 3.671A  pdb=" N   LEU F 901 " --> pdb=" O   ARG F 897 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   MET F 902 " --> pdb=" O   LEU F 898 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   VAL F 903 " --> pdb=" O   LEU F 899 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 909 through 924
      removed outlier: 3.785A  pdb=" N   ASP F 919 " --> pdb=" O   THR F 915 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 929 through 943
      removed outlier: 3.924A  pdb=" N   ASN F 935 " --> pdb=" O   PRO F 931 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 956 through 974
      removed outlier: 3.770A  pdb=" N   ALA F 966 " --> pdb=" O   GLU F 962 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 978 through 984
      removed outlier: 4.046A  pdb=" N   HIS F 982 " --> pdb=" O   GLY F 978 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLY F 984 " --> pdb=" O   SER F 980 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 988 through 1001
    Processing helix  chain 'F' and resid 1005 through 1023
      removed outlier: 3.704A  pdb=" N   GLN F1010 " --> pdb=" O   VAL F1006 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLU F1020 " --> pdb=" O   CYS F1016 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1033 through 1046
      removed outlier: 4.132A  pdb=" N   LYS F1040 " --> pdb=" O   LYS F1036 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1047 through 1049
      No H-bonds generated for 'chain 'F' and resid 1047 through 1049'
    Processing helix  chain 'F' and resid 1052 through 1058
      removed outlier: 4.126A  pdb=" N   ALA F1056 " --> pdb=" O   THR F1052 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1059 through 1062
    Processing helix  chain 'F' and resid 1063 through 1080
      removed outlier: 3.766A  pdb=" N   ASP F1067 " --> pdb=" O   CYS F1063 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU F1074 " --> pdb=" O   GLN F1070 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER F1078 " --> pdb=" O   GLU F1074 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1094 through 1117
      removed outlier: 3.513A  pdb=" N   SER F1100 " --> pdb=" O   MET F1096 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR F1106 " --> pdb=" O   LEU F1102 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU F1109 " --> pdb=" O   LYS F1105 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ASP F1116 " --> pdb=" O   ASN F1112 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   CYS F1117 " --> pdb=" O   LEU F1113 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1135 through 1156
      removed outlier: 3.694A  pdb=" N   MET F1149 " --> pdb=" O   THR F1145 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA F1155 " --> pdb=" O   ASN F1151 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN F1156 " --> pdb=" O   LEU F1152 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1160 through 1165
      removed outlier: 3.512A  pdb=" N   SER F1164 " --> pdb=" O   GLY F1160 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1166 through 1170
      removed outlier: 3.724A  pdb=" N   TYR F1169 " --> pdb=" O   GLY F1166 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1172 through 1189
      removed outlier: 3.537A  pdb=" N   ILE F1186 " --> pdb=" O   VAL F1182 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU F1187 " --> pdb=" O   LEU F1183 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1195 through 1205
      removed outlier: 4.262A  pdb=" N   ALA F1202 " --> pdb=" O   GLU F1198 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1205 through 1213
      removed outlier: 4.122A  pdb=" N   VAL F1209 " --> pdb=" O   PHE F1205 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLU F1210 " --> pdb=" O   GLU F1206 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1221 through 1231
      removed outlier: 3.589A  pdb=" N   ASN F1229 " --> pdb=" O   MET F1225 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1232 through 1234
      No H-bonds generated for 'chain 'F' and resid 1232 through 1234'
    Processing helix  chain 'F' and resid 1235 through 1250
    Processing helix  chain 'F' and resid 1252 through 1268
      removed outlier: 3.557A  pdb=" N   LEU F1256 " --> pdb=" O   LEU F1252 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS F1263 " --> pdb=" O   ASN F1259 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU F1264 " --> pdb=" O   MET F1260 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1270 through 1277
      removed outlier: 3.563A  pdb=" N   PHE F1275 " --> pdb=" O   MET F1271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1279 through 1311
      removed outlier: 3.702A  pdb=" N   MET F1285 " --> pdb=" O   ALA F1281 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA F1294 " --> pdb=" O   LYS F1290 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   THR F1295 " --> pdb=" O   VAL F1291 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   TYR F1296 " --> pdb=" O   TYR F1292 " (cutoff:3.500A)
      Proline residue:  F1303  - end of helix
      removed outlier: 3.728A  pdb=" N   ILE F1307 " --> pdb=" O   PRO F1303 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1331 through 1353
    Processing helix  chain 'F' and resid 1358 through 1379
    Processing helix  chain 'F' and resid 1400 through 1413
    Processing helix  chain 'F' and resid 1413 through 1420
      removed outlier: 4.390A  pdb=" N   ALA F1417 " --> pdb=" O   PHE F1413 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE F1418 " --> pdb=" O   ILE F1414 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1420 through 1425
      removed outlier: 3.501A  pdb=" N   ALA F1424 " --> pdb=" O   SER F1420 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1432 through 1452
      removed outlier: 3.793A  pdb=" N   GLY F1438 " --> pdb=" O   ARG F1434 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU F1439 " --> pdb=" O   ILE F1435 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA F1450 " --> pdb=" O   LEU F1446 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN F1451 " --> pdb=" O   GLN F1447 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1458 through 1463
      Proline residue:  F1463  - end of helix
    Processing helix  chain 'F' and resid 1464 through 1484
      removed outlier: 3.788A  pdb=" N   VAL F1468 " --> pdb=" O   PHE F1464 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS F1469 " --> pdb=" O   ASN F1465 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   SER F1470 " --> pdb=" O   ASP F1466 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASN F1471 " --> pdb=" O   PHE F1467 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   ASP F1473 " --> pdb=" O   LYS F1469 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ALA F1474 " --> pdb=" O   SER F1470 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE F1482 " --> pdb=" O   PHE F1478 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1500 through 1514
      removed outlier: 3.777A  pdb=" N   LEU F1505 " --> pdb=" O   ASP F1501 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ALA F1506 " --> pdb=" O   GLY F1502 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN F1513 " --> pdb=" O   ARG F1509 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN F1514 " --> pdb=" O   LEU F1510 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1514 through 1525
      removed outlier: 3.556A  pdb=" N   GLY F1519 " --> pdb=" O   GLN F1515 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ASN F1525 " --> pdb=" O   TYR F1521 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1530 through 1533
      removed outlier: 3.990A  pdb=" N   ARG F1533 " --> pdb=" O   ALA F1530 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 1530 through 1533'
    Processing helix  chain 'F' and resid 1534 through 1547
    Processing helix  chain 'F' and resid 1565 through 1576
    Processing helix  chain 'F' and resid 1577 through 1581
      removed outlier: 3.696A  pdb=" N   GLU F1580 " --> pdb=" O   GLN F1577 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1583 through 1591
      removed outlier: 3.661A  pdb=" N   LEU F1587 " --> pdb=" O   GLU F1583 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LYS F1588 " --> pdb=" O   PHE F1584 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   THR F1589 " --> pdb=" O   LYS F1585 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1619 through 1632
      removed outlier: 4.024A  pdb=" N   LEU F1623 " --> pdb=" O   ASN F1619 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE F1624 " --> pdb=" O   GLY F1620 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1655 through 1666
      removed outlier: 3.856A  pdb=" N   LYS F1661 " --> pdb=" O   ASP F1657 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   TRP F1662 " --> pdb=" O   PHE F1658 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   PHE F1663 " --> pdb=" O   LEU F1659 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   VAL F1664 " --> pdb=" O   SER F1660 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   PHE F1666 " --> pdb=" O   TRP F1662 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1668 through 1673
      removed outlier: 4.178A  pdb=" N   ASP F1672 " --> pdb=" O   GLY F1668 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN F1673 " --> pdb=" O   PHE F1669 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 1668 through 1673'
    Processing helix  chain 'F' and resid 1683 through 1693
    Processing helix  chain 'F' and resid 1693 through 1698
    Processing helix  chain 'F' and resid 1699 through 1701
      No H-bonds generated for 'chain 'F' and resid 1699 through 1701'
    Processing helix  chain 'F' and resid 1711 through 1719
      removed outlier: 4.209A  pdb=" N   LEU F1715 " --> pdb=" O   CYS F1711 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ALA F1716 " --> pdb=" O   PRO F1712 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   GLU F1717 " --> pdb=" O   GLY F1713 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1727 through 1734
      removed outlier: 3.609A  pdb=" N   GLU F1734 " --> pdb=" O   THR F1730 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1816 through 1835
      removed outlier: 3.688A  pdb=" N   ILE F1820 " --> pdb=" O   GLU F1816 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER F1823 " --> pdb=" O   ALA F1819 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1846 through 1849
    Processing helix  chain 'F' and resid 1850 through 1862
      removed outlier: 3.668A  pdb=" N   LEU F1854 " --> pdb=" O   VAL F1850 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE F1857 " --> pdb=" O   THR F1853 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1866 through 1882
      removed outlier: 3.550A  pdb=" N   SER F1871 " --> pdb=" O   PRO F1867 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   CYS F1882 " --> pdb=" O   CYS F1878 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1910 through 1919
    Processing helix  chain 'F' and resid 1922 through 1937
      removed outlier: 3.529A  pdb=" N   GLU F1928 " --> pdb=" O   LEU F1924 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU F1929 " --> pdb=" O   GLU F1925 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER F1935 " --> pdb=" O   ILE F1931 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS F1936 " --> pdb=" O   SER F1932 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1938 through 1950
      removed outlier: 3.660A  pdb=" N   HIS F1943 " --> pdb=" O   ILE F1939 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU F1944 " --> pdb=" O   GLU F1940 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR F1950 " --> pdb=" O   LEU F1946 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1951 through 1953
      No H-bonds generated for 'chain 'F' and resid 1951 through 1953'
    Processing helix  chain 'N' and resid 1958 through 1962
    Processing helix  chain 'N' and resid 1967 through 1985
      removed outlier: 3.557A  pdb=" N   VAL N1971 " --> pdb=" O   LYS N1967 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR N1972 " --> pdb=" O   ARG N1968 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA N1973 " --> pdb=" O   GLN N1969 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE N1983 " --> pdb=" O   ILE N1979 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 1988 through 2001
      removed outlier: 3.934A  pdb=" N   ALA N1994 " --> pdb=" O   PRO N1990 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TRP N1997 " --> pdb=" O   GLN N1993 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY N1998 " --> pdb=" O   ALA N1994 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2003 through 2022
      removed outlier: 4.515A  pdb=" N   ASP N2008 " --> pdb=" O   THR N2004 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   VAL N2009 " --> pdb=" O   ASP N2005 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE N2015 " --> pdb=" O   LEU N2011 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY N2021 " --> pdb=" O   THR N2017 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2025 through 2042
      removed outlier: 3.607A  pdb=" N   ALA N2032 " --> pdb=" O   ALA N2028 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP N2033 " --> pdb=" O   GLU N2029 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL N2036 " --> pdb=" O   ALA N2032 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ALA N2037 " --> pdb=" O   ASP N2033 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER N2040 " --> pdb=" O   VAL N2036 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   GLY N2041 " --> pdb=" O   ALA N2037 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ASN N2042 " --> pdb=" O   LEU N2038 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2042 through 2059
      removed outlier: 4.205A  pdb=" N   SER N2048 " --> pdb=" O   LYS N2044 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   GLY N2052 " --> pdb=" O   SER N2048 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG N2053 " --> pdb=" O   LYS N2049 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS N2056 " --> pdb=" O   GLY N2052 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2068 through 2073
      removed outlier: 6.119A  pdb=" N   LEU N2073 " --> pdb=" O   GLU N2070 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2074 through 2090
      removed outlier: 3.554A  pdb=" N   ARG N2083 " --> pdb=" O   ALA N2079 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR N2084 " --> pdb=" O   ILE N2080 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET N2085 " --> pdb=" O   LEU N2081 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE N2090 " --> pdb=" O   LEU N2086 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2091 through 2093
      No H-bonds generated for 'chain 'N' and resid 2091 through 2093'
    Processing helix  chain 'N' and resid 2095 through 2108
      Proline residue:  N2101  - end of helix
      removed outlier: 3.651A  pdb=" N   VAL N2106 " --> pdb=" O   TYR N2102 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2115 through 2135
      removed outlier: 3.607A  pdb=" N   THR N2122 " --> pdb=" O   LEU N2118 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS N2123 " --> pdb=" O   ARG N2119 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2142 through 2156
      removed outlier: 3.862A  pdb=" N   GLN N2147 " --> pdb=" O   GLU N2143 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL N2148 " --> pdb=" O   GLU N2144 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2158 through 2166
      removed outlier: 3.544A  pdb=" N   LEU N2163 " --> pdb=" O   PRO N2159 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU N2164 " --> pdb=" O   LYS N2160 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2172 through 2178
      removed outlier: 4.002A  pdb=" N   ILE N2176 " --> pdb=" O   SER N2172 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2198 through 2220
      removed outlier: 3.560A  pdb=" N   LEU N2202 " --> pdb=" O   ALA N2198 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU N2203 " --> pdb=" O   LEU N2199 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR N2204 " --> pdb=" O   THR N2200 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE N2212 " --> pdb=" O   ALA N2208 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ASP N2219 " --> pdb=" O   ALA N2215 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2224 through 2238
      removed outlier: 3.699A  pdb=" N   PHE N2236 " --> pdb=" O   LEU N2232 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   PHE N2238 " --> pdb=" O   GLN N2234 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2244 through 2256
      removed outlier: 3.599A  pdb=" N   VAL N2251 " --> pdb=" O   ARG N2247 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE N2252 " --> pdb=" O   ALA N2248 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   CYS N2254 " --> pdb=" O   VAL N2250 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2260 through 2281
      removed outlier: 3.688A  pdb=" N   GLN N2266 " --> pdb=" O   GLY N2262 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS N2273 " --> pdb=" O   ARG N2269 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU N2275 " --> pdb=" O   LEU N2271 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU N2279 " --> pdb=" O   LEU N2275 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2288 through 2302
      removed outlier: 3.998A  pdb=" N   GLU N2292 " --> pdb=" O   GLN N2288 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR N2294 " --> pdb=" O   LEU N2290 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS N2300 " --> pdb=" O   ILE N2296 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2303 through 2305
      No H-bonds generated for 'chain 'N' and resid 2303 through 2305'
    Processing helix  chain 'N' and resid 2310 through 2324
      removed outlier: 5.436A  pdb=" N   PHE N2316 " --> pdb=" O   HIS N2312 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   TRP N2317 " --> pdb=" O   LYS N2313 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL N2318 " --> pdb=" O   ALA N2314 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA N2319 " --> pdb=" O   LEU N2315 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN N2324 " --> pdb=" O   VAL N2320 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2327 through 2348
      removed outlier: 3.593A  pdb=" N   ALA N2336 " --> pdb=" O   SER N2332 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU N2337 " --> pdb=" O   ALA N2333 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN N2340 " --> pdb=" O   ALA N2336 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   SER N2347 " --> pdb=" O   HIS N2343 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2355 through 2363
    Processing helix  chain 'N' and resid 2367 through 2379
      removed outlier: 3.557A  pdb=" N   CYS N2371 " --> pdb=" O   LEU N2367 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLN N2373 " --> pdb=" O   TRP N2369 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   MET N2374 " --> pdb=" O   HIS N2370 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2385 through 2393
      removed outlier: 4.312A  pdb=" N   VAL N2391 " --> pdb=" O   ASN N2387 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   HIS N2393 " --> pdb=" O   ALA N2389 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2395 through 2400
      removed outlier: 3.637A  pdb=" N   TYR N2398 " --> pdb=" O   LEU N2395 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2402 through 2425
      removed outlier: 3.728A  pdb=" N   VAL N2406 " --> pdb=" O   SER N2402 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA N2407 " --> pdb=" O   PRO N2403 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG N2408 " --> pdb=" O   ALA N2404 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN N2421 " --> pdb=" O   LEU N2417 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYS N2422 " --> pdb=" O   THR N2418 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG N2424 " --> pdb=" O   VAL N2420 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2436 through 2442
    Processing helix  chain 'N' and resid 2446 through 2453
    Processing helix  chain 'N' and resid 2612 through 2630
      removed outlier: 4.067A  pdb=" N   LEU N2619 " --> pdb=" O   ILE N2615 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU N2620 " --> pdb=" O   GLN N2616 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU N2623 " --> pdb=" O   LEU N2619 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL N2627 " --> pdb=" O   LEU N2623 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TYR N2629 " --> pdb=" O   THR N2625 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2632 through 2650
      removed outlier: 3.517A  pdb=" N   TYR N2642 " --> pdb=" O   ILE N2638 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU N2645 " --> pdb=" O   GLU N2641 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA N2646 " --> pdb=" O   TYR N2642 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL N2648 " --> pdb=" O   ALA N2644 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2653 through 2656
    Processing helix  chain 'N' and resid 2657 through 2672
      removed outlier: 3.548A  pdb=" N   LEU N2661 " --> pdb=" O   VAL N2657 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER N2663 " --> pdb=" O   ASN N2659 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   LYS N2664 " --> pdb=" O   LEU N2660 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR N2667 " --> pdb=" O   SER N2663 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER N2670 " --> pdb=" O   ASN N2666 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2674 through 2692
      Proline residue:  N2680  - end of helix
    Processing helix  chain 'N' and resid 2699 through 2707
      removed outlier: 4.263A  pdb=" N   LEU N2703 " --> pdb=" O   THR N2700 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN N2704 " --> pdb=" O   SER N2701 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER N2705 " --> pdb=" O   TYR N2702 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY N2707 " --> pdb=" O   GLN N2704 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2710 through 2715
      removed outlier: 3.718A  pdb=" N   ALA N2715 " --> pdb=" O   LEU N2711 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2728 through 2743
      removed outlier: 3.886A  pdb=" N   LYS N2733 " --> pdb=" O   GLU N2729 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 945 through 946
      removed outlier: 3.575A  pdb=" N   ASP F 946 " --> pdb=" O   GLN F 950 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLN F 950 " --> pdb=" O   ASP F 946 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 1594 through 1598
      removed outlier: 3.844A  pdb=" N   ILE F1605 " --> pdb=" O   ALA F1596 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   VAL F1642 " --> pdb=" O   PRO F1604 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   PHE F1606 " --> pdb=" O   VAL F1642 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ASP F1644 " --> pdb=" O   PHE F1606 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   TYR F1608 " --> pdb=" O   ASP F1644 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   TYR F1639 " --> pdb=" O   SER F1675 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   VAL F1677 " --> pdb=" O   TYR F1639 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ILE F1641 " --> pdb=" O   VAL F1677 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ILE F1679 " --> pdb=" O   ILE F1641 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL F1643 " --> pdb=" O   ILE F1679 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   VAL F1707 " --> pdb=" O   SER F1675 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   VAL F1677 " --> pdb=" O   VAL F1707 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 1780 through 1784
      removed outlier: 3.919A  pdb=" N   THR F1751 " --> pdb=" O   LYS F1745 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ILE F1755 " --> pdb=" O   HIS F1741 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   HIS F1741 " --> pdb=" O   ILE F1755 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL F1757 " --> pdb=" O   VAL F1739 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL F1739 " --> pdb=" O   VAL F1757 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   THR F1811 " --> pdb=" O   LEU F1746 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   PHE F1812 " --> pdb=" O   PHE F1799 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 1770 through 1772

    792 hydrogen bonds defined for protein.
    2319 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.42

  Time building geometry restraints manager: 4.10 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 15765
        1.03 -     1.23: 47
        1.23 -     1.42: 6534
        1.42 -     1.62: 9330
        1.62 -     1.81: 155
  Bond restraints: 31831
  Sorted by residual:
  bond pdb=" C4  PEV F2901 "
       pdb=" C5  PEV F2901 "
    ideal  model  delta    sigma   weight residual
    1.511  1.547 -0.036 2.00e-02 2.50e+03 3.16e+00
  bond pdb=" C1  PEV F2901 "
       pdb=" O3P PEV F2901 "
    ideal  model  delta    sigma   weight residual
    1.407  1.443 -0.036 2.00e-02 2.50e+03 3.16e+00
  bond pdb=" O4P PEV F2901 "
       pdb=" P   PEV F2901 "
    ideal  model  delta    sigma   weight residual
    1.638  1.605  0.033 2.00e-02 2.50e+03 2.78e+00
  bond pdb=" C4  PEV F2901 "
       pdb=" O4P PEV F2901 "
    ideal  model  delta    sigma   weight residual
    1.418  1.450 -0.032 2.00e-02 2.50e+03 2.53e+00
  bond pdb=" C2  PEV F2901 "
       pdb=" O2  PEV F2901 "
    ideal  model  delta    sigma   weight residual
    1.432  1.462 -0.030 2.00e-02 2.50e+03 2.29e+00
  ... (remaining 31826 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 57501
        2.21 -     4.41: 131
        4.41 -     6.62: 3
        6.62 -     8.82: 0
        8.82 -    11.03: 1
  Bond angle restraints: 57636
  Sorted by residual:
  angle pdb=" O3P PEV F2901 "
        pdb=" P   PEV F2901 "
        pdb=" O4P PEV F2901 "
      ideal   model   delta    sigma   weight residual
      93.57  104.60  -11.03 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" N   VAL F 551 "
        pdb=" CA  VAL F 551 "
        pdb=" C   VAL F 551 "
      ideal   model   delta    sigma   weight residual
     112.35  108.77    3.58 1.41e+00 5.03e-01 6.44e+00
  angle pdb=" N   PRO F1535 "
        pdb=" CA  PRO F1535 "
        pdb=" C   PRO F1535 "
      ideal   model   delta    sigma   weight residual
     112.47  117.25   -4.78 2.06e+00 2.36e-01 5.38e+00
  angle pdb=" C   GLU F1459 "
        pdb=" N   HIS F1460 "
        pdb=" CA  HIS F1460 "
      ideal   model   delta    sigma   weight residual
     120.38  123.50   -3.12 1.37e+00 5.33e-01 5.17e+00
  angle pdb=" C2  PEV F2901 "
        pdb=" C3  PEV F2901 "
        pdb=" O3  PEV F2901 "
      ideal   model   delta    sigma   weight residual
     112.90  107.15    5.75 3.00e+00 1.11e-01 3.67e+00
  ... (remaining 57631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.28: 14632
       28.28 -    56.55: 309
       56.55 -    84.83: 33
       84.83 -   113.11: 1
      113.11 -   141.38: 1
  Dihedral angle restraints: 14976
    sinusoidal: 8182
      harmonic: 6794
  Sorted by residual:
  dihedral pdb=" C3  PEV F2901 "
           pdb=" C1  PEV F2901 "
           pdb=" C2  PEV F2901 "
           pdb=" O3P PEV F2901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.20   74.18 -141.38     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" CA  SER N2093 "
           pdb=" C   SER N2093 "
           pdb=" N   LEU N2094 "
           pdb=" CA  LEU N2094 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.54   19.46     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ARG F1534 "
           pdb=" C   ARG F1534 "
           pdb=" N   PRO F1535 "
           pdb=" CA  PRO F1535 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.08  -18.92     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 14973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 2079
       0.042 -    0.084: 353
       0.084 -    0.126: 89
       0.126 -    0.168: 2
       0.168 -    0.210: 1
  Chirality restraints: 2524
  Sorted by residual:
  chirality pdb=" C2  PEV F2901 "
            pdb=" C1  PEV F2901 "
            pdb=" C3  PEV F2901 "
            pdb=" O2  PEV F2901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.57   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  PRO F1535 "
            pdb=" N   PRO F1535 "
            pdb=" C   PRO F1535 "
            pdb=" CB  PRO F1535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE N2724 "
            pdb=" N   ILE N2724 "
            pdb=" C   ILE N2724 "
            pdb=" CB  ILE N2724 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 2521 not shown)

  Planarity restraints: 4621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR N2066 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO N2067 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO N2067 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO N2067 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F1083 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO F1084 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO F1084 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F1084 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F1866 "   -0.016 5.00e-02 4.00e+02   2.44e-02 9.51e-01
        pdb=" N   PRO F1867 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO F1867 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F1867 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 4618 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1041
        2.18 -     2.78: 62988
        2.78 -     3.39: 82866
        3.39 -     3.99: 102223
        3.99 -     4.60: 164991
  Nonbonded interactions: 414109
  Sorted by model distance:
  nonbonded pdb=" O   ALA N2644 "
            pdb=" HG  SER N2647 "
     model   vdw
     1.574 2.450
  nonbonded pdb=" O   SER F1150 "
            pdb="HD22 ASN F1154 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" OD2 ASP F1172 "
            pdb=" H   THR F1175 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" O   GLN F 912 "
            pdb="HD22 ASN F 916 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" OD1 ASP F1644 "
            pdb=" HG1 THR F1646 "
     model   vdw
     1.601 2.450
  ... (remaining 414104 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.180
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.100
  Set scattering table:                    0.090
  Process input model:                     38.070
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.040
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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      :  0.004   0.259  16027  Z= 0.161
  Angle     :  0.453  11.027  21715  Z= 0.239
  Chirality :  0.035   0.210   2524
  Planarity :  0.003   0.041   2739
  Dihedral  : 10.678 141.383   5941
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  4.60 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.19), residues: 1954
  helix:  0.40 (0.16), residues: 1142
  sheet:  0.30 (0.69), residues: 72
  loop : -0.98 (0.22), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 764 
 TYR   0.010   0.001   TYR F1948 
 PHE   0.009   0.001   PHE F1031 
 TRP   0.006   0.001   TRP F 696 
 HIS   0.005   0.001   HIS F1558 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (16024)
  covalent geometry    : angle       0.45313 (21715)
  hydrogen bonds       : bond        0.30440 (  792)
  hydrogen bonds       : angle       7.88604 ( 2319)
  metal coordination   : bond        0.19809 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  739 MET cc_start: 0.8858 (mmm) cc_final: 0.8576 (mmm)
REVERT: F  932 MET cc_start: 0.8607 (ttm) cc_final: 0.8385 (ttp)
REVERT: F 1111 MET cc_start: 0.8585 (mmm) cc_final: 0.8360 (mmm)
REVERT: F 1180 MET cc_start: 0.8935 (mtp) cc_final: 0.8720 (mtm)
REVERT: F 1225 MET cc_start: 0.8935 (mmm) cc_final: 0.8472 (mmm)
REVERT: F 1271 MET cc_start: 0.6939 (ptt) cc_final: 0.6732 (ptp)
REVERT: F 1342 MET cc_start: 0.9019 (ttp) cc_final: 0.8732 (ttp)
REVERT: F 1894 GLU cc_start: 0.8112 (pt0) cc_final: 0.7613 (pp20)
REVERT: N 2054 MET cc_start: 0.8608 (tpp) cc_final: 0.8358 (tpp)
REVERT: N 2367 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8522 (pt)
REVERT: N 2443 LEU cc_start: 0.9565 (tp) cc_final: 0.9287 (tt)
  outliers start: 16
  outliers final: 7
  residues processed: 197
  average time/residue: 0.3119
  time to fit residues: 87.5696
Evaluate side-chains
  121 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1156 ASN
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1276 ARG
Chi-restraints excluded: chain F residue 1457 LYS
Chi-restraints excluded: chain F residue 1576 HIS
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0370
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   overall best weight:    1.4662

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

Flipped N/Q/H residues before XYZ refinement:
F 682 GLN
F 697 ASN
F 959 GLN
F1577 GLN
F1683 ASN
F1875 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.106951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.076462 restraints weight = 150785.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.078957 restraints weight = 69948.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.080665 restraints weight = 47231.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.081676 restraints weight = 38183.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.082257 restraints weight = 33962.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  16027  Z= 0.181
  Angle     :  0.619   6.341  21715  Z= 0.347
  Chirality :  0.038   0.147   2524
  Planarity :  0.004   0.050   2739
  Dihedral  :  6.216 130.013   2162
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.53 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.67 %
    Favored  : 91.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.19), residues: 1954
  helix:  0.69 (0.15), residues: 1205
  sheet:  0.28 (0.67), residues: 71
  loop : -0.85 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F1437 
 TYR   0.015   0.001   TYR F1948 
 PHE   0.015   0.001   PHE F1478 
 TRP   0.014   0.001   TRP F1831 
 HIS   0.007   0.001   HIS F1718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (16024)
  covalent geometry    : angle       0.61950 (21715)
  hydrogen bonds       : bond        0.08471 (  792)
  hydrogen bonds       : angle       5.47729 ( 2319)
  metal coordination   : bond        0.01448 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  682 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8561 (tp-100)
REVERT: F  740 GLU cc_start: 0.9060 (mp0) cc_final: 0.8822 (mp0)
REVERT: F  895 MET cc_start: 0.9044 (mmm) cc_final: 0.8436 (mmm)
REVERT: F  932 MET cc_start: 0.8537 (ttm) cc_final: 0.8330 (ttt)
REVERT: F 1111 MET cc_start: 0.8736 (mmm) cc_final: 0.8464 (mmm)
REVERT: F 1271 MET cc_start: 0.6283 (ptt) cc_final: 0.5940 (ptp)
REVERT: F 1342 MET cc_start: 0.9219 (ttp) cc_final: 0.8877 (ttp)
REVERT: N 1995 LYS cc_start: 0.9103 (mttt) cc_final: 0.8832 (mtpt)
REVERT: N 2054 MET cc_start: 0.8683 (tpp) cc_final: 0.8237 (tpp)
REVERT: N 2217 MET cc_start: 0.8124 (mtp) cc_final: 0.7865 (mtp)
REVERT: N 2367 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8509 (pt)
REVERT: N 2390 LEU cc_start: 0.9497 (tp) cc_final: 0.9238 (tp)
REVERT: N 2443 LEU cc_start: 0.9572 (tp) cc_final: 0.9291 (tt)
  outliers start: 18
  outliers final: 11
  residues processed: 129
  average time/residue: 0.2572
  time to fit residues: 51.0149
Evaluate side-chains
  111 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  682 GLN
Chi-restraints excluded: chain F residue 1156 ASN
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2220 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0470
   chunk 102 optimal weight:    5.9990
   chunk 174 optimal weight:    4.9990
   chunk 194 optimal weight:    4.9990
   chunk 165 optimal weight:    2.9990
   chunk 143 optimal weight:    0.2980
   chunk 52 optimal weight:    0.8980
   chunk 91 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
** N2421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.107973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.076995 restraints weight = 149778.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.079602 restraints weight = 69247.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.081373 restraints weight = 47928.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.082446 restraints weight = 38491.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.083040 restraints weight = 34062.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  16027  Z= 0.126
  Angle     :  0.510   7.072  21715  Z= 0.277
  Chirality :  0.035   0.140   2524
  Planarity :  0.003   0.046   2739
  Dihedral  :  5.654 124.610   2152
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.30 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.50 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.19), residues: 1954
  helix:  1.11 (0.15), residues: 1211
  sheet:  0.08 (0.64), residues: 67
  loop : -0.88 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F1437 
 TYR   0.015   0.001   TYR F1948 
 PHE   0.042   0.001   PHE F 579 
 TRP   0.009   0.001   TRP F1831 
 HIS   0.005   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (16024)
  covalent geometry    : angle       0.50970 (21715)
  hydrogen bonds       : bond        0.06790 (  792)
  hydrogen bonds       : angle       4.86859 ( 2319)
  metal coordination   : bond        0.00755 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  740 GLU cc_start: 0.9195 (mp0) cc_final: 0.8904 (mp0)
REVERT: F  895 MET cc_start: 0.9019 (mmm) cc_final: 0.8327 (mmm)
REVERT: F 1111 MET cc_start: 0.8734 (mmm) cc_final: 0.8431 (mmm)
REVERT: F 1271 MET cc_start: 0.6618 (ptt) cc_final: 0.6348 (ptp)
REVERT: F 1410 PHE cc_start: 0.9071 (t80) cc_final: 0.8819 (t80)
REVERT: N 2054 MET cc_start: 0.8738 (tpp) cc_final: 0.8362 (tpp)
REVERT: N 2217 MET cc_start: 0.7892 (mtp) cc_final: 0.7631 (mtp)
REVERT: N 2367 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8440 (pt)
REVERT: N 2390 LEU cc_start: 0.9515 (tp) cc_final: 0.9257 (tp)
REVERT: N 2443 LEU cc_start: 0.9533 (tp) cc_final: 0.9281 (tt)
  outliers start: 12
  outliers final: 9
  residues processed: 113
  average time/residue: 0.2567
  time to fit residues: 45.4911
Evaluate side-chains
  105 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1457 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 122 optimal weight:    0.2980
   chunk 167 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 193 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 89 optimal weight:    8.9990
   chunk 113 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 111 optimal weight:    7.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1054 ASN
F1070 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.106248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.075793 restraints weight = 150646.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.078250 restraints weight = 71859.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.079946 restraints weight = 48751.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.080932 restraints weight = 39435.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.081344 restraints weight = 35095.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  16027  Z= 0.219
  Angle     :  0.555   6.239  21715  Z= 0.302
  Chirality :  0.036   0.136   2524
  Planarity :  0.004   0.043   2739
  Dihedral  :  5.661 117.774   2150
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.68 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.89 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.19), residues: 1954
  helix:  1.04 (0.15), residues: 1221
  sheet:  0.47 (0.67), residues: 58
  loop : -0.94 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N2247 
 TYR   0.017   0.001   TYR F1948 
 PHE   0.014   0.001   PHE F 610 
 TRP   0.010   0.001   TRP F 696 
 HIS   0.010   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (16024)
  covalent geometry    : angle       0.55491 (21715)
  hydrogen bonds       : bond        0.05625 (  792)
  hydrogen bonds       : angle       4.95386 ( 2319)
  metal coordination   : bond        0.00115 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  740 GLU cc_start: 0.9188 (mp0) cc_final: 0.8902 (mp0)
REVERT: F 1111 MET cc_start: 0.8734 (mmm) cc_final: 0.8437 (mmm)
REVERT: F 1271 MET cc_start: 0.6619 (ptt) cc_final: 0.6332 (ptp)
REVERT: F 1410 PHE cc_start: 0.9102 (t80) cc_final: 0.8834 (t80)
REVERT: N 2054 MET cc_start: 0.8878 (tpp) cc_final: 0.8556 (tpp)
REVERT: N 2217 MET cc_start: 0.7865 (mtp) cc_final: 0.7557 (mtp)
REVERT: N 2367 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8531 (pt)
REVERT: N 2443 LEU cc_start: 0.9544 (tp) cc_final: 0.9260 (tt)
  outliers start: 25
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2591
  time to fit residues: 44.9299
Evaluate side-chains
  105 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  682 GLN
Chi-restraints excluded: chain F residue 1150 SER
Chi-restraints excluded: chain F residue 1156 ASN
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1645 LEU
Chi-restraints excluded: chain F residue 1826 HIS
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0970
   chunk 109 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 187 optimal weight:    5.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N2414 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.106990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.076674 restraints weight = 150417.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.079094 restraints weight = 70236.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.080530 restraints weight = 47380.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.081540 restraints weight = 39137.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.082128 restraints weight = 34985.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16027  Z= 0.134
  Angle     :  0.491   6.283  21715  Z= 0.265
  Chirality :  0.035   0.138   2524
  Planarity :  0.003   0.043   2739
  Dihedral  :  5.506 112.421   2150
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.02 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.69 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.19), residues: 1954
  helix:  1.37 (0.15), residues: 1221
  sheet:  0.31 (0.67), residues: 58
  loop : -0.89 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 681 
 TYR   0.017   0.001   TYR F1948 
 PHE   0.015   0.001   PHE F 610 
 TRP   0.009   0.001   TRP F1831 
 HIS   0.012   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (16024)
  covalent geometry    : angle       0.49052 (21715)
  hydrogen bonds       : bond        0.05103 (  792)
  hydrogen bonds       : angle       4.57164 ( 2319)
  metal coordination   : bond        0.00042 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  740 GLU cc_start: 0.9288 (mp0) cc_final: 0.8970 (mp0)
REVERT: F 1111 MET cc_start: 0.8729 (mmm) cc_final: 0.8406 (mmm)
REVERT: F 1225 MET cc_start: 0.9103 (mmm) cc_final: 0.8619 (mmm)
REVERT: F 1271 MET cc_start: 0.6943 (ptt) cc_final: 0.6617 (ptp)
REVERT: F 1410 PHE cc_start: 0.9079 (t80) cc_final: 0.8802 (t80)
REVERT: N 2054 MET cc_start: 0.8847 (tpp) cc_final: 0.8543 (tpp)
REVERT: N 2217 MET cc_start: 0.7873 (mtp) cc_final: 0.7508 (mtp)
REVERT: N 2367 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8522 (pt)
REVERT: N 2443 LEU cc_start: 0.9534 (tp) cc_final: 0.9234 (tt)
  outliers start: 17
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2547
  time to fit residues: 43.5818
Evaluate side-chains
  104 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2312 HIS
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   chunk 152 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   chunk 187 optimal weight:    6.9990
   chunk 180 optimal weight:    5.9990
   chunk 176 optimal weight:    0.4980
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.107026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.076502 restraints weight = 150209.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.079015 restraints weight = 70843.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.080781 restraints weight = 48263.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.081755 restraints weight = 38959.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.082354 restraints weight = 34538.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16027  Z= 0.119
  Angle     :  0.482   8.016  21715  Z= 0.256
  Chirality :  0.035   0.202   2524
  Planarity :  0.003   0.042   2739
  Dihedral  :  5.415 108.935   2150
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.53 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.63 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.19), residues: 1954
  helix:  1.54 (0.15), residues: 1226
  sheet:  0.29 (0.67), residues: 58
  loop : -0.92 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F1611 
 TYR   0.016   0.001   TYR F1948 
 PHE   0.012   0.001   PHE F 610 
 TRP   0.008   0.001   TRP F1831 
 HIS   0.009   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (16024)
  covalent geometry    : angle       0.48150 (21715)
  hydrogen bonds       : bond        0.04622 (  792)
  hydrogen bonds       : angle       4.39114 ( 2319)
  metal coordination   : bond        0.00041 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  740 GLU cc_start: 0.9298 (mp0) cc_final: 0.8872 (mp0)
REVERT: F 1111 MET cc_start: 0.8729 (mmm) cc_final: 0.8399 (mmm)
REVERT: F 1225 MET cc_start: 0.9030 (mmm) cc_final: 0.8633 (mmm)
REVERT: F 1410 PHE cc_start: 0.9073 (t80) cc_final: 0.8776 (t80)
REVERT: F 1813 MET cc_start: 0.5021 (tpp) cc_final: 0.4707 (tpp)
REVERT: N 2054 MET cc_start: 0.8847 (tpp) cc_final: 0.8552 (tpp)
REVERT: N 2217 MET cc_start: 0.7861 (mtp) cc_final: 0.7469 (mtp)
REVERT: N 2367 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8577 (pt)
REVERT: N 2443 LEU cc_start: 0.9537 (tp) cc_final: 0.9233 (tt)
  outliers start: 19
  outliers final: 16
  residues processed: 111
  average time/residue: 0.2534
  time to fit residues: 43.9709
Evaluate side-chains
  108 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1576 HIS
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1645 LEU
Chi-restraints excluded: chain F residue 1826 HIS
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2268 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2312 HIS
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 164 optimal weight:    0.7980
   chunk 146 optimal weight:    0.9990
   chunk 195 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 191 optimal weight:   10.0000
   chunk 156 optimal weight:    0.0470
   chunk 126 optimal weight:    2.9990
   chunk 119 optimal weight:   10.0000
   chunk 174 optimal weight:    3.9990
   chunk 190 optimal weight:    8.9990
   chunk 144 optimal weight:    0.7980
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.107279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.076734 restraints weight = 151216.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.079306 restraints weight = 70984.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.081137 restraints weight = 48163.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.082138 restraints weight = 38670.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.082725 restraints weight = 34296.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  16027  Z= 0.112
  Angle     :  0.475   7.675  21715  Z= 0.251
  Chirality :  0.035   0.136   2524
  Planarity :  0.003   0.042   2739
  Dihedral  :  5.333 105.627   2150
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.12 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.97 %
    Favored  : 89.89 %
  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:  1.17 (0.19), residues: 1954
  helix:  1.70 (0.15), residues: 1227
  sheet:  0.27 (0.67), residues: 58
  loop : -0.92 (0.24), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F1477 
 TYR   0.014   0.001   TYR F1948 
 PHE   0.012   0.001   PHE F 610 
 TRP   0.007   0.001   TRP F1831 
 HIS   0.007   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (16024)
  covalent geometry    : angle       0.47537 (21715)
  hydrogen bonds       : bond        0.04266 (  792)
  hydrogen bonds       : angle       4.23718 ( 2319)
  metal coordination   : bond        0.00086 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  599 TRP cc_start: 0.8293 (t60) cc_final: 0.8004 (t60)
REVERT: F  740 GLU cc_start: 0.9304 (mp0) cc_final: 0.8832 (mp0)
REVERT: F 1111 MET cc_start: 0.8731 (mmm) cc_final: 0.8408 (mmm)
REVERT: F 1225 MET cc_start: 0.9043 (mmm) cc_final: 0.8516 (mmm)
REVERT: F 1410 PHE cc_start: 0.9060 (t80) cc_final: 0.8756 (t80)
REVERT: N 2054 MET cc_start: 0.8835 (tpp) cc_final: 0.8555 (tpp)
REVERT: N 2217 MET cc_start: 0.7817 (mtp) cc_final: 0.7408 (mtp)
REVERT: N 2367 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8586 (pt)
REVERT: N 2443 LEU cc_start: 0.9517 (tp) cc_final: 0.9244 (tt)
  outliers start: 20
  outliers final: 17
  residues processed: 110
  average time/residue: 0.2516
  time to fit residues: 43.2378
Evaluate side-chains
  111 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1150 SER
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1576 HIS
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1645 LEU
Chi-restraints excluded: chain F residue 1826 HIS
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2268 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2312 HIS
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 169 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 119 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 135 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1525 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.105266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.074554 restraints weight = 152246.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.076930 restraints weight = 73593.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.078514 restraints weight = 50282.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.079432 restraints weight = 41413.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.079913 restraints weight = 37108.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  16027  Z= 0.255
  Angle     :  0.558   6.922  21715  Z= 0.301
  Chirality :  0.037   0.166   2524
  Planarity :  0.004   0.044   2739
  Dihedral  :  5.592 103.198   2150
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.45 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.31 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.19), residues: 1954
  helix:  1.26 (0.15), residues: 1230
  sheet:  0.24 (0.66), residues: 58
  loop : -1.11 (0.24), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N2247 
 TYR   0.014   0.001   TYR F1948 
 PHE   0.015   0.002   PHE F 579 
 TRP   0.011   0.001   TRP F 696 
 HIS   0.006   0.001   HIS N2099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (16024)
  covalent geometry    : angle       0.55774 (21715)
  hydrogen bonds       : bond        0.04697 (  792)
  hydrogen bonds       : angle       4.67817 ( 2319)
  metal coordination   : bond        0.00206 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  599 TRP cc_start: 0.8430 (t60) cc_final: 0.8199 (t60)
REVERT: F 1111 MET cc_start: 0.8718 (mmm) cc_final: 0.8391 (mmm)
REVERT: F 1225 MET cc_start: 0.9106 (mmm) cc_final: 0.8602 (mmm)
REVERT: F 1410 PHE cc_start: 0.9106 (t80) cc_final: 0.8790 (t80)
REVERT: N 2054 MET cc_start: 0.8918 (tpp) cc_final: 0.8626 (tpp)
REVERT: N 2217 MET cc_start: 0.7827 (mtp) cc_final: 0.7433 (mtp)
REVERT: N 2367 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8622 (pt)
REVERT: N 2443 LEU cc_start: 0.9522 (tp) cc_final: 0.9218 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 107
  average time/residue: 0.2574
  time to fit residues: 42.8927
Evaluate side-chains
  104 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  688 GLU
Chi-restraints excluded: chain F residue 1150 SER
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1826 HIS
Chi-restraints excluded: chain F residue 1895 THR
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2312 HIS
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 69 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 115 optimal weight:    8.9990
   chunk 112 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 164 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 153 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.106462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.076052 restraints weight = 150713.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.078588 restraints weight = 71281.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.080321 restraints weight = 48252.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.081305 restraints weight = 39148.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.081878 restraints weight = 34791.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16027  Z= 0.118
  Angle     :  0.480   6.352  21715  Z= 0.255
  Chirality :  0.035   0.129   2524
  Planarity :  0.003   0.042   2739
  Dihedral  :  5.403  99.043   2150
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.68 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  9.88 %
    Favored  : 89.27 %
  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:  1.01 (0.19), residues: 1954
  helix:  1.57 (0.15), residues: 1239
  sheet:  0.29 (0.67), residues: 58
  loop : -1.02 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F1038 
 TYR   0.017   0.001   TYR F1948 
 PHE   0.011   0.001   PHE F 579 
 TRP   0.007   0.001   TRP F1831 
 HIS   0.006   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (16024)
  covalent geometry    : angle       0.48033 (21715)
  hydrogen bonds       : bond        0.04325 (  792)
  hydrogen bonds       : angle       4.25036 ( 2319)
  metal coordination   : bond        0.00091 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  740 GLU cc_start: 0.9331 (mp0) cc_final: 0.8892 (mp0)
REVERT: F 1111 MET cc_start: 0.8714 (mmm) cc_final: 0.8379 (mmm)
REVERT: F 1225 MET cc_start: 0.9060 (mmm) cc_final: 0.8538 (mmm)
REVERT: F 1410 PHE cc_start: 0.9064 (t80) cc_final: 0.8746 (t80)
REVERT: N 2054 MET cc_start: 0.8899 (tpp) cc_final: 0.8630 (tpp)
REVERT: N 2217 MET cc_start: 0.7809 (mtp) cc_final: 0.7401 (mtp)
REVERT: N 2367 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8613 (pt)
REVERT: N 2443 LEU cc_start: 0.9515 (tp) cc_final: 0.9234 (tt)
  outliers start: 15
  outliers final: 14
  residues processed: 103
  average time/residue: 0.2553
  time to fit residues: 40.9744
Evaluate side-chains
  106 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1150 SER
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1576 HIS
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1826 HIS
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2312 HIS
Chi-restraints excluded: chain N residue 2367 LEU
Chi-restraints excluded: chain N residue 2432 ASN
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 146 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 193 optimal weight:    3.9990
   chunk 171 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 196 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 974 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.106968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.076872 restraints weight = 150482.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.079447 restraints weight = 70217.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.081001 restraints weight = 47427.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.082097 restraints weight = 39011.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.082652 restraints weight = 34271.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  16027  Z= 0.105
  Angle     :  0.466   7.041  21715  Z= 0.245
  Chirality :  0.034   0.139   2524
  Planarity :  0.003   0.042   2739
  Dihedral  :  5.192  96.242   2150
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.09 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  9.88 %
    Favored  : 89.27 %
  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:  1.27 (0.20), residues: 1954
  helix:  1.80 (0.15), residues: 1242
  sheet:  0.23 (0.67), residues: 58
  loop : -0.99 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 720 
 TYR   0.017   0.001   TYR F1948 
 PHE   0.010   0.001   PHE F 610 
 TRP   0.014   0.001   TRP F 599 
 HIS   0.003   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (16024)
  covalent geometry    : angle       0.46611 (21715)
  hydrogen bonds       : bond        0.03855 (  792)
  hydrogen bonds       : angle       4.05900 ( 2319)
  metal coordination   : bond        0.00060 (    3)

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

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

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3908 Ramachandran restraints generated.
    1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  740 GLU cc_start: 0.9360 (mp0) cc_final: 0.8864 (mp0)
REVERT: F 1111 MET cc_start: 0.8736 (mmm) cc_final: 0.8389 (mmm)
REVERT: F 1225 MET cc_start: 0.9056 (mmm) cc_final: 0.8723 (mmp)
REVERT: F 1410 PHE cc_start: 0.9040 (t80) cc_final: 0.8719 (t80)
REVERT: N 2054 MET cc_start: 0.8896 (tpp) cc_final: 0.8633 (tpp)
REVERT: N 2443 LEU cc_start: 0.9512 (tp) cc_final: 0.9234 (tt)
  outliers start: 15
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2602
  time to fit residues: 41.1704
Evaluate side-chains
  103 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1150 SER
Chi-restraints excluded: chain F residue 1201 LEU
Chi-restraints excluded: chain F residue 1285 MET
Chi-restraints excluded: chain F residue 1430 LYS
Chi-restraints excluded: chain F residue 1534 ARG
Chi-restraints excluded: chain F residue 1576 HIS
Chi-restraints excluded: chain F residue 1635 TYR
Chi-restraints excluded: chain F residue 1826 HIS
Chi-restraints excluded: chain F residue 1908 ILE
Chi-restraints excluded: chain N residue 2268 ILE
Chi-restraints excluded: chain N residue 2294 THR
Chi-restraints excluded: chain N residue 2436 VAL
Chi-restraints excluded: chain N residue 2638 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 197
   random chunks:
   chunk 148 optimal weight:    1.9990
   chunk 152 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 184 optimal weight:    4.9990
   chunk 192 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:    4.9990
   chunk 189 optimal weight:    6.9990
   chunk 196 optimal weight:    0.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.106958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.076716 restraints weight = 150534.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.079238 restraints weight = 70481.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080977 restraints weight = 47779.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.081952 restraints weight = 38602.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.082515 restraints weight = 34339.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  16027  Z= 0.113
  Angle     :  0.473   8.971  21715  Z= 0.247
  Chirality :  0.035   0.131   2524
  Planarity :  0.003   0.042   2739
  Dihedral  :  5.016  92.727   2146
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.53 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.16 %
    Favored  : 89.10 %
  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:  1.33 (0.19), residues: 1954
  helix:  1.85 (0.15), residues: 1243
  sheet:  0.30 (0.68), residues: 58
  loop : -0.98 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N2269 
 TYR   0.017   0.001   TYR F1948 
 PHE   0.010   0.001   PHE F 610 
 TRP   0.008   0.001   TRP F 599 
 HIS   0.003   0.001   HIS F1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (16024)
  covalent geometry    : angle       0.47320 (21715)
  hydrogen bonds       : bond        0.03778 (  792)
  hydrogen bonds       : angle       4.03490 ( 2319)
  metal coordination   : bond        0.00049 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4742.86 seconds
wall clock time: 81 minutes 33.47 seconds (4893.47 seconds total)