Starting phenix.real_space_refine
on Fri Mar  6 07:38:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z8s_14562/03_2026/7z8s_14562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z8s_14562/03_2026/7z8s_14562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z8s_14562/03_2026/7z8s_14562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z8s_14562/03_2026/7z8s_14562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z8s_14562/03_2026/7z8s_14562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z8s_14562/03_2026/7z8s_14562.cif"
  }
  resolution = 3.9
  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=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P      72      5.49       5
     S      70      5.16       5
     C    9171      2.51       5
     N    2614      2.21       5
     O    2871      1.98       5
     H   14473      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  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: 29271
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 1144
          Classifications: {'DNA': 36}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 35}
    Chain: "B"
      Number of atoms: 1135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 1135
          Classifications: {'DNA': 36}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 35}
    Chain: "D"
      Number of atoms: 2907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 2907
          Classifications: {'peptide': 178}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 169}
    Chain: "E"
      Number of atoms: 24085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1514, 24085
          Classifications: {'peptide': 1514}
          Link IDs: {'PTRANS': 76, 'TRANS': 1437}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 4.60, per 1000 atoms: 0.16
  Number of scatterers: 29271
  At special positions: 0
  Unit cell: (142.965, 136.611, 140.847, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      70     16.00
     P      72     15.00
     O    2871      8.00
     N    2614      7.00
     C    9171      6.00
     H   14473      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: 2.35
  Conformation dependent library (CDL) restraints added in 732.5 milliseconds
  

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3212

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 3 sheets defined
      68.0% alpha, 5.0% beta
      35 base pairs and 63 stacking pairs defined.
    Time for finding SS restraints: 5.63
  Creating SS restraints...
    Processing helix  chain 'D' and resid 97 through 104
      removed outlier: 3.653A  pdb=" N   ALA D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 161
    Processing helix  chain 'D' and resid 187 through 193
    Processing helix  chain 'D' and resid 234 through 250
      removed outlier: 4.200A  pdb=" N   ILE D 238 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   TYR D 239 " --> pdb=" O   ARG D 235 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET D 244 " --> pdb=" O   GLN D 240 " (cutoff:3.500A)
      Proline residue:  D 247  - end of helix
    Processing helix  chain 'D' and resid 251 through 253
      No H-bonds generated for 'chain 'D' and resid 251 through 253'
    Processing helix  chain 'E' and resid 3 through 11
      removed outlier: 3.789A  pdb=" N   ILE E  11 " --> pdb=" O   ARG E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 35
      removed outlier: 3.708A  pdb=" N   THR E  23 " --> pdb=" O   LEU E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 47
      removed outlier: 3.731A  pdb=" N   LEU E  42 " --> pdb=" O   GLU E  38 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ARG E  45 " --> pdb=" O   ASN E  41 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 52
    Processing helix  chain 'E' and resid 54 through 70
      removed outlier: 3.809A  pdb=" N   THR E  60 " --> pdb=" O   GLU E  56 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE E  69 " --> pdb=" O   ILE E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 313 through 324
      removed outlier: 3.688A  pdb=" N   VAL E 322 " --> pdb=" O   GLU E 318 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 329 through 347
    Processing helix  chain 'E' and resid 348 through 350
      No H-bonds generated for 'chain 'E' and resid 348 through 350'
    Processing helix  chain 'E' and resid 357 through 383
      removed outlier: 4.691A  pdb=" N   ASP E 363 " --> pdb=" O   LYS E 359 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LEU E 364 " --> pdb=" O   GLU E 360 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 395 through 409
    Processing helix  chain 'E' and resid 413 through 428
      removed outlier: 4.012A  pdb=" N   ALA E 419 " --> pdb=" O   GLU E 415 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 447 through 457
      removed outlier: 3.542A  pdb=" N   ARG E 451 " --> pdb=" O   MET E 447 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 458 through 464
      removed outlier: 3.845A  pdb=" N   LEU E 462 " --> pdb=" O   LYS E 458 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP E 464 " --> pdb=" O   LEU E 460 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 464 through 480
      removed outlier: 4.484A  pdb=" N   ILE E 468 " --> pdb=" O   ASP E 464 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY E 480 " --> pdb=" O   MET E 476 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 483 through 495
      removed outlier: 3.572A  pdb=" N   THR E 493 " --> pdb=" O   VAL E 489 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU E 494 " --> pdb=" O   SER E 490 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE E 495 " --> pdb=" O   ALA E 491 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 497 through 502
    Processing helix  chain 'E' and resid 505 through 522
      removed outlier: 3.780A  pdb=" N   LEU E 509 " --> pdb=" O   ARG E 505 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASN E 514 " --> pdb=" O   ASP E 510 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 529 through 542
      removed outlier: 4.071A  pdb=" N   LYS E 533 " --> pdb=" O   ALA E 529 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 544 through 558
    Processing helix  chain 'E' and resid 559 through 561
      No H-bonds generated for 'chain 'E' and resid 559 through 561'
    Processing helix  chain 'E' and resid 562 through 567
    Processing helix  chain 'E' and resid 568 through 576
      Proline residue:  E 572  - end of helix
      removed outlier: 4.228A  pdb=" N   ARG E 575 " --> pdb=" O   PRO E 572 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 578 through 594
      removed outlier: 3.805A  pdb=" N   LEU E 586 " --> pdb=" O   ARG E 582 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN E 594 " --> pdb=" O   MET E 590 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 605 through 619
      removed outlier: 3.619A  pdb=" N   LEU E 609 " --> pdb=" O   ASN E 605 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 621 through 643
      removed outlier: 3.982A  pdb=" N   ASP E 643 " --> pdb=" O   LEU E 639 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 643 through 652
      removed outlier: 3.610A  pdb=" N   LEU E 647 " --> pdb=" O   ASP E 643 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 654 through 663
    Processing helix  chain 'E' and resid 676 through 680
    Processing helix  chain 'E' and resid 732 through 736
      removed outlier: 3.593A  pdb=" N   MET E 735 " --> pdb=" O   ASP E 732 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 744 through 766
      removed outlier: 4.181A  pdb=" N   LEU E 761 " --> pdb=" O   LYS E 757 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE E 762 " --> pdb=" O   ALA E 758 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER E 764 " --> pdb=" O   GLY E 760 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 767 through 770
    Processing helix  chain 'E' and resid 771 through 782
      removed outlier: 3.601A  pdb=" N   ALA E 777 " --> pdb=" O   SER E 773 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 786 through 804
    Processing helix  chain 'E' and resid 806 through 812
      removed outlier: 4.661A  pdb=" N   ARG E 812 " --> pdb=" O   VAL E 809 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 813 through 823
      removed outlier: 3.678A  pdb=" N   ILE E 820 " --> pdb=" O   PRO E 816 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 829 through 831
      No H-bonds generated for 'chain 'E' and resid 829 through 831'
    Processing helix  chain 'E' and resid 832 through 853
      removed outlier: 3.809A  pdb=" N   VAL E 836 " --> pdb=" O   LEU E 832 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG E 851 " --> pdb=" O   ILE E 847 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 880 through 899
      removed outlier: 3.553A  pdb=" N   ASN E 889 " --> pdb=" O   GLU E 885 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP E 891 " --> pdb=" O   VAL E 887 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   PHE E 892 " --> pdb=" O   VAL E 888 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU E 898 " --> pdb=" O   ARG E 894 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 903 through 947
      Proline residue:  E 909  - end of helix
      removed outlier: 3.517A  pdb=" N   GLU E 924 " --> pdb=" O   GLU E 920 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA E 943 " --> pdb=" O   ALA E 939 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 954 through 968
      removed outlier: 3.593A  pdb=" N   SER E 964 " --> pdb=" O   ALA E 960 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 970 through 991
      removed outlier: 4.373A  pdb=" N   ARG E 976 " --> pdb=" O   GLU E 972 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER E 977 " --> pdb=" O   LEU E 973 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA E 982 " --> pdb=" O   ALA E 978 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 994 through 1009
      removed outlier: 3.927A  pdb=" N   CYS E1009 " --> pdb=" O   VAL E1005 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1010 through 1015
      removed outlier: 5.739A  pdb=" N   ALA E1013 " --> pdb=" O   VAL E1010 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1017 through 1022
    Processing helix  chain 'E' and resid 1028 through 1035
      removed outlier: 4.563A  pdb=" N   LYS E1033 " --> pdb=" O   SER E1030 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1044 through 1072
      removed outlier: 3.850A  pdb=" N   ARG E1054 " --> pdb=" O   ALA E1050 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLY E1059 " --> pdb=" O   ILE E1055 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU E1062 " --> pdb=" O   ARG E1058 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1074 through 1079
      removed outlier: 3.543A  pdb=" N   ARG E1078 " --> pdb=" O   GLU E1074 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1080 through 1095
      removed outlier: 3.880A  pdb=" N   MET E1086 " --> pdb=" O   LEU E1082 " (cutoff:3.500A)
      Proline residue:  E1089  - end of helix
    Processing helix  chain 'E' and resid 1099 through 1104
      removed outlier: 3.551A  pdb=" N   ASP E1104 " --> pdb=" O   GLU E1101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1107 through 1124
      removed outlier: 4.349A  pdb=" N   GLN E1111 " --> pdb=" O   ASN E1107 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE E1113 " --> pdb=" O   PHE E1109 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL E1114 " --> pdb=" O   GLY E1110 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   MET E1117 " --> pdb=" O   ILE E1113 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER E1118 " --> pdb=" O   VAL E1114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1125 through 1127
      No H-bonds generated for 'chain 'E' and resid 1125 through 1127'
    Processing helix  chain 'E' and resid 1128 through 1130
      No H-bonds generated for 'chain 'E' and resid 1128 through 1130'
    Processing helix  chain 'E' and resid 1131 through 1147
      removed outlier: 3.539A  pdb=" N   GLN E1138 " --> pdb=" O   PHE E1134 " (cutoff:3.500A)
      Proline residue:  E1140  - end of helix
    Processing helix  chain 'E' and resid 1150 through 1168
      removed outlier: 3.539A  pdb=" N   SER E1166 " --> pdb=" O   ALA E1162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1169 through 1180
    Processing helix  chain 'E' and resid 1181 through 1186
    Processing helix  chain 'E' and resid 1190 through 1208
      removed outlier: 3.930A  pdb=" N   ILE E1200 " --> pdb=" O   ALA E1196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1209 through 1212
      removed outlier: 4.148A  pdb=" N   LEU E1212 " --> pdb=" O   ASP E1209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 1209 through 1212'
    Processing helix  chain 'E' and resid 1214 through 1226
      removed outlier: 3.880A  pdb=" N   LEU E1218 " --> pdb=" O   TYR E1214 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   VAL E1220 " --> pdb=" O   ILE E1216 " (cutoff:3.500A)
      Proline residue:  E1221  - end of helix
    Processing helix  chain 'E' and resid 1230 through 1248
      removed outlier: 4.081A  pdb=" N   THR E1243 " --> pdb=" O   THR E1239 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   LYS E1246 " --> pdb=" O   ALA E1242 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU E1247 " --> pdb=" O   THR E1243 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL E1248 " --> pdb=" O   LEU E1244 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1249 through 1251
      No H-bonds generated for 'chain 'E' and resid 1249 through 1251'
    Processing helix  chain 'E' and resid 1261 through 1280
      removed outlier: 3.679A  pdb=" N   GLY E1267 " --> pdb=" O   GLU E1263 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLN E1277 " --> pdb=" O   THR E1273 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   LEU E1278 " --> pdb=" O   PHE E1274 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1298 through 1315
      removed outlier: 3.667A  pdb=" N   TYR E1314 " --> pdb=" O   PHE E1310 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1327 through 1350
      removed outlier: 3.582A  pdb=" N   GLU E1346 " --> pdb=" O   GLN E1342 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE E1347 " --> pdb=" O   ARG E1343 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1352 through 1356
    Processing helix  chain 'E' and resid 1365 through 1367
      No H-bonds generated for 'chain 'E' and resid 1365 through 1367'
    Processing helix  chain 'E' and resid 1368 through 1380
    Processing helix  chain 'E' and resid 1391 through 1396
    Processing helix  chain 'E' and resid 1397 through 1399
      No H-bonds generated for 'chain 'E' and resid 1397 through 1399'
    Processing helix  chain 'E' and resid 1400 through 1404
      removed outlier: 3.748A  pdb=" N   ASP E1403 " --> pdb=" O   ASP E1400 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1412 through 1416
    Processing helix  chain 'E' and resid 1418 through 1423
    Processing helix  chain 'E' and resid 1434 through 1439
      removed outlier: 3.510A  pdb=" N   LEU E1437 " --> pdb=" O   GLU E1434 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS E1439 " --> pdb=" O   HIS E1436 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1443 through 1450
    Processing helix  chain 'E' and resid 1468 through 1480
      removed outlier: 3.982A  pdb=" N   LEU E1472 " --> pdb=" O   ASN E1468 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1486 through 1494
    Processing helix  chain 'E' and resid 1494 through 1501
      removed outlier: 3.993A  pdb=" N   SER E1501 " --> pdb=" O   PRO E1497 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1502 through 1504
      No H-bonds generated for 'chain 'E' and resid 1502 through 1504'
    Processing helix  chain 'E' and resid 1508 through 1526
      removed outlier: 4.182A  pdb=" N   GLY E1514 " --> pdb=" O   GLU E1510 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU E1519 " --> pdb=" O   ALA E1515 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN E1524 " --> pdb=" O   ALA E1520 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1527 through 1529
      No H-bonds generated for 'chain 'E' and resid 1527 through 1529'
    Processing helix  chain 'E' and resid 1533 through 1538
    Processing helix  chain 'E' and resid 1554 through 1566
    Processing helix  chain 'E' and resid 1587 through 1598
    Processing helix  chain 'E' and resid 1632 through 1643
    Processing helix  chain 'E' and resid 1645 through 1650
    Processing helix  chain 'E' and resid 1673 through 1685
      removed outlier: 3.532A  pdb=" N   THR E1683 " --> pdb=" O   MET E1679 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU E1685 " --> pdb=" O   GLN E1681 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1705 through 1714
    Processing helix  chain 'E' and resid 1749 through 1758
    Processing helix  chain 'E' and resid 1779 through 1798
      removed outlier: 4.174A  pdb=" N   LYS E1783 " --> pdb=" O   THR E1779 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1811 through 1816
      removed outlier: 3.754A  pdb=" N   ASP E1816 " --> pdb=" O   ASP E1812 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1856 through 1861
      removed outlier: 4.069A  pdb=" N   LEU E1860 " --> pdb=" O   LYS E1856 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLU E1861 " --> pdb=" O   ALA E1857 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 1856 through 1861'
    Processing helix  chain 'E' and resid 1869 through 1877
      removed outlier: 3.920A  pdb=" N   GLU E1873 " --> pdb=" O   ASN E1869 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER E1875 " --> pdb=" O   GLN E1871 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1877 through 1885
      removed outlier: 3.625A  pdb=" N   PHE E1881 " --> pdb=" O   ASP E1877 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 117 through 121
      removed outlier: 6.781A  pdb=" N   VAL D 176 " --> pdb=" O   GLN D  83 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ILE D  85 " --> pdb=" O   ASN D 174 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ASN D 174 " --> pdb=" O   ILE D  85 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ALA D  87 " --> pdb=" O   ILE D 172 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE D 172 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   VAL D  89 " --> pdb=" O   PHE D 170 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   PHE D 170 " --> pdb=" O   VAL D  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 1318 through 1319
      removed outlier: 7.000A  pdb=" N   GLY E1318 " --> pdb=" O   ILE E1459 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LEU E1361 " --> pdb=" O   TYR E1429 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 1544 through 1551
      removed outlier: 6.166A  pdb=" N   VAL E1741 " --> pdb=" O   TYR E1772 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ILE E1774 " --> pdb=" O   VAL E1741 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   PHE E1743 " --> pdb=" O   ILE E1774 " (cutoff:3.500A)
      removed outlier: 8.775A  pdb=" N   THR E1776 " --> pdb=" O   PHE E1743 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU E1695 " --> pdb=" O   LEU E1723 " (cutoff:3.500A)
      removed outlier: 8.906A  pdb=" N   THR E1725 " --> pdb=" O   LEU E1695 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   LEU E1697 " --> pdb=" O   THR E1725 " (cutoff:3.500A)

    722 hydrogen bonds defined for protein.
    2073 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      95 hydrogen bonds
      190 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      63 stacking parallelities
  Total time for adding SS restraints: 7.96

  Time building geometry restraints manager: 3.32 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: 14452
        1.03 -     1.23: 42
        1.23 -     1.42: 6150
        1.42 -     1.62: 8926
        1.62 -     1.81: 119
  Bond restraints: 29689
  Sorted by residual:
  bond pdb=" N   SER D  76 "
       pdb=" CA  SER D  76 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" C1'  DC B  29 "
       pdb=" N1   DC B  29 "
    ideal  model  delta    sigma   weight residual
    1.490  1.542 -0.052 3.00e-02 1.11e+03 3.05e+00
  bond pdb=" N   ALA E   2 "
       pdb=" CA  ALA E   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.82e+00
  bond pdb=" C1'  DT B  10 "
       pdb=" N1   DT B  10 "
    ideal  model  delta    sigma   weight residual
    1.490  1.539 -0.049 3.00e-02 1.11e+03 2.64e+00
  bond pdb=" C1'  DC B  34 "
       pdb=" N1   DC B  34 "
    ideal  model  delta    sigma   weight residual
    1.490  1.538 -0.048 3.00e-02 1.11e+03 2.54e+00
  ... (remaining 29684 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 51175
        1.52 -     3.05: 2494
        3.05 -     4.57: 210
        4.57 -     6.09: 33
        6.09 -     7.61: 3
  Bond angle restraints: 53915
  Sorted by residual:
  angle pdb=" C   VAL E  46 "
        pdb=" N   VAL E  47 "
        pdb=" CA  VAL E  47 "
      ideal   model   delta    sigma   weight residual
     120.24  123.45   -3.21 6.30e-01 2.52e+00 2.60e+01
  angle pdb=" C   VAL E  47 "
        pdb=" CA  VAL E  47 "
        pdb=" CB  VAL E  47 "
      ideal   model   delta    sigma   weight residual
     114.35  110.06    4.29 1.06e+00 8.90e-01 1.64e+01
  angle pdb=" C   VAL E1525 "
        pdb=" N   LEU E1526 "
        pdb=" CA  LEU E1526 "
      ideal   model   delta    sigma   weight residual
     120.97  125.17   -4.20 1.48e+00 4.57e-01 8.06e+00
  angle pdb=" N   VAL E1248 "
        pdb=" CA  VAL E1248 "
        pdb=" C   VAL E1248 "
      ideal   model   delta    sigma   weight residual
     108.88  114.87   -5.99 2.16e+00 2.14e-01 7.69e+00
  angle pdb=" N   LEU E  39 "
        pdb=" CA  LEU E  39 "
        pdb=" C   LEU E  39 "
      ideal   model   delta    sigma   weight residual
     111.11  114.20   -3.09 1.20e+00 6.94e-01 6.64e+00
  ... (remaining 53910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 11895
       17.86 -    35.73: 1115
       35.73 -    53.59: 388
       53.59 -    71.46: 115
       71.46 -    89.32: 11
  Dihedral angle restraints: 13524
    sinusoidal: 7933
      harmonic: 5591
  Sorted by residual:
  dihedral pdb=" CA  PHE E 501 "
           pdb=" C   PHE E 501 "
           pdb=" N   VAL E 502 "
           pdb=" CA  VAL E 502 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.07  -21.93     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ILE E1113 "
           pdb=" C   ILE E1113 "
           pdb=" N   VAL E1114 "
           pdb=" CA  VAL E1114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.53   20.47     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ILE D 121 "
           pdb=" C   ILE D 121 "
           pdb=" N   ARG D 122 "
           pdb=" CA  ARG D 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.79  -20.21     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 13521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1628
       0.038 -    0.075: 576
       0.075 -    0.113: 174
       0.113 -    0.150: 36
       0.150 -    0.188: 4
  Chirality restraints: 2418
  Sorted by residual:
  chirality pdb=" CA  THR E1124 "
            pdb=" N   THR E1124 "
            pdb=" C   THR E1124 "
            pdb=" CB  THR E1124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.81e-01
  chirality pdb=" CA  ILE E 766 "
            pdb=" N   ILE E 766 "
            pdb=" C   ILE E 766 "
            pdb=" CB  ILE E 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.59e-01
  chirality pdb=" CA  ILE E 673 "
            pdb=" N   ILE E 673 "
            pdb=" C   ILE E 673 "
            pdb=" CB  ILE E 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.43e-01
  ... (remaining 2415 not shown)

  Planarity restraints: 4093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E1083 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.87e+00
        pdb=" C   ARG E1083 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ARG E1083 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR E1084 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E1491 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.85e+00
        pdb=" C   LEU E1491 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LEU E1491 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP E1492 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 332 "    0.144 9.50e-02 1.11e+02   4.80e-02 2.58e+00
        pdb=" NE  ARG E 332 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 332 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 332 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 332 "   -0.005 2.00e-02 2.50e+03
        pdb="HH11 ARG E 332 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG E 332 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG E 332 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG E 332 "    0.007 2.00e-02 2.50e+03
  ... (remaining 4090 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 3364
        2.26 -     2.85: 64594
        2.85 -     3.43: 75085
        3.43 -     4.02: 100778
        4.02 -     4.60: 154122
  Nonbonded interactions: 397943
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E1323 "
            pdb="HH12 ARG E1531 "
     model   vdw
     1.677 2.450
  nonbonded pdb=" H   ARG E1666 "
            pdb=" OD2 ASP E1739 "
     model   vdw
     1.686 2.450
  nonbonded pdb=" O   VAL E1684 "
            pdb=" H   LEU E1689 "
     model   vdw
     1.688 2.450
  nonbonded pdb="HD22 ASN D 106 "
            pdb=" O   ARG D 120 "
     model   vdw
     1.692 2.450
  nonbonded pdb=" O   LEU E 761 "
            pdb=" HG  SER E 764 "
     model   vdw
     1.695 2.450
  ... (remaining 397938 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.900
  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:             0.130
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     31.670
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
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   0.056  15216  Z= 0.194
  Angle     :  0.743   7.613  20906  Z= 0.415
  Chirality :  0.042   0.188   2418
  Planarity :  0.005   0.059   2430
  Dihedral  : 16.373  89.319   5890
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  6.26 %
    Favored  : 92.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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: -0.90 (0.20), residues: 1674
  helix: -0.41 (0.16), residues: 972
  sheet: -0.85 (0.47), residues: 114
  loop : -0.57 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 825 
 TYR   0.016   0.002   TYR E1214 
 PHE   0.018   0.002   PHE E 892 
 TRP   0.012   0.002   TRP E  55 
 HIS   0.007   0.001   HIS E 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (15216)
  covalent geometry    : angle       0.74321 (20906)
  hydrogen bonds       : bond        0.15406 (  817)
  hydrogen bonds       : angle       5.99477 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  373 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 358
  time to evaluate  : 0.689 
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: D  194 HIS cc_start: 0.5303 (m90) cc_final: 0.4588 (m-70)
REVERT: D  212 MET cc_start: 0.7885 (tmm) cc_final: 0.7600 (tmm)
REVERT: E   43 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8532 (mp)
REVERT: E  315 ARG cc_start: 0.7122 (ptt-90) cc_final: 0.6798 (ptp-110)
REVERT: E  385 PHE cc_start: 0.5313 (m-80) cc_final: 0.5070 (m-80)
REVERT: E  583 LEU cc_start: 0.9261 (tt) cc_final: 0.8882 (tt)
REVERT: E  735 MET cc_start: 0.8506 (tpt) cc_final: 0.8227 (tpt)
REVERT: E 1411 SER cc_start: 0.9327 (t) cc_final: 0.8983 (p)
REVERT: E 1413 ASP cc_start: 0.7363 (m-30) cc_final: 0.6937 (m-30)
REVERT: E 1564 PHE cc_start: 0.6157 (t80) cc_final: 0.5897 (t80)
REVERT: E 1733 LEU cc_start: 0.8937 (tp) cc_final: 0.8645 (tp)
REVERT: E 1763 ILE cc_start: 0.8646 (tt) cc_final: 0.8324 (mm)
  outliers start: 15
  outliers final: 4
  residues processed: 370
  average time/residue: 0.3211
  time to fit residues: 164.4906
Evaluate side-chains
  225 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 220
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1694 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.2980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
D  90 ASN
E 418 HIS
E 671 HIS
** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1373 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.130413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.097026 restraints weight = 80432.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.100948 restraints weight = 37225.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103430 restraints weight = 22294.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.104967 restraints weight = 15953.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.105941 restraints weight = 12878.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15216  Z= 0.174
  Angle     :  0.631   8.252  20906  Z= 0.349
  Chirality :  0.040   0.174   2418
  Planarity :  0.005   0.055   2430
  Dihedral  : 17.272  73.318   2592
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.59 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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: -0.58 (0.20), residues: 1674
  helix:  0.05 (0.16), residues: 982
  sheet: -1.02 (0.49), residues: 101
  loop : -0.80 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E1343 
 TYR   0.017   0.002   TYR E 452 
 PHE   0.023   0.002   PHE E 501 
 TRP   0.014   0.001   TRP E 311 
 HIS   0.005   0.001   HIS E1746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (15216)
  covalent geometry    : angle       0.63105 (20906)
  hydrogen bonds       : bond        0.05366 (  817)
  hydrogen bonds       : angle       4.72080 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  260 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 227
  time to evaluate  : 0.692 
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: D  194 HIS cc_start: 0.6198 (m90) cc_final: 0.5299 (m-70)
REVERT: E   43 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: E  315 ARG cc_start: 0.7008 (ptt-90) cc_final: 0.6776 (ptp-110)
REVERT: E  735 MET cc_start: 0.8706 (tpt) cc_final: 0.8454 (tpt)
REVERT: E  799 GLU cc_start: 0.7485 (tp30) cc_final: 0.7069 (tp30)
REVERT: E 1185 ASN cc_start: 0.8433 (m-40) cc_final: 0.8055 (p0)
REVERT: E 1594 MET cc_start: 0.8881 (mtt) cc_final: 0.8673 (mtt)
REVERT: E 1676 MET cc_start: 0.9378 (tpp) cc_final: 0.8898 (tpp)
REVERT: E 1733 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8677 (tp)
REVERT: E 1747 ASP cc_start: 0.8296 (t70) cc_final: 0.8089 (t0)
REVERT: E 1763 ILE cc_start: 0.8549 (tt) cc_final: 0.8195 (mm)
  outliers start: 33
  outliers final: 22
  residues processed: 249
  average time/residue: 0.2327
  time to fit residues: 88.8143
Evaluate side-chains
  231 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 207
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  311 TRP
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  895 LEU
Chi-restraints excluded: chain E residue  998 GLU
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1200 ILE
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1733 LEU
Chi-restraints excluded: chain E residue 1744 VAL
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 153 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 166 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 154 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   chunk 134 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
D  90 ASN
E 671 HIS
** E 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1277 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.128808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.095484 restraints weight = 80725.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.099331 restraints weight = 37665.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.101776 restraints weight = 22665.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103357 restraints weight = 16267.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.104222 restraints weight = 13171.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  15216  Z= 0.174
  Angle     :  0.595   6.649  20906  Z= 0.327
  Chirality :  0.040   0.176   2418
  Planarity :  0.005   0.077   2430
  Dihedral  : 17.303  67.499   2590
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.08 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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: -0.35 (0.20), residues: 1674
  helix:  0.32 (0.16), residues: 992
  sheet: -1.09 (0.49), residues: 102
  loop : -0.85 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 211 
 TYR   0.014   0.001   TYR E1214 
 PHE   0.016   0.002   PHE E 385 
 TRP   0.016   0.002   TRP E 329 
 HIS   0.004   0.001   HIS E1746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (15216)
  covalent geometry    : angle       0.59510 (20906)
  hydrogen bonds       : bond        0.04701 (  817)
  hydrogen bonds       : angle       4.49197 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  248 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 209
  time to evaluate  : 0.693 
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: D   84 ASN cc_start: 0.8815 (t0) cc_final: 0.8594 (t0)
REVERT: D  194 HIS cc_start: 0.6361 (m90) cc_final: 0.5320 (m-70)
REVERT: E   43 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8265 (mp)
REVERT: E  315 ARG cc_start: 0.7020 (ptt-90) cc_final: 0.6811 (ptp-110)
REVERT: E  735 MET cc_start: 0.8727 (tpt) cc_final: 0.8480 (tpt)
REVERT: E  917 GLN cc_start: 0.8712 (tp40) cc_final: 0.8267 (tm-30)
REVERT: E 1028 ILE cc_start: 0.8579 (mt) cc_final: 0.7728 (tt)
REVERT: E 1185 ASN cc_start: 0.8435 (m-40) cc_final: 0.7967 (p0)
REVERT: E 1676 MET cc_start: 0.9341 (tpp) cc_final: 0.8960 (tpp)
REVERT: E 1733 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (tp)
REVERT: E 1763 ILE cc_start: 0.8571 (tt) cc_final: 0.8237 (mm)
  outliers start: 39
  outliers final: 28
  residues processed: 237
  average time/residue: 0.2377
  time to fit residues: 85.5316
Evaluate side-chains
  223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 193
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  311 TRP
Chi-restraints excluded: chain E residue  383 ASP
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  895 LEU
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue  998 GLU
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1733 LEU
Chi-restraints excluded: chain E residue 1744 VAL
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 145 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 116 optimal weight:    0.4980
   chunk 134 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
E 858 GLN
E1277 GLN
E1803 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.129636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.096278 restraints weight = 80577.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.100118 restraints weight = 37497.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.102535 restraints weight = 22596.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.104109 restraints weight = 16285.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.105024 restraints weight = 13208.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  15216  Z= 0.145
  Angle     :  0.564   6.510  20906  Z= 0.310
  Chirality :  0.039   0.173   2418
  Planarity :  0.004   0.052   2430
  Dihedral  : 17.224  59.928   2590
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.18 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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: -0.15 (0.21), residues: 1674
  helix:  0.55 (0.17), residues: 999
  sheet: -1.05 (0.49), residues: 102
  loop : -0.93 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 915 
 TYR   0.010   0.001   TYR E 421 
 PHE   0.014   0.001   PHE E1347 
 TRP   0.014   0.001   TRP E 311 
 HIS   0.027   0.001   HIS E 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (15216)
  covalent geometry    : angle       0.56398 (20906)
  hydrogen bonds       : bond        0.04155 (  817)
  hydrogen bonds       : angle       4.27167 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  233 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.761 
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: D   84 ASN cc_start: 0.8847 (t0) cc_final: 0.8613 (t0)
REVERT: D  194 HIS cc_start: 0.6261 (m90) cc_final: 0.5210 (m-70)
REVERT: E   43 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8239 (mp)
REVERT: E  735 MET cc_start: 0.8697 (tpt) cc_final: 0.8495 (tpt)
REVERT: E  759 MET cc_start: 0.8329 (tpt) cc_final: 0.8080 (tpp)
REVERT: E  917 GLN cc_start: 0.8651 (tp40) cc_final: 0.8389 (tm-30)
REVERT: E  924 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: E 1014 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7447 (mp0)
REVERT: E 1185 ASN cc_start: 0.8396 (m-40) cc_final: 0.7935 (p0)
REVERT: E 1280 ASP cc_start: 0.3863 (OUTLIER) cc_final: 0.3658 (t0)
REVERT: E 1594 MET cc_start: 0.8879 (mtt) cc_final: 0.8677 (mtt)
REVERT: E 1676 MET cc_start: 0.9311 (tpp) cc_final: 0.8990 (tpp)
REVERT: E 1763 ILE cc_start: 0.8591 (tt) cc_final: 0.8271 (mm)
REVERT: E 1772 TYR cc_start: 0.7838 (m-80) cc_final: 0.7619 (m-80)
  outliers start: 32
  outliers final: 27
  residues processed: 224
  average time/residue: 0.2305
  time to fit residues: 79.7000
Evaluate side-chains
  219 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  311 TRP
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  895 LEU
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue  998 GLU
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1280 ASP
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1744 VAL
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 155 optimal weight:    5.9990
   chunk 126 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.128239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094871 restraints weight = 81521.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.098652 restraints weight = 38307.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.101045 restraints weight = 23194.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.102491 restraints weight = 16761.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.103540 restraints weight = 13633.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  15216  Z= 0.169
  Angle     :  0.577   8.312  20906  Z= 0.314
  Chirality :  0.039   0.146   2418
  Planarity :  0.004   0.040   2430
  Dihedral  : 17.187  59.914   2590
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.38 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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: -0.14 (0.21), residues: 1674
  helix:  0.60 (0.17), residues: 998
  sheet: -1.03 (0.50), residues: 102
  loop : -1.04 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 904 
 TYR   0.013   0.001   TYR E 421 
 PHE   0.026   0.002   PHE E1347 
 TRP   0.014   0.001   TRP E 311 
 HIS   0.004   0.001   HIS E1746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (15216)
  covalent geometry    : angle       0.57656 (20906)
  hydrogen bonds       : bond        0.04146 (  817)
  hydrogen bonds       : angle       4.27508 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  237 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 199
  time to evaluate  : 0.745 
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: D   84 ASN cc_start: 0.8825 (t0) cc_final: 0.8589 (t0)
REVERT: D  194 HIS cc_start: 0.6395 (m90) cc_final: 0.5330 (m-70)
REVERT: E   43 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8247 (mp)
REVERT: E  917 GLN cc_start: 0.8632 (tp40) cc_final: 0.8243 (tm-30)
REVERT: E  924 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: E 1185 ASN cc_start: 0.8409 (m-40) cc_final: 0.7973 (p0)
REVERT: E 1320 LEU cc_start: 0.9445 (tp) cc_final: 0.9190 (tt)
REVERT: E 1480 MET cc_start: 0.9018 (ptp) cc_final: 0.8734 (mtp)
REVERT: E 1594 MET cc_start: 0.8880 (mtt) cc_final: 0.8670 (mtt)
REVERT: E 1676 MET cc_start: 0.9325 (tpp) cc_final: 0.9052 (tpp)
REVERT: E 1763 ILE cc_start: 0.8626 (tt) cc_final: 0.8314 (mm)
REVERT: E 1772 TYR cc_start: 0.7837 (m-80) cc_final: 0.7594 (m-80)
  outliers start: 38
  outliers final: 30
  residues processed: 226
  average time/residue: 0.2390
  time to fit residues: 83.2435
Evaluate side-chains
  216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 185
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  311 TRP
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  467 MET
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  888 VAL
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue  998 GLU
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1744 VAL
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 168 optimal weight:    5.9990
   chunk 172 optimal weight:    0.9990
   chunk 131 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 152 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
E1765 GLN
E1803 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.127835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.094612 restraints weight = 81978.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.098437 restraints weight = 37598.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.100888 restraints weight = 22445.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.102401 restraints weight = 16065.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.103189 restraints weight = 13049.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  15216  Z= 0.179
  Angle     :  0.585   7.343  20906  Z= 0.319
  Chirality :  0.040   0.180   2418
  Planarity :  0.004   0.040   2430
  Dihedral  : 17.162  59.966   2590
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.14 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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: -0.12 (0.21), residues: 1674
  helix:  0.66 (0.17), residues: 996
  sheet: -1.06 (0.50), residues: 102
  loop : -1.07 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 904 
 TYR   0.010   0.001   TYR E1549 
 PHE   0.017   0.002   PHE E1561 
 TRP   0.015   0.001   TRP E 311 
 HIS   0.004   0.001   HIS E 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (15216)
  covalent geometry    : angle       0.58483 (20906)
  hydrogen bonds       : bond        0.04150 (  817)
  hydrogen bonds       : angle       4.28120 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  226 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.743 
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: D  194 HIS cc_start: 0.6500 (m90) cc_final: 0.5415 (m-70)
REVERT: E   43 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8178 (mp)
REVERT: E  917 GLN cc_start: 0.8675 (tp40) cc_final: 0.8247 (tm-30)
REVERT: E  923 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8403 (tm-30)
REVERT: E  924 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: E 1014 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7544 (mp0)
REVERT: E 1185 ASN cc_start: 0.8437 (m-40) cc_final: 0.7947 (p0)
REVERT: E 1594 MET cc_start: 0.8913 (mtt) cc_final: 0.8667 (mtt)
REVERT: E 1676 MET cc_start: 0.9349 (tpp) cc_final: 0.9116 (tpp)
REVERT: E 1757 MET cc_start: 0.8849 (mtm) cc_final: 0.8527 (mtt)
REVERT: E 1763 ILE cc_start: 0.8638 (tt) cc_final: 0.8322 (mm)
REVERT: E 1772 TYR cc_start: 0.7809 (m-80) cc_final: 0.7572 (m-80)
  outliers start: 37
  outliers final: 30
  residues processed: 218
  average time/residue: 0.2185
  time to fit residues: 74.2094
Evaluate side-chains
  217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 185
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  311 TRP
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  888 VAL
Chi-restraints excluded: chain E residue  922 ILE
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue  998 GLU
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1725 THR
Chi-restraints excluded: chain E residue 1744 VAL
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 145 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 163 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0370
   chunk 127 optimal weight:    2.9990
   overall best weight:    1.0862

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

Flipped N/Q/H residues before XYZ refinement:
E1026 ASN
E1803 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.129062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.096285 restraints weight = 80997.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.100073 restraints weight = 37728.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.102417 restraints weight = 22684.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.103950 restraints weight = 16297.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.104842 restraints weight = 13255.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15216  Z= 0.139
  Angle     :  0.555   8.705  20906  Z= 0.300
  Chirality :  0.039   0.165   2418
  Planarity :  0.004   0.039   2430
  Dihedral  : 17.113  59.790   2590
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.76 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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:  0.03 (0.21), residues: 1674
  helix:  0.79 (0.17), residues: 992
  sheet: -1.00 (0.50), residues: 102
  loop : -1.03 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 904 
 TYR   0.014   0.001   TYR E 452 
 PHE   0.018   0.001   PHE E1561 
 TRP   0.013   0.001   TRP E 311 
 HIS   0.003   0.001   HIS E1746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (15216)
  covalent geometry    : angle       0.55521 (20906)
  hydrogen bonds       : bond        0.03850 (  817)
  hydrogen bonds       : angle       4.09495 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  224 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 189
  time to evaluate  : 0.676 
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: D   84 ASN cc_start: 0.8853 (t0) cc_final: 0.8649 (t0)
REVERT: D  194 HIS cc_start: 0.6410 (m90) cc_final: 0.5398 (m-70)
REVERT: E   43 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8168 (mp)
REVERT: E  330 GLU cc_start: 0.7915 (mp0) cc_final: 0.7705 (mp0)
REVERT: E  917 GLN cc_start: 0.8691 (tp40) cc_final: 0.8338 (tm-30)
REVERT: E  923 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8341 (tm-30)
REVERT: E  924 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8310 (tm-30)
REVERT: E 1014 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7481 (mp0)
REVERT: E 1185 ASN cc_start: 0.8405 (m-40) cc_final: 0.7899 (p0)
REVERT: E 1594 MET cc_start: 0.8867 (mtt) cc_final: 0.8627 (mtt)
REVERT: E 1676 MET cc_start: 0.9312 (tpp) cc_final: 0.9108 (tpp)
REVERT: E 1757 MET cc_start: 0.8847 (mtm) cc_final: 0.8518 (mtt)
REVERT: E 1763 ILE cc_start: 0.8671 (tt) cc_final: 0.8361 (mm)
REVERT: E 1772 TYR cc_start: 0.7668 (m-80) cc_final: 0.7397 (m-80)
  outliers start: 35
  outliers final: 29
  residues processed: 214
  average time/residue: 0.2313
  time to fit residues: 76.0172
Evaluate side-chains
  213 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 182
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  311 TRP
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  888 VAL
Chi-restraints excluded: chain E residue  912 ASN
Chi-restraints excluded: chain E residue  922 ILE
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1725 THR
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 162 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 132 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
E 671 HIS
E1026 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.129281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.096040 restraints weight = 80842.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.099880 restraints weight = 37172.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.102351 restraints weight = 22279.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.103984 restraints weight = 15911.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.105008 restraints weight = 12735.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15216  Z= 0.137
  Angle     :  0.553   8.059  20906  Z= 0.298
  Chirality :  0.039   0.152   2418
  Planarity :  0.004   0.035   2430
  Dihedral  : 17.069  59.797   2590
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.79 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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:  0.14 (0.21), residues: 1674
  helix:  0.90 (0.17), residues: 992
  sheet: -1.01 (0.50), residues: 102
  loop : -1.01 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 904 
 TYR   0.009   0.001   TYR E 452 
 PHE   0.019   0.001   PHE E1561 
 TRP   0.012   0.001   TRP E 311 
 HIS   0.003   0.001   HIS E 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (15216)
  covalent geometry    : angle       0.55251 (20906)
  hydrogen bonds       : bond        0.03714 (  817)
  hydrogen bonds       : angle       4.03075 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 186
  time to evaluate  : 0.626 
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: D   84 ASN cc_start: 0.8869 (t0) cc_final: 0.8657 (t0)
REVERT: D  194 HIS cc_start: 0.6420 (m90) cc_final: 0.5498 (m-70)
REVERT: E   43 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8158 (mp)
REVERT: E  330 GLU cc_start: 0.7971 (mp0) cc_final: 0.7752 (mp0)
REVERT: E  917 GLN cc_start: 0.8659 (tp40) cc_final: 0.8317 (tm-30)
REVERT: E  923 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8347 (tm-30)
REVERT: E  924 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: E 1014 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7488 (mp0)
REVERT: E 1185 ASN cc_start: 0.8406 (m-40) cc_final: 0.7894 (p0)
REVERT: E 1594 MET cc_start: 0.8873 (mtt) cc_final: 0.8642 (mtt)
REVERT: E 1757 MET cc_start: 0.8856 (mtm) cc_final: 0.8526 (mtt)
REVERT: E 1763 ILE cc_start: 0.8674 (tt) cc_final: 0.8370 (mm)
REVERT: E 1772 TYR cc_start: 0.7635 (m-80) cc_final: 0.7388 (m-80)
  outliers start: 30
  outliers final: 26
  residues processed: 206
  average time/residue: 0.2391
  time to fit residues: 75.3906
Evaluate side-chains
  210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  912 ASN
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1516 LEU
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1725 THR
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 165 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 147 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
E 671 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.128631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.095506 restraints weight = 80276.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.099194 restraints weight = 37769.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.101611 restraints weight = 22935.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.103175 restraints weight = 16486.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.104146 restraints weight = 13304.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  15216  Z= 0.140
  Angle     :  0.553   8.909  20906  Z= 0.298
  Chirality :  0.038   0.149   2418
  Planarity :  0.004   0.035   2430
  Dihedral  : 17.049  59.889   2590
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.66 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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:  0.20 (0.21), residues: 1674
  helix:  0.95 (0.17), residues: 992
  sheet: -0.96 (0.50), residues: 102
  loop : -1.00 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 904 
 TYR   0.012   0.001   TYR D 154 
 PHE   0.023   0.001   PHE E1347 
 TRP   0.011   0.001   TRP E 311 
 HIS   0.015   0.001   HIS E 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (15216)
  covalent geometry    : angle       0.55275 (20906)
  hydrogen bonds       : bond        0.03679 (  817)
  hydrogen bonds       : angle       3.99097 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  218 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 186
  time to evaluate  : 0.617 
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: D   84 ASN cc_start: 0.8875 (t0) cc_final: 0.8666 (t0)
REVERT: D  194 HIS cc_start: 0.6421 (m90) cc_final: 0.5515 (m-70)
REVERT: E   43 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8179 (mp)
REVERT: E  330 GLU cc_start: 0.7908 (mp0) cc_final: 0.7700 (mp0)
REVERT: E  743 VAL cc_start: 0.8764 (t) cc_final: 0.8531 (m)
REVERT: E  917 GLN cc_start: 0.8641 (tp40) cc_final: 0.8252 (tm-30)
REVERT: E  923 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: E  924 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8282 (tm-30)
REVERT: E 1014 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7492 (mp0)
REVERT: E 1112 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8359 (tt0)
REVERT: E 1185 ASN cc_start: 0.8404 (m-40) cc_final: 0.7884 (p0)
REVERT: E 1594 MET cc_start: 0.8916 (mtt) cc_final: 0.8676 (mtt)
REVERT: E 1757 MET cc_start: 0.8851 (mtm) cc_final: 0.8518 (mtt)
REVERT: E 1763 ILE cc_start: 0.8704 (tt) cc_final: 0.8407 (mm)
REVERT: E 1772 TYR cc_start: 0.7555 (m-80) cc_final: 0.7317 (m-80)
  outliers start: 32
  outliers final: 24
  residues processed: 210
  average time/residue: 0.2251
  time to fit residues: 72.1703
Evaluate side-chains
  209 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  912 ASN
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1112 GLU
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1289 ILE
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1725 THR
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 170 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
E1026 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.129532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.096258 restraints weight = 80615.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.100113 restraints weight = 37040.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.102568 restraints weight = 22187.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.104034 restraints weight = 15928.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.105123 restraints weight = 12908.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15216  Z= 0.137
  Angle     :  0.561   8.424  20906  Z= 0.301
  Chirality :  0.039   0.148   2418
  Planarity :  0.004   0.037   2430
  Dihedral  : 17.030  59.939   2590
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.34 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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 (0.21), residues: 1674
  helix:  0.99 (0.17), residues: 992
  sheet: -0.93 (0.50), residues: 102
  loop : -1.00 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 915 
 TYR   0.018   0.001   TYR D 154 
 PHE   0.020   0.001   PHE E1561 
 TRP   0.010   0.001   TRP E 311 
 HIS   0.003   0.001   HIS E1746 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (15216)
  covalent geometry    : angle       0.56053 (20906)
  hydrogen bonds       : bond        0.03593 (  817)
  hydrogen bonds       : angle       3.95680 ( 2263)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  507 is missing expected H atoms. Skipping.
Residue SER 1261 is missing expected H atoms. Skipping.
Evaluate side-chains
  213 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.782 
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: D   84 ASN cc_start: 0.8870 (t0) cc_final: 0.8667 (t0)
REVERT: D  194 HIS cc_start: 0.6464 (m90) cc_final: 0.5563 (m-70)
REVERT: E   43 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8148 (mp)
REVERT: E  330 GLU cc_start: 0.7881 (mp0) cc_final: 0.7679 (mp0)
REVERT: E  743 VAL cc_start: 0.8746 (t) cc_final: 0.8507 (m)
REVERT: E  917 GLN cc_start: 0.8584 (tp40) cc_final: 0.8225 (tm-30)
REVERT: E  923 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: E  924 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: E 1014 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: E 1185 ASN cc_start: 0.8420 (m-40) cc_final: 0.7868 (p0)
REVERT: E 1207 MET cc_start: 0.8249 (tpp) cc_final: 0.8026 (mmm)
REVERT: E 1594 MET cc_start: 0.8917 (mtt) cc_final: 0.8674 (mtt)
REVERT: E 1757 MET cc_start: 0.8868 (mtm) cc_final: 0.8527 (mtt)
REVERT: E 1763 ILE cc_start: 0.8712 (tt) cc_final: 0.8420 (mm)
REVERT: E 1772 TYR cc_start: 0.7410 (m-80) cc_final: 0.7178 (m-80)
  outliers start: 28
  outliers final: 24
  residues processed: 204
  average time/residue: 0.2254
  time to fit residues: 71.3643
Evaluate side-chains
  202 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 176
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  208 LEU
Chi-restraints excluded: chain D residue  245 ILE
Chi-restraints excluded: chain D residue  248 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  420 ILE
Chi-restraints excluded: chain E residue  471 VAL
Chi-restraints excluded: chain E residue  589 LEU
Chi-restraints excluded: chain E residue  617 ILE
Chi-restraints excluded: chain E residue  671 HIS
Chi-restraints excluded: chain E residue  814 ILE
Chi-restraints excluded: chain E residue  880 SER
Chi-restraints excluded: chain E residue  912 ASN
Chi-restraints excluded: chain E residue  965 ILE
Chi-restraints excluded: chain E residue 1014 GLU
Chi-restraints excluded: chain E residue 1068 SER
Chi-restraints excluded: chain E residue 1091 VAL
Chi-restraints excluded: chain E residue 1163 THR
Chi-restraints excluded: chain E residue 1223 LEU
Chi-restraints excluded: chain E residue 1361 LEU
Chi-restraints excluded: chain E residue 1429 TYR
Chi-restraints excluded: chain E residue 1694 TYR
Chi-restraints excluded: chain E residue 1725 THR
Chi-restraints excluded: chain E residue 1746 HIS
Chi-restraints excluded: chain E residue 1793 ASP
Chi-restraints excluded: chain E residue 1794 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 163 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 81 optimal weight:    0.3980
   chunk 117 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 126 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 169 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** E1026 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 = 0.3809 r_free = 0.3809 target = 0.128848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.095516 restraints weight = 81191.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.099318 restraints weight = 37433.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.101809 restraints weight = 22448.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.103376 restraints weight = 16035.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104187 restraints weight = 12956.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  15216  Z= 0.156
  Angle     :  0.565   8.987  20906  Z= 0.304
  Chirality :  0.039   0.148   2418
  Planarity :  0.004   0.034   2430
  Dihedral  : 17.027  59.919   2590
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.62 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.20 %
    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:  0.21 (0.21), residues: 1674
  helix:  0.97 (0.17), residues: 996
  sheet: -1.11 (0.50), residues: 105
  loop : -1.01 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 915 
 TYR   0.017   0.001   TYR D 154 
 PHE   0.020   0.001   PHE E1561 
 TRP   0.011   0.001   TRP E 311 
 HIS   0.003   0.001   HIS E 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (15216)
  covalent geometry    : angle       0.56460 (20906)
  hydrogen bonds       : bond        0.03683 (  817)
  hydrogen bonds       : angle       3.99015 ( 2263)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4613.12 seconds
wall clock time: 79 minutes 8.71 seconds (4748.71 seconds total)