Starting phenix.real_space_refine on Tue Feb 20 03:52:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6u_10106/02_2024/6s6u_10106_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6u_10106/02_2024/6s6u_10106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6u_10106/02_2024/6s6u_10106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6u_10106/02_2024/6s6u_10106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6u_10106/02_2024/6s6u_10106_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6u_10106/02_2024/6s6u_10106_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.020 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 Fe 50 7.16 5 P 14 5.49 5 S 484 5.16 5 C 51864 2.51 5 N 14916 2.21 5 O 15650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 1156": "NH1" <-> "NH2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A ARG 1186": "NH1" <-> "NH2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A ARG 1252": "NH1" <-> "NH2" Residue "A GLU 1316": "OE1" <-> "OE2" Residue "A ARG 1345": "NH1" <-> "NH2" Residue "A GLU 1408": "OE1" <-> "OE2" Residue "A ARG 1449": "NH1" <-> "NH2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "A ARG 1465": "NH1" <-> "NH2" Residue "A GLU 1467": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B ARG 782": "NH1" <-> "NH2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B ARG 893": "NH1" <-> "NH2" Residue "B GLU 940": "OE1" <-> "OE2" Residue "B GLU 1145": "OE1" <-> "OE2" Residue "B ARG 1156": "NH1" <-> "NH2" Residue "B ARG 1173": "NH1" <-> "NH2" Residue "B ARG 1186": "NH1" <-> "NH2" Residue "B GLU 1206": "OE1" <-> "OE2" Residue "B ARG 1214": "NH1" <-> "NH2" Residue "B GLU 1225": "OE1" <-> "OE2" Residue "B ARG 1252": "NH1" <-> "NH2" Residue "B GLU 1316": "OE1" <-> "OE2" Residue "B GLU 1344": "OE1" <-> "OE2" Residue "B ARG 1345": "NH1" <-> "NH2" Residue "B GLU 1434": "OE1" <-> "OE2" Residue "B ARG 1449": "NH1" <-> "NH2" Residue "B GLU 1461": "OE1" <-> "OE2" Residue "B ARG 1465": "NH1" <-> "NH2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C ARG 782": "NH1" <-> "NH2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C GLU 844": "OE1" <-> "OE2" Residue "C ARG 893": "NH1" <-> "NH2" Residue "C GLU 927": "OE1" <-> "OE2" Residue "C GLU 1145": "OE1" <-> "OE2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C ARG 1173": "NH1" <-> "NH2" Residue "C ARG 1186": "NH1" <-> "NH2" Residue "C ARG 1214": "NH1" <-> "NH2" Residue "C GLU 1225": "OE1" <-> "OE2" Residue "C ARG 1252": "NH1" <-> "NH2" Residue "C ARG 1345": "NH1" <-> "NH2" Residue "C GLU 1408": "OE1" <-> "OE2" Residue "C GLU 1434": "OE1" <-> "OE2" Residue "C ARG 1449": "NH1" <-> "NH2" Residue "C GLU 1450": "OE1" <-> "OE2" Residue "C ARG 1465": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D ARG 782": "NH1" <-> "NH2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D ARG 893": "NH1" <-> "NH2" Residue "D ARG 1156": "NH1" <-> "NH2" Residue "D ARG 1173": "NH1" <-> "NH2" Residue "D GLU 1176": "OE1" <-> "OE2" Residue "D ARG 1186": "NH1" <-> "NH2" Residue "D ARG 1214": "NH1" <-> "NH2" Residue "D GLU 1225": "OE1" <-> "OE2" Residue "D ARG 1252": "NH1" <-> "NH2" Residue "D GLU 1316": "OE1" <-> "OE2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "D GLU 1408": "OE1" <-> "OE2" Residue "D ARG 1449": "NH1" <-> "NH2" Residue "D GLU 1461": "OE1" <-> "OE2" Residue "D ARG 1465": "NH1" <-> "NH2" Residue "D GLU 1467": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E GLU 428": "OE1" <-> "OE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E ARG 556": "NH1" <-> "NH2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E ARG 745": "NH1" <-> "NH2" Residue "E ARG 782": "NH1" <-> "NH2" Residue "E GLU 842": "OE1" <-> "OE2" Residue "E GLU 844": "OE1" <-> "OE2" Residue "E ARG 893": "NH1" <-> "NH2" Residue "E GLU 927": "OE1" <-> "OE2" Residue "E GLU 1145": "OE1" <-> "OE2" Residue "E ARG 1156": "NH1" <-> "NH2" Residue "E ARG 1173": "NH1" <-> "NH2" Residue "E ARG 1186": "NH1" <-> "NH2" Residue "E ARG 1214": "NH1" <-> "NH2" Residue "E GLU 1225": "OE1" <-> "OE2" Residue "E ARG 1252": "NH1" <-> "NH2" Residue "E ARG 1345": "NH1" <-> "NH2" Residue "E GLU 1408": "OE1" <-> "OE2" Residue "E GLU 1434": "OE1" <-> "OE2" Residue "E ARG 1449": "NH1" <-> "NH2" Residue "E GLU 1450": "OE1" <-> "OE2" Residue "E ARG 1465": "NH1" <-> "NH2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 474": "OE1" <-> "OE2" Residue "F GLU 516": "OE1" <-> "OE2" Residue "F GLU 535": "OE1" <-> "OE2" Residue "F GLU 537": "OE1" <-> "OE2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F ARG 556": "NH1" <-> "NH2" Residue "F GLU 568": "OE1" <-> "OE2" Residue "F GLU 592": "OE1" <-> "OE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "F GLU 677": "OE1" <-> "OE2" Residue "F GLU 726": "OE1" <-> "OE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F ARG 782": "NH1" <-> "NH2" Residue "F GLU 815": "OE1" <-> "OE2" Residue "F GLU 830": "OE1" <-> "OE2" Residue "F GLU 842": "OE1" <-> "OE2" Residue "F GLU 886": "OE1" <-> "OE2" Residue "F ARG 893": "NH1" <-> "NH2" Residue "F GLU 940": "OE1" <-> "OE2" Residue "F GLU 1145": "OE1" <-> "OE2" Residue "F ARG 1156": "NH1" <-> "NH2" Residue "F ARG 1173": "NH1" <-> "NH2" Residue "F ARG 1186": "NH1" <-> "NH2" Residue "F GLU 1206": "OE1" <-> "OE2" Residue "F ARG 1214": "NH1" <-> "NH2" Residue "F GLU 1225": "OE1" <-> "OE2" Residue "F ARG 1252": "NH1" <-> "NH2" Residue "F GLU 1316": "OE1" <-> "OE2" Residue "F GLU 1344": "OE1" <-> "OE2" Residue "F ARG 1345": "NH1" <-> "NH2" Residue "F GLU 1434": "OE1" <-> "OE2" Residue "F ARG 1449": "NH1" <-> "NH2" Residue "F GLU 1461": "OE1" <-> "OE2" Residue "F ARG 1465": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G ARG 47": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G ARG 311": "NH1" <-> "NH2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G ARG 333": "NH1" <-> "NH2" Residue "G GLU 344": "OE1" <-> "OE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 429": "NH1" <-> "NH2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "G GLU 474": "OE1" <-> "OE2" Residue "H ARG 5": "NH1" <-> "NH2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H ARG 47": "NH1" <-> "NH2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H GLU 282": "OE1" <-> "OE2" Residue "H ARG 311": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ARG 333": "NH1" <-> "NH2" Residue "H GLU 339": "OE1" <-> "OE2" Residue "H GLU 344": "OE1" <-> "OE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 367": "NH1" <-> "NH2" Residue "H GLU 385": "OE1" <-> "OE2" Residue "H GLU 413": "OE1" <-> "OE2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H GLU 474": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 223": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "I GLU 279": "OE1" <-> "OE2" Residue "I GLU 282": "OE1" <-> "OE2" Residue "I ARG 311": "NH1" <-> "NH2" Residue "I ARG 325": "NH1" <-> "NH2" Residue "I ARG 333": "NH1" <-> "NH2" Residue "I GLU 344": "OE1" <-> "OE2" Residue "I ARG 364": "NH1" <-> "NH2" Residue "I ARG 367": "NH1" <-> "NH2" Residue "I ARG 420": "NH1" <-> "NH2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I GLU 463": "OE1" <-> "OE2" Residue "I GLU 474": "OE1" <-> "OE2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J ARG 179": "NH1" <-> "NH2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J ARG 223": "NH1" <-> "NH2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J GLU 282": "OE1" <-> "OE2" Residue "J ARG 311": "NH1" <-> "NH2" Residue "J ARG 325": "NH1" <-> "NH2" Residue "J ARG 333": "NH1" <-> "NH2" Residue "J GLU 339": "OE1" <-> "OE2" Residue "J GLU 344": "OE1" <-> "OE2" Residue "J GLU 352": "OE1" <-> "OE2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J ARG 367": "NH1" <-> "NH2" Residue "J GLU 385": "OE1" <-> "OE2" Residue "J GLU 413": "OE1" <-> "OE2" Residue "J ARG 420": "NH1" <-> "NH2" Residue "J ARG 429": "NH1" <-> "NH2" Residue "J GLU 474": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 82978 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "B" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "C" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "D" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "E" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "F" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "G" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "H" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "J" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8585 SG CYS A1113 41.041 82.516 61.334 1.00 29.90 S ATOM 8499 SG CYS A1102 47.235 80.483 61.432 1.00 28.69 S ATOM 8548 SG CYS A1108 45.394 85.935 58.506 1.00 30.37 S ATOM 19922 SG CYS B1113 43.164 74.577 140.930 1.00126.63 S ATOM 19836 SG CYS B1102 49.563 75.428 142.758 1.00125.07 S ATOM 19885 SG CYS B1108 47.306 70.791 138.856 1.00117.42 S ATOM 31259 SG CYS C1113 38.199 152.736 98.979 1.00 36.02 S ATOM 31173 SG CYS C1102 44.365 153.473 97.407 1.00 32.69 S ATOM 31222 SG CYS C1108 42.756 154.559 103.398 1.00 39.38 S ATOM 42596 SG CYS D1113 150.126 128.510 61.319 1.00 29.60 S ATOM 42510 SG CYS D1102 143.935 130.551 61.395 1.00 28.67 S ATOM 42559 SG CYS D1108 145.778 125.094 58.480 1.00 30.76 S ATOM 53933 SG CYS E1113 152.892 58.510 99.088 1.00 35.61 S ATOM 53847 SG CYS E1102 146.733 57.753 97.499 1.00 31.76 S ATOM 53896 SG CYS E1108 148.327 56.683 103.497 1.00 38.72 S ATOM 65270 SG CYS F1113 147.817 136.573 141.068 1.00127.21 S ATOM 65184 SG CYS F1102 141.417 135.740 142.899 1.00124.68 S ATOM 65233 SG CYS F1108 143.683 140.363 138.987 1.00116.85 S ATOM 68418 SG CYS G 51 41.376 75.244 52.957 1.00 29.19 S ATOM 68453 SG CYS G 56 40.750 70.316 50.215 1.00 27.90 S ATOM 68397 SG CYS G 48 37.185 75.118 49.430 1.00 31.15 S ATOM 68868 SG CYS G 109 36.560 70.667 54.650 1.00 30.52 S ATOM 68841 SG CYS G 105 36.561 62.909 50.760 1.00 39.20 S ATOM 68485 SG CYS G 60 41.624 62.213 47.490 1.00 30.83 S ATOM 68792 SG CYS G 99 37.031 58.130 49.596 1.00 45.88 S ATOM 72031 SG CYS H 51 38.673 163.138 96.031 1.00 41.80 S ATOM 72066 SG CYS H 56 37.907 167.821 92.248 1.00 41.09 S ATOM 72010 SG CYS H 48 34.558 166.622 97.286 1.00 43.94 S ATOM 72481 SG CYS H 109 33.797 163.067 91.718 1.00 42.18 S ATOM 72454 SG CYS H 105 33.808 169.713 85.553 1.00 54.55 S ATOM 72098 SG CYS H 60 38.674 173.310 85.525 1.00 45.34 S ATOM 72405 SG CYS H 99 34.308 173.463 81.019 1.00 61.40 S ATOM 75644 SG CYS I 51 149.550 135.808 52.879 1.00 30.01 S ATOM 75679 SG CYS I 56 150.195 140.735 50.138 1.00 28.81 S ATOM 75623 SG CYS I 48 153.752 135.925 49.364 1.00 32.09 S ATOM 76094 SG CYS I 109 154.370 140.375 54.587 1.00 30.59 S ATOM 76067 SG CYS I 105 154.397 148.132 50.696 1.00 38.75 S ATOM 75711 SG CYS I 60 149.346 148.839 47.410 1.00 31.64 S ATOM 76018 SG CYS I 99 153.942 152.913 49.530 1.00 45.31 S ATOM 79257 SG CYS J 51 152.437 47.851 96.064 1.00 41.77 S ATOM 79292 SG CYS J 56 153.232 43.164 92.291 1.00 42.27 S ATOM 79236 SG CYS J 48 156.559 44.383 97.339 1.00 44.30 S ATOM 79707 SG CYS J 109 157.327 47.931 91.768 1.00 42.64 S ATOM 79680 SG CYS J 105 157.361 41.275 85.614 1.00 54.72 S ATOM 79324 SG CYS J 60 152.508 37.661 85.575 1.00 45.71 S ATOM 79631 SG CYS J 99 156.891 37.515 81.084 1.00 60.54 S Time building chain proxies: 30.65, per 1000 atoms: 0.37 Number of scatterers: 82978 At special positions: 0 Unit cell: (192.51, 212.474, 179.676, 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) Fe 50 26.01 S 484 16.00 P 14 15.00 O 15650 8.00 N 14916 7.00 C 51864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 23.26 Conformation dependent library (CDL) restraints added in 11.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A1502 " pdb="FE1 F3S A1502 " - pdb=" SG CYS A1113 " pdb="FE3 F3S A1502 " - pdb=" SG CYS A1102 " pdb="FE4 F3S A1502 " - pdb=" SG CYS A1108 " pdb=" F3S B1502 " pdb="FE4 F3S B1502 " - pdb=" SG CYS B1108 " pdb="FE3 F3S B1502 " - pdb=" SG CYS B1102 " pdb="FE1 F3S B1502 " - pdb=" SG CYS B1113 " pdb=" F3S C1502 " pdb="FE1 F3S C1502 " - pdb=" SG CYS C1113 " pdb="FE3 F3S C1502 " - pdb=" SG CYS C1102 " pdb="FE4 F3S C1502 " - pdb=" SG CYS C1108 " pdb=" F3S D1502 " pdb="FE1 F3S D1502 " - pdb=" SG CYS D1113 " pdb="FE3 F3S D1502 " - pdb=" SG CYS D1102 " pdb="FE4 F3S D1502 " - pdb=" SG CYS D1108 " pdb=" F3S E1502 " pdb="FE1 F3S E1502 " - pdb=" SG CYS E1113 " pdb="FE3 F3S E1502 " - pdb=" SG CYS E1102 " pdb="FE4 F3S E1502 " - pdb=" SG CYS E1108 " pdb=" F3S F1502 " pdb="FE4 F3S F1502 " - pdb=" SG CYS F1108 " pdb="FE3 F3S F1502 " - pdb=" SG CYS F1102 " pdb="FE1 F3S F1502 " - pdb=" SG CYS F1113 " pdb=" SF4 G 501 " pdb="FE2 SF4 G 501 " - pdb=" SG CYS G 56 " pdb="FE1 SF4 G 501 " - pdb=" SG CYS G 51 " pdb="FE3 SF4 G 501 " - pdb=" SG CYS G 48 " pdb="FE4 SF4 G 501 " - pdb=" SG CYS G 109 " pdb=" SF4 G 502 " pdb="FE2 SF4 G 502 " - pdb=" SG CYS G 60 " pdb="FE1 SF4 G 502 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G 502 " - pdb=" SG CYS G 99 " pdb=" SF4 H 501 " pdb="FE3 SF4 H 501 " - pdb=" SG CYS H 48 " pdb="FE2 SF4 H 501 " - pdb=" SG CYS H 56 " pdb="FE4 SF4 H 501 " - pdb=" SG CYS H 109 " pdb="FE1 SF4 H 501 " - pdb=" SG CYS H 51 " pdb=" SF4 H 502 " pdb="FE2 SF4 H 502 " - pdb=" SG CYS H 60 " pdb="FE1 SF4 H 502 " - pdb=" SG CYS H 105 " pdb="FE4 SF4 H 502 " - pdb=" SG CYS H 99 " pdb=" SF4 I 501 " pdb="FE2 SF4 I 501 " - pdb=" SG CYS I 56 " pdb="FE1 SF4 I 501 " - pdb=" SG CYS I 51 " pdb="FE3 SF4 I 501 " - pdb=" SG CYS I 48 " pdb="FE4 SF4 I 501 " - pdb=" SG CYS I 109 " pdb=" SF4 I 502 " pdb="FE2 SF4 I 502 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 502 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 502 " - pdb=" SG CYS I 99 " pdb=" SF4 J 501 " pdb="FE3 SF4 J 501 " - pdb=" SG CYS J 48 " pdb="FE2 SF4 J 501 " - pdb=" SG CYS J 56 " pdb="FE4 SF4 J 501 " - pdb=" SG CYS J 109 " pdb="FE1 SF4 J 501 " - pdb=" SG CYS J 51 " pdb=" SF4 J 502 " pdb="FE2 SF4 J 502 " - pdb=" SG CYS J 60 " pdb="FE1 SF4 J 502 " - pdb=" SG CYS J 105 " pdb="FE4 SF4 J 502 " - pdb=" SG CYS J 99 " Number of angles added : 138 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 436 helices and 78 sheets defined 35.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.14 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.819A pdb=" N ALA A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.781A pdb=" N ALA A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 141 through 161 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.320A pdb=" N THR A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.585A pdb=" N ASP A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.848A pdb=" N THR A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.733A pdb=" N GLN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.630A pdb=" N ALA A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.559A pdb=" N GLU A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 552 through 565 removed outlier: 6.341A pdb=" N ASP A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 598 removed outlier: 3.914A pdb=" N GLU A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.599A pdb=" N ALA A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 680 Processing helix chain 'A' and resid 689 through 710 Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 751 through 766 Processing helix chain 'A' and resid 792 through 804 Processing helix chain 'A' and resid 807 through 818 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.640A pdb=" N ARG A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.718A pdb=" N ILE A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 1006 through 1015 removed outlier: 3.715A pdb=" N LYS A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1045 through 1058 removed outlier: 3.540A pdb=" N GLN A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1064 No H-bonds generated for 'chain 'A' and resid 1062 through 1064' Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1093 through 1099 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 4.316A pdb=" N LYS A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1153 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1183 through 1187 Processing helix chain 'A' and resid 1211 through 1218 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1245 through 1253 Processing helix chain 'A' and resid 1317 through 1319 No H-bonds generated for 'chain 'A' and resid 1317 through 1319' Processing helix chain 'A' and resid 1401 through 1404 No H-bonds generated for 'chain 'A' and resid 1401 through 1404' Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.870A pdb=" N GLN A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A1424 " --> pdb=" O TYR A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1445 Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 4.709A pdb=" N THR A1452 " --> pdb=" O ALA A1448 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.781A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 141 through 161 Processing helix chain 'B' and resid 188 through 191 No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.866A pdb=" N ASN B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 273 through 287 removed outlier: 4.013A pdb=" N ALA B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 403 through 412 removed outlier: 4.122A pdb=" N THR B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.976A pdb=" N GLN B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.864A pdb=" N PHE B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 462 No H-bonds generated for 'chain 'B' and resid 459 through 462' Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 552 through 565 removed outlier: 6.441A pdb=" N ASP B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR B 565 " --> pdb=" O TYR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 599 removed outlier: 3.672A pdb=" N GLU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 633 Processing helix chain 'B' and resid 652 through 661 removed outlier: 3.536A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 680 Processing helix chain 'B' and resid 689 through 709 Processing helix chain 'B' and resid 716 through 719 No H-bonds generated for 'chain 'B' and resid 716 through 719' Processing helix chain 'B' and resid 732 through 738 Processing helix chain 'B' and resid 751 through 766 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 807 through 817 Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 847 through 852 removed outlier: 4.932A pdb=" N ARG B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 878 removed outlier: 4.190A pdb=" N ILE B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 921 through 923 No H-bonds generated for 'chain 'B' and resid 921 through 923' Processing helix chain 'B' and resid 951 through 957 Processing helix chain 'B' and resid 977 through 990 Processing helix chain 'B' and resid 1006 through 1016 removed outlier: 3.766A pdb=" N LYS B1015 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B1016 " --> pdb=" O GLY B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1045 through 1058 Processing helix chain 'B' and resid 1062 through 1064 No H-bonds generated for 'chain 'B' and resid 1062 through 1064' Processing helix chain 'B' and resid 1076 through 1085 Processing helix chain 'B' and resid 1093 through 1100 Processing helix chain 'B' and resid 1125 through 1127 No H-bonds generated for 'chain 'B' and resid 1125 through 1127' Processing helix chain 'B' and resid 1132 through 1153 Processing helix chain 'B' and resid 1158 through 1160 No H-bonds generated for 'chain 'B' and resid 1158 through 1160' Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1184 through 1187 No H-bonds generated for 'chain 'B' and resid 1184 through 1187' Processing helix chain 'B' and resid 1211 through 1218 Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1245 through 1253 Processing helix chain 'B' and resid 1317 through 1319 No H-bonds generated for 'chain 'B' and resid 1317 through 1319' Processing helix chain 'B' and resid 1401 through 1404 No H-bonds generated for 'chain 'B' and resid 1401 through 1404' Processing helix chain 'B' and resid 1418 through 1435 removed outlier: 3.648A pdb=" N GLN B1423 " --> pdb=" O HIS B1419 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B1424 " --> pdb=" O TYR B1420 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1445 Processing helix chain 'B' and resid 1447 through 1453 removed outlier: 4.782A pdb=" N THR B1452 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS B1453 " --> pdb=" O ARG B1449 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.622A pdb=" N ALA C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 141 through 162 Processing helix chain 'C' and resid 185 through 191 removed outlier: 4.911A pdb=" N THR C 189 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 238 through 250 removed outlier: 3.864A pdb=" N ASN C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.058A pdb=" N ALA C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 403 through 412 removed outlier: 3.722A pdb=" N THR C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.867A pdb=" N GLN C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN C 422 " --> pdb=" O LYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 444 through 454 removed outlier: 3.536A pdb=" N ALA C 453 " --> pdb=" O ARG C 449 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 462 Processing helix chain 'C' and resid 466 through 470 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 552 through 562 Processing helix chain 'C' and resid 581 through 599 removed outlier: 3.753A pdb=" N GLU C 594 " --> pdb=" O ARG C 590 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 633 Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.822A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 680 Processing helix chain 'C' and resid 689 through 709 Processing helix chain 'C' and resid 716 through 719 No H-bonds generated for 'chain 'C' and resid 716 through 719' Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 751 through 766 Processing helix chain 'C' and resid 792 through 804 Processing helix chain 'C' and resid 807 through 817 Processing helix chain 'C' and resid 825 through 827 No H-bonds generated for 'chain 'C' and resid 825 through 827' Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 847 through 852 removed outlier: 4.801A pdb=" N ARG C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 877 Processing helix chain 'C' and resid 891 through 893 No H-bonds generated for 'chain 'C' and resid 891 through 893' Processing helix chain 'C' and resid 946 through 948 No H-bonds generated for 'chain 'C' and resid 946 through 948' Processing helix chain 'C' and resid 951 through 956 Processing helix chain 'C' and resid 977 through 990 Processing helix chain 'C' and resid 1006 through 1016 removed outlier: 3.615A pdb=" N LYS C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C1016 " --> pdb=" O GLY C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'C' and resid 1045 through 1058 Processing helix chain 'C' and resid 1062 through 1064 No H-bonds generated for 'chain 'C' and resid 1062 through 1064' Processing helix chain 'C' and resid 1076 through 1085 Processing helix chain 'C' and resid 1093 through 1100 Processing helix chain 'C' and resid 1108 through 1110 No H-bonds generated for 'chain 'C' and resid 1108 through 1110' Processing helix chain 'C' and resid 1125 through 1127 No H-bonds generated for 'chain 'C' and resid 1125 through 1127' Processing helix chain 'C' and resid 1132 through 1153 removed outlier: 3.546A pdb=" N VAL C1146 " --> pdb=" O LEU C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1160 No H-bonds generated for 'chain 'C' and resid 1158 through 1160' Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing helix chain 'C' and resid 1184 through 1187 No H-bonds generated for 'chain 'C' and resid 1184 through 1187' Processing helix chain 'C' and resid 1211 through 1218 Processing helix chain 'C' and resid 1220 through 1224 Processing helix chain 'C' and resid 1245 through 1253 Processing helix chain 'C' and resid 1317 through 1319 No H-bonds generated for 'chain 'C' and resid 1317 through 1319' Processing helix chain 'C' and resid 1401 through 1404 No H-bonds generated for 'chain 'C' and resid 1401 through 1404' Processing helix chain 'C' and resid 1418 through 1435 Processing helix chain 'C' and resid 1439 through 1445 Processing helix chain 'C' and resid 1447 through 1453 removed outlier: 4.767A pdb=" N THR C1452 " --> pdb=" O ALA C1448 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS C1453 " --> pdb=" O ARG C1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.819A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.780A pdb=" N ALA D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 141 through 161 Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 240 through 249 removed outlier: 4.320A pdb=" N THR D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.585A pdb=" N ASP D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.848A pdb=" N THR D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.733A pdb=" N GLN D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 444 through 454 removed outlier: 3.631A pdb=" N ALA D 453 " --> pdb=" O ARG D 449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 462 removed outlier: 3.560A pdb=" N GLU D 462 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 552 through 565 removed outlier: 6.341A pdb=" N ASP D 564 " --> pdb=" O ASP D 560 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR D 565 " --> pdb=" O TYR D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.914A pdb=" N GLU D 594 " --> pdb=" O ARG D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 633 Processing helix chain 'D' and resid 652 through 661 removed outlier: 3.599A pdb=" N ALA D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 680 Processing helix chain 'D' and resid 689 through 710 Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 751 through 766 Processing helix chain 'D' and resid 792 through 804 Processing helix chain 'D' and resid 807 through 818 Processing helix chain 'D' and resid 825 through 827 No H-bonds generated for 'chain 'D' and resid 825 through 827' Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 846 through 852 removed outlier: 4.641A pdb=" N ARG D 852 " --> pdb=" O ALA D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 878 removed outlier: 3.718A pdb=" N ILE D 878 " --> pdb=" O ALA D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 893 No H-bonds generated for 'chain 'D' and resid 891 through 893' Processing helix chain 'D' and resid 951 through 957 Processing helix chain 'D' and resid 977 through 990 Processing helix chain 'D' and resid 1006 through 1015 removed outlier: 3.715A pdb=" N LYS D1015 " --> pdb=" O ALA D1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 1035 through 1039 Processing helix chain 'D' and resid 1045 through 1058 removed outlier: 3.541A pdb=" N GLN D1054 " --> pdb=" O SER D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1064 No H-bonds generated for 'chain 'D' and resid 1062 through 1064' Processing helix chain 'D' and resid 1076 through 1085 Processing helix chain 'D' and resid 1093 through 1099 Processing helix chain 'D' and resid 1122 through 1127 removed outlier: 4.316A pdb=" N LYS D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1153 Processing helix chain 'D' and resid 1165 through 1167 No H-bonds generated for 'chain 'D' and resid 1165 through 1167' Processing helix chain 'D' and resid 1183 through 1187 Processing helix chain 'D' and resid 1211 through 1218 Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1245 through 1253 Processing helix chain 'D' and resid 1317 through 1319 No H-bonds generated for 'chain 'D' and resid 1317 through 1319' Processing helix chain 'D' and resid 1401 through 1404 No H-bonds generated for 'chain 'D' and resid 1401 through 1404' Processing helix chain 'D' and resid 1418 through 1435 removed outlier: 3.869A pdb=" N GLN D1423 " --> pdb=" O HIS D1419 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D1424 " --> pdb=" O TYR D1420 " (cutoff:3.500A) Processing helix chain 'D' and resid 1439 through 1445 Processing helix chain 'D' and resid 1447 through 1453 removed outlier: 4.708A pdb=" N THR D1452 " --> pdb=" O ALA D1448 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS D1453 " --> pdb=" O ARG D1449 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.622A pdb=" N ALA E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 141 through 162 Processing helix chain 'E' and resid 185 through 191 removed outlier: 4.911A pdb=" N THR E 189 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 196 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.864A pdb=" N ASN E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR E 249 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 273 through 287 removed outlier: 4.058A pdb=" N ALA E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 311 through 323 Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.721A pdb=" N THR E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.867A pdb=" N GLN E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN E 422 " --> pdb=" O LYS E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 444 through 454 removed outlier: 3.536A pdb=" N ALA E 453 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 462 Processing helix chain 'E' and resid 466 through 470 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 538 through 540 No H-bonds generated for 'chain 'E' and resid 538 through 540' Processing helix chain 'E' and resid 552 through 562 Processing helix chain 'E' and resid 581 through 599 removed outlier: 3.754A pdb=" N GLU E 594 " --> pdb=" O ARG E 590 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY E 599 " --> pdb=" O ASP E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 633 Processing helix chain 'E' and resid 652 through 661 removed outlier: 3.821A pdb=" N ALA E 656 " --> pdb=" O THR E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 680 Processing helix chain 'E' and resid 689 through 709 Processing helix chain 'E' and resid 716 through 719 No H-bonds generated for 'chain 'E' and resid 716 through 719' Processing helix chain 'E' and resid 732 through 738 Processing helix chain 'E' and resid 751 through 766 Processing helix chain 'E' and resid 792 through 804 Processing helix chain 'E' and resid 807 through 817 Processing helix chain 'E' and resid 825 through 827 No H-bonds generated for 'chain 'E' and resid 825 through 827' Processing helix chain 'E' and resid 840 through 842 No H-bonds generated for 'chain 'E' and resid 840 through 842' Processing helix chain 'E' and resid 847 through 852 removed outlier: 4.801A pdb=" N ARG E 852 " --> pdb=" O ALA E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 877 Processing helix chain 'E' and resid 891 through 893 No H-bonds generated for 'chain 'E' and resid 891 through 893' Processing helix chain 'E' and resid 946 through 948 No H-bonds generated for 'chain 'E' and resid 946 through 948' Processing helix chain 'E' and resid 951 through 956 Processing helix chain 'E' and resid 977 through 990 Processing helix chain 'E' and resid 1006 through 1016 removed outlier: 3.616A pdb=" N LYS E1015 " --> pdb=" O ALA E1011 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E1016 " --> pdb=" O GLY E1012 " (cutoff:3.500A) Processing helix chain 'E' and resid 1035 through 1039 Processing helix chain 'E' and resid 1045 through 1058 Processing helix chain 'E' and resid 1062 through 1064 No H-bonds generated for 'chain 'E' and resid 1062 through 1064' Processing helix chain 'E' and resid 1076 through 1085 Processing helix chain 'E' and resid 1093 through 1100 Processing helix chain 'E' and resid 1108 through 1110 No H-bonds generated for 'chain 'E' and resid 1108 through 1110' 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 1132 through 1153 removed outlier: 3.546A pdb=" N VAL E1146 " --> pdb=" O LEU E1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 1158 through 1160 No H-bonds generated for 'chain 'E' and resid 1158 through 1160' Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1184 through 1187 No H-bonds generated for 'chain 'E' and resid 1184 through 1187' Processing helix chain 'E' and resid 1211 through 1218 Processing helix chain 'E' and resid 1220 through 1224 Processing helix chain 'E' and resid 1245 through 1253 Processing helix chain 'E' and resid 1317 through 1319 No H-bonds generated for 'chain 'E' and resid 1317 through 1319' Processing helix chain 'E' and resid 1401 through 1404 No H-bonds generated for 'chain 'E' and resid 1401 through 1404' Processing helix chain 'E' and resid 1418 through 1435 Processing helix chain 'E' and resid 1439 through 1445 Processing helix chain 'E' and resid 1447 through 1453 removed outlier: 4.767A pdb=" N THR E1452 " --> pdb=" O ALA E1448 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS E1453 " --> pdb=" O ARG E1449 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 27 removed outlier: 3.781A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 85 through 97 Processing helix chain 'F' and resid 141 through 161 Processing helix chain 'F' and resid 188 through 191 No H-bonds generated for 'chain 'F' and resid 188 through 191' Processing helix chain 'F' and resid 193 through 196 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 238 through 250 removed outlier: 3.866A pdb=" N ASN F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 273 through 287 removed outlier: 4.012A pdb=" N ALA F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 376 through 378 No H-bonds generated for 'chain 'F' and resid 376 through 378' Processing helix chain 'F' and resid 403 through 412 removed outlier: 4.122A pdb=" N THR F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.976A pdb=" N GLN F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASN F 422 " --> pdb=" O LYS F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 444 through 454 removed outlier: 3.864A pdb=" N PHE F 454 " --> pdb=" O ARG F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 462 No H-bonds generated for 'chain 'F' and resid 459 through 462' Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 537 through 540 Processing helix chain 'F' and resid 552 through 565 removed outlier: 6.440A pdb=" N ASP F 564 " --> pdb=" O ASP F 560 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR F 565 " --> pdb=" O TYR F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 599 removed outlier: 3.672A pdb=" N GLU F 594 " --> pdb=" O ARG F 590 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 599 " --> pdb=" O ASP F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 633 Processing helix chain 'F' and resid 652 through 661 removed outlier: 3.536A pdb=" N ALA F 656 " --> pdb=" O THR F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 680 Processing helix chain 'F' and resid 689 through 709 Processing helix chain 'F' and resid 716 through 719 No H-bonds generated for 'chain 'F' and resid 716 through 719' Processing helix chain 'F' and resid 732 through 738 Processing helix chain 'F' and resid 751 through 766 Processing helix chain 'F' and resid 792 through 804 Processing helix chain 'F' and resid 807 through 817 Processing helix chain 'F' and resid 825 through 827 No H-bonds generated for 'chain 'F' and resid 825 through 827' Processing helix chain 'F' and resid 840 through 842 No H-bonds generated for 'chain 'F' and resid 840 through 842' Processing helix chain 'F' and resid 847 through 852 removed outlier: 4.933A pdb=" N ARG F 852 " --> pdb=" O ALA F 848 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 878 removed outlier: 4.190A pdb=" N ILE F 878 " --> pdb=" O ALA F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 894 Processing helix chain 'F' and resid 921 through 923 No H-bonds generated for 'chain 'F' and resid 921 through 923' Processing helix chain 'F' and resid 951 through 957 Processing helix chain 'F' and resid 977 through 990 Processing helix chain 'F' and resid 1006 through 1016 removed outlier: 3.766A pdb=" N LYS F1015 " --> pdb=" O ALA F1011 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F1016 " --> pdb=" O GLY F1012 " (cutoff:3.500A) Processing helix chain 'F' and resid 1035 through 1039 Processing helix chain 'F' and resid 1045 through 1058 Processing helix chain 'F' and resid 1062 through 1064 No H-bonds generated for 'chain 'F' and resid 1062 through 1064' Processing helix chain 'F' and resid 1076 through 1085 Processing helix chain 'F' and resid 1093 through 1100 Processing helix chain 'F' and resid 1125 through 1127 No H-bonds generated for 'chain 'F' and resid 1125 through 1127' Processing helix chain 'F' and resid 1132 through 1153 Processing helix chain 'F' and resid 1158 through 1160 No H-bonds generated for 'chain 'F' and resid 1158 through 1160' Processing helix chain 'F' and resid 1165 through 1167 No H-bonds generated for 'chain 'F' and resid 1165 through 1167' Processing helix chain 'F' and resid 1184 through 1187 No H-bonds generated for 'chain 'F' and resid 1184 through 1187' Processing helix chain 'F' and resid 1211 through 1218 Processing helix chain 'F' and resid 1220 through 1224 Processing helix chain 'F' and resid 1245 through 1253 Processing helix chain 'F' and resid 1317 through 1319 No H-bonds generated for 'chain 'F' and resid 1317 through 1319' Processing helix chain 'F' and resid 1401 through 1404 No H-bonds generated for 'chain 'F' and resid 1401 through 1404' Processing helix chain 'F' and resid 1418 through 1435 removed outlier: 3.648A pdb=" N GLN F1423 " --> pdb=" O HIS F1419 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F1424 " --> pdb=" O TYR F1420 " (cutoff:3.500A) Processing helix chain 'F' and resid 1439 through 1445 Processing helix chain 'F' and resid 1447 through 1453 removed outlier: 4.782A pdb=" N THR F1452 " --> pdb=" O ALA F1448 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS F1453 " --> pdb=" O ARG F1449 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 25 No H-bonds generated for 'chain 'G' and resid 22 through 25' Processing helix chain 'G' and resid 38 through 47 removed outlier: 3.687A pdb=" N GLU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN G 46 " --> pdb=" O ASN G 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 58 No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.666A pdb=" N SER G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 4.232A pdb=" N THR G 88 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 110 through 113 No H-bonds generated for 'chain 'G' and resid 110 through 113' Processing helix chain 'G' and resid 121 through 135 removed outlier: 4.401A pdb=" N ALA G 132 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN G 135 " --> pdb=" O THR G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 185 through 189 removed outlier: 3.787A pdb=" N TYR G 189 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 211 removed outlier: 3.923A pdb=" N GLU G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'G' and resid 279 through 282 No H-bonds generated for 'chain 'G' and resid 279 through 282' Processing helix chain 'G' and resid 299 through 311 Processing helix chain 'G' and resid 333 through 341 Processing helix chain 'G' and resid 407 through 411 Processing helix chain 'G' and resid 451 through 474 Processing helix chain 'H' and resid 8 through 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 22 through 25 No H-bonds generated for 'chain 'H' and resid 22 through 25' Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.854A pdb=" N GLU H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN H 46 " --> pdb=" O ASN H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.637A pdb=" N SER H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 121 through 130 Processing helix chain 'H' and resid 158 through 170 Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.752A pdb=" N TYR H 189 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 211 Processing helix chain 'H' and resid 227 through 233 Processing helix chain 'H' and resid 262 through 274 Processing helix chain 'H' and resid 279 through 282 No H-bonds generated for 'chain 'H' and resid 279 through 282' Processing helix chain 'H' and resid 300 through 312 removed outlier: 3.708A pdb=" N GLN H 312 " --> pdb=" O THR H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 327 No H-bonds generated for 'chain 'H' and resid 325 through 327' Processing helix chain 'H' and resid 333 through 341 Processing helix chain 'H' and resid 407 through 410 No H-bonds generated for 'chain 'H' and resid 407 through 410' Processing helix chain 'H' and resid 451 through 474 Processing helix chain 'I' and resid 22 through 25 No H-bonds generated for 'chain 'I' and resid 22 through 25' Processing helix chain 'I' and resid 38 through 47 removed outlier: 3.687A pdb=" N GLU I 43 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG I 47 " --> pdb=" O GLU I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 58 No H-bonds generated for 'chain 'I' and resid 55 through 58' Processing helix chain 'I' and resid 66 through 74 removed outlier: 3.665A pdb=" N SER I 74 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 88 removed outlier: 4.232A pdb=" N THR I 88 " --> pdb=" O VAL I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 98 Processing helix chain 'I' and resid 110 through 113 No H-bonds generated for 'chain 'I' and resid 110 through 113' Processing helix chain 'I' and resid 121 through 135 removed outlier: 4.401A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP I 133 " --> pdb=" O ASN I 129 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 170 Processing helix chain 'I' and resid 185 through 189 removed outlier: 3.788A pdb=" N TYR I 189 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 211 removed outlier: 3.922A pdb=" N GLU I 202 " --> pdb=" O LYS I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 233 Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 279 through 282 No H-bonds generated for 'chain 'I' and resid 279 through 282' Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 333 through 341 Processing helix chain 'I' and resid 407 through 411 Processing helix chain 'I' and resid 451 through 474 Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 22 through 25 No H-bonds generated for 'chain 'J' and resid 22 through 25' Processing helix chain 'J' and resid 38 through 46 removed outlier: 3.854A pdb=" N GLU J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN J 46 " --> pdb=" O ASN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 58 No H-bonds generated for 'chain 'J' and resid 55 through 58' Processing helix chain 'J' and resid 66 through 75 removed outlier: 3.638A pdb=" N SER J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU J 75 " --> pdb=" O LYS J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 92 through 98 Processing helix chain 'J' and resid 121 through 130 Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'J' and resid 185 through 189 removed outlier: 3.753A pdb=" N TYR J 189 " --> pdb=" O LEU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 211 Processing helix chain 'J' and resid 227 through 233 Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 279 through 282 No H-bonds generated for 'chain 'J' and resid 279 through 282' Processing helix chain 'J' and resid 300 through 312 removed outlier: 3.709A pdb=" N GLN J 312 " --> pdb=" O THR J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 327 No H-bonds generated for 'chain 'J' and resid 325 through 327' Processing helix chain 'J' and resid 333 through 341 Processing helix chain 'J' and resid 407 through 410 No H-bonds generated for 'chain 'J' and resid 407 through 410' Processing helix chain 'J' and resid 451 through 474 Processing sheet with id= A, first strand: chain 'A' and resid 379 through 384 removed outlier: 6.932A pdb=" N ILE A 357 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS A 382 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR A 355 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE A 204 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 49 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.630A pdb=" N GLN A 75 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 172 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 73 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 106 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY A 134 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE A 104 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 230 through 232 Processing sheet with id= D, first strand: chain 'A' and resid 499 through 501 Processing sheet with id= E, first strand: chain 'A' and resid 524 through 526 Processing sheet with id= F, first strand: chain 'A' and resid 566 through 570 removed outlier: 6.691A pdb=" N HIS A 603 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A 569 " --> pdb=" O HIS A 603 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 605 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN A 643 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 665 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR A 646 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 667 " --> pdb=" O THR A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 572 through 574 Processing sheet with id= H, first strand: chain 'A' and resid 829 through 831 Processing sheet with id= I, first strand: chain 'A' and resid 907 through 910 removed outlier: 6.576A pdb=" N GLU A 927 " --> pdb=" O LYS A 908 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL A 910 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 929 " --> pdb=" O VAL A 910 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LYS A 995 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE A 930 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 997 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A1020 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A1000 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A1022 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A1066 " --> pdb=" O ILE A1021 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE A1023 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG A1068 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A1089 " --> pdb=" O THR A1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 1229 through 1234 removed outlier: 3.790A pdb=" N THR A1265 " --> pdb=" O MET A1229 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1269 " --> pdb=" O TYR A1233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A1291 " --> pdb=" O GLY A1270 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A1304 " --> pdb=" O LEU A1286 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A1288 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A1306 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY A1290 " --> pdb=" O VAL A1306 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG A1308 " --> pdb=" O GLY A1290 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA A1292 " --> pdb=" O ARG A1308 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS A1335 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL A1307 " --> pdb=" O LYS A1335 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A1337 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A1372 " --> pdb=" O ALA A1353 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET A1391 " --> pdb=" O ALA A1373 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE A1375 " --> pdb=" O MET A1391 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A1393 " --> pdb=" O ILE A1375 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 379 through 382 removed outlier: 6.926A pdb=" N ILE B 357 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS B 382 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR B 355 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE B 204 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA B 49 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.694A pdb=" N GLN B 75 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU B 172 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 73 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 106 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 134 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE B 104 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 230 through 232 Processing sheet with id= N, first strand: chain 'B' and resid 524 through 526 Processing sheet with id= O, first strand: chain 'B' and resid 566 through 569 removed outlier: 6.575A pdb=" N HIS B 603 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 569 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 605 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'B' and resid 643 through 646 removed outlier: 6.758A pdb=" N THR B 665 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR B 646 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN B 667 " --> pdb=" O THR B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 829 through 831 Processing sheet with id= S, first strand: chain 'B' and resid 997 through 1001 removed outlier: 6.671A pdb=" N ILE B1020 " --> pdb=" O VAL B 998 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU B1000 " --> pdb=" O ILE B1020 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B1022 " --> pdb=" O LEU B1000 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B1066 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE B1023 " --> pdb=" O ARG B1066 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B1068 " --> pdb=" O ILE B1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'B' and resid 1229 through 1233 removed outlier: 3.511A pdb=" N ARG B1269 " --> pdb=" O TYR B1233 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B1304 " --> pdb=" O LEU B1286 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL B1288 " --> pdb=" O THR B1304 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B1306 " --> pdb=" O VAL B1288 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B1335 " --> pdb=" O ILE B1305 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL B1307 " --> pdb=" O LYS B1335 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B1337 " --> pdb=" O VAL B1307 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR B1354 " --> pdb=" O LEU B1336 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA B1338 " --> pdb=" O THR B1354 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B1356 " --> pdb=" O ALA B1338 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR B1372 " --> pdb=" O VAL B1355 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL B1357 " --> pdb=" O THR B1372 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B1374 " --> pdb=" O VAL B1357 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET B1391 " --> pdb=" O ALA B1373 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ILE B1375 " --> pdb=" O MET B1391 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR B1393 " --> pdb=" O ILE B1375 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 379 through 384 removed outlier: 6.884A pdb=" N ILE C 357 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS C 382 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR C 355 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE C 204 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA C 49 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.631A pdb=" N GLN C 75 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 172 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 73 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 106 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY C 134 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE C 104 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 230 through 232 Processing sheet with id= X, first strand: chain 'C' and resid 499 through 501 Processing sheet with id= Y, first strand: chain 'C' and resid 524 through 526 Processing sheet with id= Z, first strand: chain 'C' and resid 566 through 570 removed outlier: 6.875A pdb=" N HIS C 603 " --> pdb=" O ALA C 567 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE C 569 " --> pdb=" O HIS C 603 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 605 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER C 641 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 606 " --> pdb=" O SER C 641 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN C 643 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR C 665 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR C 646 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN C 667 " --> pdb=" O THR C 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'C' and resid 572 through 574 Processing sheet with id= AB, first strand: chain 'C' and resid 829 through 831 Processing sheet with id= AC, first strand: chain 'C' and resid 927 through 931 removed outlier: 5.875A pdb=" N LYS C 995 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE C 930 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR C 997 " --> pdb=" O ILE C 930 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C1020 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU C1000 " --> pdb=" O ILE C1020 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C1022 " --> pdb=" O LEU C1000 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'C' and resid 1068 through 1070 removed outlier: 6.674A pdb=" N GLU C1089 " --> pdb=" O THR C1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'C' and resid 1229 through 1234 removed outlier: 3.977A pdb=" N ASP C1291 " --> pdb=" O GLY C1270 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C1304 " --> pdb=" O LEU C1286 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL C1288 " --> pdb=" O THR C1304 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1306 " --> pdb=" O VAL C1288 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY C1290 " --> pdb=" O VAL C1306 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG C1308 " --> pdb=" O GLY C1290 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS C1335 " --> pdb=" O ILE C1305 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL C1307 " --> pdb=" O LYS C1335 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE C1337 " --> pdb=" O VAL C1307 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR C1354 " --> pdb=" O LEU C1336 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA C1338 " --> pdb=" O THR C1354 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C1356 " --> pdb=" O ALA C1338 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C1372 " --> pdb=" O VAL C1355 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL C1357 " --> pdb=" O THR C1372 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C1374 " --> pdb=" O VAL C1357 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET C1391 " --> pdb=" O ALA C1373 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE C1375 " --> pdb=" O MET C1391 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C1393 " --> pdb=" O ILE C1375 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 379 through 384 removed outlier: 6.933A pdb=" N ILE D 357 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS D 382 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR D 355 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE D 204 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 49 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.631A pdb=" N GLN D 75 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU D 172 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL D 73 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 106 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY D 134 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE D 104 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 230 through 232 Processing sheet with id= AI, first strand: chain 'D' and resid 499 through 501 Processing sheet with id= AJ, first strand: chain 'D' and resid 524 through 526 Processing sheet with id= AK, first strand: chain 'D' and resid 566 through 570 removed outlier: 6.690A pdb=" N HIS D 603 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE D 569 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE D 605 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN D 643 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 665 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR D 646 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN D 667 " --> pdb=" O THR D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'D' and resid 572 through 574 Processing sheet with id= AM, first strand: chain 'D' and resid 829 through 831 Processing sheet with id= AN, first strand: chain 'D' and resid 907 through 910 removed outlier: 6.576A pdb=" N GLU D 927 " --> pdb=" O LYS D 908 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL D 910 " --> pdb=" O GLU D 927 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU D 929 " --> pdb=" O VAL D 910 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS D 995 " --> pdb=" O LEU D 928 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE D 930 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 997 " --> pdb=" O ILE D 930 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D1020 " --> pdb=" O VAL D 998 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU D1000 " --> pdb=" O ILE D1020 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D1022 " --> pdb=" O LEU D1000 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG D1066 " --> pdb=" O ILE D1021 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE D1023 " --> pdb=" O ARG D1066 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG D1068 " --> pdb=" O ILE D1023 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU D1089 " --> pdb=" O THR D1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'D' and resid 1229 through 1234 removed outlier: 3.790A pdb=" N THR D1265 " --> pdb=" O MET D1229 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D1269 " --> pdb=" O TYR D1233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D1291 " --> pdb=" O GLY D1270 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR D1304 " --> pdb=" O LEU D1286 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL D1288 " --> pdb=" O THR D1304 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D1306 " --> pdb=" O VAL D1288 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLY D1290 " --> pdb=" O VAL D1306 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG D1308 " --> pdb=" O GLY D1290 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA D1292 " --> pdb=" O ARG D1308 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS D1335 " --> pdb=" O ILE D1305 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D1307 " --> pdb=" O LYS D1335 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D1337 " --> pdb=" O VAL D1307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D1372 " --> pdb=" O ALA D1353 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET D1391 " --> pdb=" O ALA D1373 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE D1375 " --> pdb=" O MET D1391 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR D1393 " --> pdb=" O ILE D1375 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 379 through 384 removed outlier: 6.884A pdb=" N ILE E 357 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS E 382 " --> pdb=" O TYR E 355 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR E 355 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE E 204 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA E 49 " --> pdb=" O PHE E 204 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 168 through 173 removed outlier: 6.631A pdb=" N GLN E 75 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 172 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL E 73 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 106 " --> pdb=" O ILE E 132 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY E 134 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE E 104 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= AS, first strand: chain 'E' and resid 499 through 501 Processing sheet with id= AT, first strand: chain 'E' and resid 524 through 526 Processing sheet with id= AU, first strand: chain 'E' and resid 566 through 570 removed outlier: 6.875A pdb=" N HIS E 603 " --> pdb=" O ALA E 567 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE E 569 " --> pdb=" O HIS E 603 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE E 605 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER E 641 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU E 606 " --> pdb=" O SER E 641 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN E 643 " --> pdb=" O LEU E 606 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR E 665 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR E 646 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN E 667 " --> pdb=" O THR E 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'E' and resid 572 through 574 Processing sheet with id= AW, first strand: chain 'E' and resid 829 through 831 Processing sheet with id= AX, first strand: chain 'E' and resid 927 through 931 removed outlier: 5.876A pdb=" N LYS E 995 " --> pdb=" O LEU E 928 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE E 930 " --> pdb=" O LYS E 995 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR E 997 " --> pdb=" O ILE E 930 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E1020 " --> pdb=" O VAL E 998 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU E1000 " --> pdb=" O ILE E1020 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU E1022 " --> pdb=" O LEU E1000 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'E' and resid 1068 through 1070 removed outlier: 6.673A pdb=" N GLU E1089 " --> pdb=" O THR E1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'E' and resid 1229 through 1234 removed outlier: 3.977A pdb=" N ASP E1291 " --> pdb=" O GLY E1270 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR E1304 " --> pdb=" O LEU E1286 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL E1288 " --> pdb=" O THR E1304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL E1306 " --> pdb=" O VAL E1288 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E1290 " --> pdb=" O VAL E1306 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG E1308 " --> pdb=" O GLY E1290 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS E1335 " --> pdb=" O ILE E1305 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL E1307 " --> pdb=" O LYS E1335 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE E1337 " --> pdb=" O VAL E1307 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR E1354 " --> pdb=" O LEU E1336 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA E1338 " --> pdb=" O THR E1354 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E1356 " --> pdb=" O ALA E1338 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR E1372 " --> pdb=" O VAL E1355 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL E1357 " --> pdb=" O THR E1372 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL E1374 " --> pdb=" O VAL E1357 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET E1391 " --> pdb=" O ALA E1373 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE E1375 " --> pdb=" O MET E1391 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR E1393 " --> pdb=" O ILE E1375 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'F' and resid 379 through 382 removed outlier: 6.925A pdb=" N ILE F 357 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS F 382 " --> pdb=" O TYR F 355 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR F 355 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE F 204 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA F 49 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'F' and resid 168 through 173 removed outlier: 6.694A pdb=" N GLN F 75 " --> pdb=" O CYS F 170 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU F 172 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL F 73 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 106 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY F 134 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE F 104 " --> pdb=" O GLY F 134 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 230 through 232 Processing sheet with id= BD, first strand: chain 'F' and resid 524 through 526 Processing sheet with id= BE, first strand: chain 'F' and resid 566 through 569 removed outlier: 6.575A pdb=" N HIS F 603 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE F 569 " --> pdb=" O HIS F 603 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE F 605 " --> pdb=" O ILE F 569 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'F' and resid 572 through 574 Processing sheet with id= BG, first strand: chain 'F' and resid 643 through 646 removed outlier: 6.757A pdb=" N THR F 665 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR F 646 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN F 667 " --> pdb=" O THR F 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'F' and resid 829 through 831 Processing sheet with id= BI, first strand: chain 'F' and resid 997 through 1001 removed outlier: 6.671A pdb=" N ILE F1020 " --> pdb=" O VAL F 998 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F1000 " --> pdb=" O ILE F1020 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F1022 " --> pdb=" O LEU F1000 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG F1066 " --> pdb=" O ILE F1021 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE F1023 " --> pdb=" O ARG F1066 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG F1068 " --> pdb=" O ILE F1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'F' and resid 1229 through 1233 removed outlier: 3.512A pdb=" N ARG F1269 " --> pdb=" O TYR F1233 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR F1304 " --> pdb=" O LEU F1286 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL F1288 " --> pdb=" O THR F1304 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F1306 " --> pdb=" O VAL F1288 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS F1335 " --> pdb=" O ILE F1305 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL F1307 " --> pdb=" O LYS F1335 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F1337 " --> pdb=" O VAL F1307 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR F1354 " --> pdb=" O LEU F1336 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA F1338 " --> pdb=" O THR F1354 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL F1356 " --> pdb=" O ALA F1338 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR F1372 " --> pdb=" O VAL F1355 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL F1357 " --> pdb=" O THR F1372 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL F1374 " --> pdb=" O VAL F1357 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET F1391 " --> pdb=" O ALA F1373 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE F1375 " --> pdb=" O MET F1391 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR F1393 " --> pdb=" O ILE F1375 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.231A pdb=" N ALA G 236 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE G 154 " --> pdb=" O ALA G 236 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU G 238 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.565A pdb=" N VAL G 396 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER G 316 " --> pdb=" O VAL G 293 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL G 295 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS G 318 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU G 344 " --> pdb=" O CYS G 319 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'G' and resid 388 through 392 removed outlier: 5.877A pdb=" N VAL G 366 " --> pdb=" O PRO G 351 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'G' and resid 368 through 370 Processing sheet with id= BO, first strand: chain 'H' and resid 173 through 177 removed outlier: 6.088A pdb=" N ALA H 236 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE H 154 " --> pdb=" O ALA H 236 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU H 238 " --> pdb=" O ILE H 154 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 259 through 261 removed outlier: 6.686A pdb=" N VAL H 396 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER H 316 " --> pdb=" O VAL H 293 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL H 295 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS H 318 " --> pdb=" O VAL H 295 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU H 344 " --> pdb=" O CYS H 319 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 388 through 392 removed outlier: 6.180A pdb=" N VAL H 366 " --> pdb=" O PRO H 351 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'H' and resid 368 through 370 Processing sheet with id= BS, first strand: chain 'I' and resid 173 through 177 removed outlier: 6.231A pdb=" N ALA I 236 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE I 154 " --> pdb=" O ALA I 236 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU I 238 " --> pdb=" O ILE I 154 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.566A pdb=" N VAL I 396 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER I 316 " --> pdb=" O VAL I 293 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL I 295 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS I 318 " --> pdb=" O VAL I 295 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU I 344 " --> pdb=" O CYS I 319 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'I' and resid 388 through 392 removed outlier: 5.877A pdb=" N VAL I 366 " --> pdb=" O PRO I 351 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'I' and resid 368 through 370 Processing sheet with id= BW, first strand: chain 'J' and resid 173 through 177 removed outlier: 6.088A pdb=" N ALA J 236 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE J 154 " --> pdb=" O ALA J 236 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU J 238 " --> pdb=" O ILE J 154 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'J' and resid 259 through 261 removed outlier: 6.685A pdb=" N VAL J 396 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER J 316 " --> pdb=" O VAL J 293 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL J 295 " --> pdb=" O SER J 316 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS J 318 " --> pdb=" O VAL J 295 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLU J 344 " --> pdb=" O CYS J 319 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'J' and resid 388 through 392 removed outlier: 6.180A pdb=" N VAL J 366 " --> pdb=" O PRO J 351 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'J' and resid 368 through 370 2614 hydrogen bonds defined for protein. 7326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 38.12 Time building geometry restraints manager: 25.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 83686 1.76 - 2.31: 864 2.31 - 2.86: 6 2.86 - 3.41: 0 3.41 - 3.95: 18 Bond restraints: 84574 Sorted by residual: bond pdb=" S4 F3S B1502 " pdb="FE1 F3S B1502 " ideal model delta sigma weight residual 2.233 3.942 -1.709 2.00e-02 2.50e+03 7.31e+03 bond pdb=" S4 F3S F1502 " pdb="FE1 F3S F1502 " ideal model delta sigma weight residual 2.233 3.942 -1.709 2.00e-02 2.50e+03 7.30e+03 bond pdb=" S4 F3S C1502 " pdb="FE1 F3S C1502 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S4 F3S E1502 " pdb="FE1 F3S E1502 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S4 F3S D1502 " pdb="FE1 F3S D1502 " ideal model delta sigma weight residual 2.233 3.926 -1.693 2.00e-02 2.50e+03 7.16e+03 ... (remaining 84569 not shown) Histogram of bond angle deviations from ideal: 41.31 - 59.88: 24 59.88 - 78.46: 144 78.46 - 97.03: 0 97.03 - 115.61: 55268 115.61 - 134.18: 59132 Bond angle restraints: 114568 Sorted by residual: angle pdb=" S1 F3S A1502 " pdb="FE4 F3S A1502 " pdb=" S3 F3S A1502 " ideal model delta sigma weight residual 114.75 64.87 49.88 3.00e+00 1.11e-01 2.76e+02 angle pdb=" S1 F3S D1502 " pdb="FE4 F3S D1502 " pdb=" S3 F3S D1502 " ideal model delta sigma weight residual 114.75 64.89 49.86 3.00e+00 1.11e-01 2.76e+02 angle pdb=" S1 F3S B1502 " pdb="FE4 F3S B1502 " pdb=" S3 F3S B1502 " ideal model delta sigma weight residual 114.75 64.95 49.80 3.00e+00 1.11e-01 2.76e+02 angle pdb=" S1 F3S F1502 " pdb="FE4 F3S F1502 " pdb=" S3 F3S F1502 " ideal model delta sigma weight residual 114.75 64.97 49.78 3.00e+00 1.11e-01 2.75e+02 angle pdb=" S1 F3S C1502 " pdb="FE4 F3S C1502 " pdb=" S3 F3S C1502 " ideal model delta sigma weight residual 114.75 65.05 49.70 3.00e+00 1.11e-01 2.74e+02 ... (remaining 114563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 49862 33.44 - 66.87: 877 66.87 - 100.31: 119 100.31 - 133.75: 3 133.75 - 167.19: 1 Dihedral angle restraints: 50862 sinusoidal: 20564 harmonic: 30298 Sorted by residual: dihedral pdb=" O5' FAD G 503 " pdb=" O3P FAD G 503 " pdb=" P FAD G 503 " pdb=" PA FAD G 503 " ideal model delta sinusoidal sigma weight residual -61.77 105.42 -167.19 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O5' FAD J 503 " pdb=" O3P FAD J 503 " pdb=" P FAD J 503 " pdb=" PA FAD J 503 " ideal model delta sinusoidal sigma weight residual -61.77 67.81 -129.58 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA LYS C 12 " pdb=" C LYS C 12 " pdb=" N PRO C 13 " pdb=" CA PRO C 13 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 50859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 12754 0.990 - 1.981: 0 1.981 - 2.971: 0 2.971 - 3.962: 6 3.962 - 4.952: 2 Chirality restraints: 12762 Sorted by residual: chirality pdb=" C4' FAD H 503 " pdb=" C3' FAD H 503 " pdb=" C5' FAD H 503 " pdb=" O4' FAD H 503 " both_signs ideal model delta sigma weight residual False -2.48 2.47 -4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" C3' FAD H 503 " pdb=" C2' FAD H 503 " pdb=" C4' FAD H 503 " pdb=" O3' FAD H 503 " both_signs ideal model delta sigma weight residual False -2.55 2.38 -4.93 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" S2 F3S A1502 " pdb="FE1 F3S A1502 " pdb="FE3 F3S A1502 " pdb="FE4 F3S A1502 " both_signs ideal model delta sigma weight residual False 10.77 7.23 3.54 2.00e-01 2.50e+01 3.13e+02 ... (remaining 12759 not shown) Planarity restraints: 14992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 460 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.31e+01 pdb=" CG ASP B 460 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP B 460 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP B 460 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 460 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" CG ASP F 460 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP F 460 " 0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP F 460 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 443 " -0.013 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" CG ASP B 443 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP B 443 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 443 " -0.017 2.00e-02 2.50e+03 ... (remaining 14989 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 868 2.63 - 3.19: 72728 3.19 - 3.76: 117862 3.76 - 4.33: 170538 4.33 - 4.90: 286175 Nonbonded interactions: 648171 Sorted by model distance: nonbonded pdb=" OD1 ASN D 235 " pdb=" ND2 ASN D 508 " model vdw 2.058 2.520 nonbonded pdb=" OD1 ASN A 235 " pdb=" ND2 ASN A 508 " model vdw 2.058 2.520 nonbonded pdb=" OE1 GLU H 125 " pdb="FE3 SF4 H 502 " model vdw 2.156 3.000 nonbonded pdb=" OE1 GLU J 125 " pdb="FE3 SF4 J 502 " model vdw 2.157 3.000 nonbonded pdb=" O2' FAD H 503 " pdb=" O4' FAD H 503 " model vdw 2.181 2.440 ... (remaining 648166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.640 Check model and map are aligned: 0.910 Set scattering table: 0.550 Process input model: 181.350 Find NCS groups from input model: 4.480 Set up NCS constraints: 0.570 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: 0.020 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.024 1.709 84574 Z= 1.618 Angle : 0.992 49.876 114568 Z= 0.421 Chirality : 0.106 4.952 12762 Planarity : 0.003 0.042 14992 Dihedral : 13.342 167.187 31530 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.44 % Allowed : 3.22 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.07), residues: 10700 helix: -0.86 (0.08), residues: 3786 sheet: -1.69 (0.11), residues: 1654 loop : -2.77 (0.07), residues: 5260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 133 HIS 0.004 0.001 HIS H 116 PHE 0.023 0.001 PHE I 36 TYR 0.012 0.001 TYR B 319 ARG 0.003 0.000 ARG C1449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1227 time to evaluate : 7.105 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: A 479 MET cc_start: 0.8889 (tpp) cc_final: 0.8686 (tpt) REVERT: A 514 LEU cc_start: 0.8644 (mt) cc_final: 0.8397 (mp) REVERT: A 539 GLN cc_start: 0.7828 (mt0) cc_final: 0.7593 (mt0) REVERT: A 693 MET cc_start: 0.8342 (mmm) cc_final: 0.8136 (mmm) REVERT: A 1089 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 1387 MET cc_start: 0.9213 (ttt) cc_final: 0.8979 (ttt) REVERT: B 410 LEU cc_start: 0.9085 (tp) cc_final: 0.8863 (tp) REVERT: B 438 GLU cc_start: 0.4396 (OUTLIER) cc_final: 0.3694 (mp0) REVERT: B 823 MET cc_start: 0.7180 (mtp) cc_final: 0.6039 (ptt) REVERT: B 926 ARG cc_start: 0.7523 (mtm110) cc_final: 0.6952 (mtm-85) REVERT: B 952 MET cc_start: 0.6001 (tmm) cc_final: 0.5633 (tmm) REVERT: B 1204 ARG cc_start: 0.8098 (ptt180) cc_final: 0.7366 (ptt-90) REVERT: B 1462 MET cc_start: 0.7344 (tpp) cc_final: 0.7122 (tpp) REVERT: C 92 ILE cc_start: 0.8755 (mt) cc_final: 0.8539 (mm) REVERT: C 94 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7266 (mt-10) REVERT: C 221 LEU cc_start: 0.9512 (mt) cc_final: 0.9304 (mt) REVERT: C 376 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7419 (mp0) REVERT: C 1256 MET cc_start: 0.8052 (mtp) cc_final: 0.7749 (ttm) REVERT: C 1294 ASP cc_start: 0.8082 (m-30) cc_final: 0.7834 (m-30) REVERT: C 1368 MET cc_start: 0.8739 (ttt) cc_final: 0.8488 (ttp) REVERT: C 1387 MET cc_start: 0.8299 (ttt) cc_final: 0.7998 (ttm) REVERT: D 427 ASP cc_start: 0.8051 (p0) cc_final: 0.7687 (p0) REVERT: D 514 LEU cc_start: 0.8649 (mt) cc_final: 0.8424 (mp) REVERT: D 1294 ASP cc_start: 0.6794 (m-30) cc_final: 0.6446 (m-30) REVERT: D 1387 MET cc_start: 0.9142 (ttt) cc_final: 0.8806 (ttt) REVERT: E 94 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7285 (mt-10) REVERT: E 479 MET cc_start: 0.8642 (tpp) cc_final: 0.8439 (mmm) REVERT: E 562 MET cc_start: 0.7820 (mtt) cc_final: 0.7507 (mtm) REVERT: E 693 MET cc_start: 0.8191 (mmm) cc_final: 0.7882 (mmm) REVERT: E 851 LYS cc_start: 0.9407 (mttt) cc_final: 0.9157 (mtpp) REVERT: E 982 GLN cc_start: 0.7080 (tp40) cc_final: 0.6483 (tp-100) REVERT: E 1256 MET cc_start: 0.8236 (mtp) cc_final: 0.7936 (ttm) REVERT: E 1368 MET cc_start: 0.8848 (ttt) cc_final: 0.8565 (ttp) REVERT: E 1381 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8093 (t0) REVERT: E 1387 MET cc_start: 0.8493 (ttt) cc_final: 0.8288 (ttm) REVERT: E 1407 ASP cc_start: 0.8406 (p0) cc_final: 0.8180 (p0) REVERT: F 293 MET cc_start: 0.7814 (mmm) cc_final: 0.7522 (mmm) REVERT: F 438 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.3636 (mp0) REVERT: F 468 MET cc_start: 0.8688 (mtt) cc_final: 0.8433 (mtp) REVERT: F 479 MET cc_start: 0.7806 (tpp) cc_final: 0.7600 (mmt) REVERT: F 492 TYR cc_start: 0.7685 (t80) cc_final: 0.7418 (t80) REVERT: F 562 MET cc_start: 0.6951 (mtp) cc_final: 0.6582 (mtp) REVERT: F 807 TYR cc_start: 0.5042 (t80) cc_final: 0.4836 (t80) REVERT: F 858 MET cc_start: 0.6755 (mtm) cc_final: 0.6217 (mtt) REVERT: F 952 MET cc_start: 0.6494 (tmm) cc_final: 0.5987 (tmm) REVERT: F 973 ASP cc_start: 0.8565 (t0) cc_final: 0.8301 (t0) REVERT: G 6 MET cc_start: 0.8254 (ptm) cc_final: 0.8014 (ptp) REVERT: G 432 MET cc_start: 0.8609 (ttp) cc_final: 0.8312 (ttp) REVERT: H 472 LYS cc_start: 0.7624 (tmmt) cc_final: 0.7345 (tppt) REVERT: J 186 LEU cc_start: 0.6898 (pp) cc_final: 0.6524 (mt) REVERT: J 472 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7700 (tppt) outliers start: 38 outliers final: 10 residues processed: 1255 average time/residue: 0.8885 time to fit residues: 1811.5958 Evaluate side-chains 785 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 772 time to evaluate : 6.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain C residue 1332 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain E residue 1332 THR Chi-restraints excluded: chain E residue 1381 ASP Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 438 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain J residue 213 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 903 optimal weight: 8.9990 chunk 811 optimal weight: 9.9990 chunk 450 optimal weight: 0.6980 chunk 277 optimal weight: 7.9990 chunk 547 optimal weight: 3.9990 chunk 433 optimal weight: 6.9990 chunk 838 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 509 optimal weight: 3.9990 chunk 624 optimal weight: 9.9990 chunk 971 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 52 GLN A 208 HIS A 231 ASN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN A 643 ASN A 653 HIS A 667 ASN A 738 HIS A 762 HIS A 767 ASN A 824 GLN ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN A1159 ASN B 30 HIS B 52 GLN B 143 GLN B 259 HIS B 497 HIS ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN B 643 ASN B 653 HIS B 695 ASN B 762 HIS B 800 GLN B 824 GLN B1159 ASN B1177 HIS B1184 ASN B1234 ASN B1260 GLN C 52 GLN C 143 GLN C 165 ASN C 505 GLN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C 653 HIS C 762 HIS C 824 GLN C 872 ASN ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1026 ASN C1063 HIS C1195 ASN C1325 ASN C1363 ASN ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 52 GLN D 143 GLN D 208 HIS D 231 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN D 643 ASN D 653 HIS D 667 ASN D 738 HIS D 762 HIS D 767 ASN D 824 GLN ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1026 ASN D1159 ASN D1363 ASN E 52 GLN E 143 GLN E 165 ASN E 635 ASN E 653 HIS E 762 HIS E 824 GLN E 872 ASN ** E 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1026 ASN E1195 ASN E1325 ASN E1363 ASN ** E1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 HIS F 52 GLN F 165 ASN F 259 HIS F 261 GLN F 422 ASN F 497 HIS F 635 ASN F 653 HIS F 695 ASN F 762 HIS F 800 GLN F 868 HIS F 909 GLN F1177 HIS F1274 GLN G 46 ASN G 64 ASN G 108 ASN G 218 ASN G 234 HIS G 270 ASN G 392 GLN G 409 ASN G 434 ASN H 46 ASN H 108 ASN ** H 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 HIS I 46 ASN I 64 ASN I 108 ASN I 218 ASN I 234 HIS I 270 ASN I 392 GLN I 409 ASN I 434 ASN J 46 ASN J 108 ASN ** J 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 HIS ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 84574 Z= 0.437 Angle : 0.899 83.560 114568 Z= 0.381 Chirality : 0.059 1.798 12762 Planarity : 0.004 0.061 14992 Dihedral : 6.089 165.845 11953 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.21 % Allowed : 9.89 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.08), residues: 10700 helix: -0.05 (0.09), residues: 3770 sheet: -1.36 (0.12), residues: 1630 loop : -2.43 (0.07), residues: 5300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 69 HIS 0.008 0.001 HIS C 972 PHE 0.025 0.002 PHE G 36 TYR 0.023 0.002 TYR D 211 ARG 0.014 0.001 ARG J 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 790 time to evaluate : 7.268 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: A 478 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8448 (t) REVERT: A 479 MET cc_start: 0.8817 (tpp) cc_final: 0.8614 (tpt) REVERT: A 539 GLN cc_start: 0.7902 (mt0) cc_final: 0.7643 (mt0) REVERT: A 687 MET cc_start: 0.7155 (ptm) cc_final: 0.6923 (ptp) REVERT: B 293 MET cc_start: 0.7845 (mmm) cc_final: 0.7504 (mmm) REVERT: B 813 TYR cc_start: 0.8464 (t80) cc_final: 0.8007 (t80) REVERT: B 952 MET cc_start: 0.6065 (tmm) cc_final: 0.5717 (tmm) REVERT: B 1164 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.7021 (mmt90) REVERT: B 1198 TYR cc_start: 0.8232 (p90) cc_final: 0.7751 (p90) REVERT: C 94 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7331 (mt-10) REVERT: C 96 GLU cc_start: 0.8007 (tp30) cc_final: 0.7501 (tp30) REVERT: C 221 LEU cc_start: 0.9476 (mt) cc_final: 0.9037 (mt) REVERT: C 376 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7432 (mp0) REVERT: C 461 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8516 (mmt) REVERT: C 478 SER cc_start: 0.8166 (p) cc_final: 0.7721 (t) REVERT: C 562 MET cc_start: 0.8233 (mtt) cc_final: 0.8006 (mtm) REVERT: C 1173 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6463 (mtm-85) REVERT: C 1294 ASP cc_start: 0.8094 (m-30) cc_final: 0.7778 (m-30) REVERT: C 1434 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6361 (mm-30) REVERT: D 427 ASP cc_start: 0.8002 (p0) cc_final: 0.7605 (p0) REVERT: D 478 SER cc_start: 0.8725 (p) cc_final: 0.8460 (t) REVERT: D 711 MET cc_start: 0.8573 (ttm) cc_final: 0.8315 (ttm) REVERT: D 760 GLU cc_start: 0.7295 (tm-30) cc_final: 0.7053 (tm-30) REVERT: D 875 MET cc_start: 0.9089 (tpp) cc_final: 0.8751 (tpp) REVERT: D 1186 ARG cc_start: 0.7678 (ptp-110) cc_final: 0.7421 (ptp-110) REVERT: D 1294 ASP cc_start: 0.7126 (m-30) cc_final: 0.6923 (m-30) REVERT: E 94 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7357 (mt-10) REVERT: E 251 MET cc_start: 0.8780 (ptp) cc_final: 0.8565 (ptp) REVERT: E 478 SER cc_start: 0.7924 (p) cc_final: 0.7281 (t) REVERT: E 479 MET cc_start: 0.8754 (tpp) cc_final: 0.8319 (mmm) REVERT: E 562 MET cc_start: 0.7715 (mtt) cc_final: 0.7429 (mtm) REVERT: E 672 GLN cc_start: 0.7305 (tt0) cc_final: 0.7030 (tt0) REVERT: E 693 MET cc_start: 0.8313 (mmm) cc_final: 0.8083 (mmm) REVERT: E 768 GLU cc_start: 0.7955 (mp0) cc_final: 0.7622 (mp0) REVERT: E 982 GLN cc_start: 0.7122 (tp40) cc_final: 0.6896 (tp-100) REVERT: E 1227 GLU cc_start: 0.7124 (pm20) cc_final: 0.6792 (pm20) REVERT: E 1256 MET cc_start: 0.8386 (mtp) cc_final: 0.8122 (ttm) REVERT: E 1294 ASP cc_start: 0.8111 (m-30) cc_final: 0.7873 (m-30) REVERT: E 1381 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8167 (t0) REVERT: E 1387 MET cc_start: 0.8441 (ttt) cc_final: 0.8162 (ttm) REVERT: F 160 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8223 (ttmt) REVERT: F 389 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7202 (mm-30) REVERT: F 468 MET cc_start: 0.8592 (mtt) cc_final: 0.8217 (mtp) REVERT: F 492 TYR cc_start: 0.8019 (t80) cc_final: 0.7561 (t80) REVERT: F 810 PHE cc_start: 0.8754 (t80) cc_final: 0.8552 (t80) REVERT: F 858 MET cc_start: 0.7021 (mtm) cc_final: 0.6161 (mtt) REVERT: F 931 LYS cc_start: 0.8501 (tttm) cc_final: 0.8243 (tttm) REVERT: F 1159 ASN cc_start: 0.8535 (m-40) cc_final: 0.8083 (t0) REVERT: F 1204 ARG cc_start: 0.8136 (ptt180) cc_final: 0.7435 (ptt-90) REVERT: F 1229 MET cc_start: 0.9218 (mmt) cc_final: 0.8996 (mmt) REVERT: H 472 LYS cc_start: 0.7694 (tmmt) cc_final: 0.7304 (tppt) REVERT: I 68 ASP cc_start: 0.8673 (m-30) cc_final: 0.8398 (m-30) REVERT: J 208 LEU cc_start: 0.8385 (tp) cc_final: 0.8171 (tp) REVERT: J 472 LYS cc_start: 0.8110 (tmmt) cc_final: 0.7455 (tppt) outliers start: 105 outliers final: 82 residues processed: 860 average time/residue: 0.7915 time to fit residues: 1157.9521 Evaluate side-chains 798 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 712 time to evaluate : 7.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 1026 ASN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1433 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 1026 ASN Chi-restraints excluded: chain C residue 1057 THR Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1332 THR Chi-restraints excluded: chain C residue 1434 GLU Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 1013 VAL Chi-restraints excluded: chain D residue 1026 ASN Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1242 ILE Chi-restraints excluded: chain E residue 1251 THR Chi-restraints excluded: chain E residue 1332 THR Chi-restraints excluded: chain E residue 1381 ASP Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 764 THR Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1104 MET Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1433 THR Chi-restraints excluded: chain F residue 1462 MET Chi-restraints excluded: chain G residue 429 ARG Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 540 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 808 optimal weight: 7.9990 chunk 661 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 973 optimal weight: 6.9990 chunk 1051 optimal weight: 0.0370 chunk 866 optimal weight: 0.0030 chunk 965 optimal weight: 8.9990 chunk 331 optimal weight: 8.9990 chunk 780 optimal weight: 9.9990 overall best weight: 0.5668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 240 ASN A 421 GLN A 539 GLN ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN B 508 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS D 240 ASN D 497 HIS D 528 ASN ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 738 HIS ** E 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 HIS F 165 ASN F 240 ASN F 422 ASN F 508 ASN F 868 HIS F1169 HIS H 64 ASN H 216 HIS J 64 ASN J 216 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.111 84574 Z= 0.156 Angle : 0.810 81.938 114568 Z= 0.323 Chirality : 0.052 1.543 12762 Planarity : 0.003 0.050 14992 Dihedral : 5.310 161.936 11943 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.83 % Allowed : 11.76 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.08), residues: 10700 helix: 0.59 (0.09), residues: 3746 sheet: -0.91 (0.13), residues: 1536 loop : -2.01 (0.08), residues: 5418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 69 HIS 0.006 0.000 HIS F1169 PHE 0.018 0.001 PHE D 894 TYR 0.016 0.001 TYR C 207 ARG 0.009 0.000 ARG C1220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 814 time to evaluate : 7.066 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: B 813 TYR cc_start: 0.8590 (t80) cc_final: 0.8060 (t80) REVERT: B 952 MET cc_start: 0.6128 (tmm) cc_final: 0.5586 (tmm) REVERT: B 1153 LEU cc_start: 0.7665 (mm) cc_final: 0.7057 (mm) REVERT: B 1164 ARG cc_start: 0.7440 (mmm-85) cc_final: 0.6950 (mmt90) REVERT: C 94 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7095 (mt-10) REVERT: C 96 GLU cc_start: 0.7598 (tp30) cc_final: 0.7231 (tp30) REVERT: C 221 LEU cc_start: 0.9423 (mt) cc_final: 0.9194 (mt) REVERT: C 461 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8472 (mmm) REVERT: C 478 SER cc_start: 0.8012 (p) cc_final: 0.7451 (t) REVERT: C 516 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: C 562 MET cc_start: 0.8126 (mtt) cc_final: 0.7817 (mtm) REVERT: C 659 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8669 (mp) REVERT: C 851 LYS cc_start: 0.9400 (mttt) cc_final: 0.9184 (mtpp) REVERT: C 982 GLN cc_start: 0.7082 (tp40) cc_final: 0.6446 (tp-100) REVERT: C 1182 ASP cc_start: 0.8099 (p0) cc_final: 0.7897 (p0) REVERT: C 1294 ASP cc_start: 0.8077 (m-30) cc_final: 0.7665 (m-30) REVERT: C 1407 ASP cc_start: 0.8385 (p0) cc_final: 0.8138 (p0) REVERT: D 427 ASP cc_start: 0.8014 (p0) cc_final: 0.7616 (p0) REVERT: D 711 MET cc_start: 0.8328 (ttm) cc_final: 0.7895 (ttm) REVERT: D 724 ASN cc_start: 0.8223 (m110) cc_final: 0.8009 (m110) REVERT: D 1186 ARG cc_start: 0.7535 (ptp-110) cc_final: 0.7334 (ptp-110) REVERT: E 94 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7251 (mt-10) REVERT: E 182 MET cc_start: 0.7614 (tpp) cc_final: 0.6622 (mmt) REVERT: E 478 SER cc_start: 0.7676 (p) cc_final: 0.7012 (t) REVERT: E 479 MET cc_start: 0.8753 (tpp) cc_final: 0.8425 (mmm) REVERT: E 516 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: E 562 MET cc_start: 0.7743 (mtt) cc_final: 0.7481 (mtm) REVERT: E 693 MET cc_start: 0.8230 (mmm) cc_final: 0.7884 (mmm) REVERT: E 830 GLU cc_start: 0.8285 (tt0) cc_final: 0.7957 (tt0) REVERT: E 982 GLN cc_start: 0.6916 (tp40) cc_final: 0.6615 (tp-100) REVERT: E 1104 MET cc_start: 0.9004 (mmt) cc_final: 0.8790 (mmt) REVERT: E 1294 ASP cc_start: 0.8074 (m-30) cc_final: 0.7855 (m-30) REVERT: F 160 LYS cc_start: 0.8580 (tmmt) cc_final: 0.7994 (ttmt) REVERT: F 216 PHE cc_start: 0.8270 (m-80) cc_final: 0.8002 (m-80) REVERT: F 468 MET cc_start: 0.8710 (mtt) cc_final: 0.8336 (mtp) REVERT: F 492 TYR cc_start: 0.7903 (t80) cc_final: 0.7540 (t80) REVERT: F 858 MET cc_start: 0.6938 (mtm) cc_final: 0.6058 (mtt) REVERT: F 931 LYS cc_start: 0.8367 (tttm) cc_final: 0.8142 (tttm) REVERT: F 1159 ASN cc_start: 0.8491 (m-40) cc_final: 0.8014 (t0) REVERT: F 1212 ASP cc_start: 0.7646 (m-30) cc_final: 0.7422 (m-30) REVERT: F 1229 MET cc_start: 0.9070 (mmt) cc_final: 0.8838 (mmt) REVERT: H 428 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6955 (t70) REVERT: I 303 MET cc_start: 0.8112 (mmp) cc_final: 0.7768 (mmm) REVERT: J 472 LYS cc_start: 0.8115 (tmmt) cc_final: 0.7478 (tppt) outliers start: 72 outliers final: 49 residues processed: 864 average time/residue: 0.7874 time to fit residues: 1157.7500 Evaluate side-chains 787 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 733 time to evaluate : 6.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1332 THR Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1332 THR Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1256 MET Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 428 HIS Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 961 optimal weight: 5.9990 chunk 731 optimal weight: 9.9990 chunk 505 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 464 optimal weight: 0.9980 chunk 653 optimal weight: 3.9990 chunk 976 optimal weight: 0.5980 chunk 1034 optimal weight: 6.9990 chunk 510 optimal weight: 2.9990 chunk 925 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1026 ASN ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1026 ASN E 208 HIS ** E 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 868 HIS F1120 GLN H 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 84574 Z= 0.244 Angle : 0.831 82.125 114568 Z= 0.336 Chirality : 0.053 1.547 12762 Planarity : 0.004 0.045 14992 Dihedral : 5.228 163.157 11941 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.63 % Allowed : 12.61 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.08), residues: 10700 helix: 0.79 (0.09), residues: 3728 sheet: -0.70 (0.13), residues: 1532 loop : -1.82 (0.08), residues: 5440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 69 HIS 0.009 0.001 HIS D 603 PHE 0.017 0.001 PHE I 36 TYR 0.019 0.001 TYR C1367 ARG 0.009 0.000 ARG E1220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 756 time to evaluate : 7.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8801 (mtt) cc_final: 0.8564 (mtt) REVERT: A 479 MET cc_start: 0.8498 (tpp) cc_final: 0.8187 (tpt) REVERT: B 160 LYS cc_start: 0.8691 (tmmt) cc_final: 0.8173 (ttmt) REVERT: B 952 MET cc_start: 0.6070 (tmm) cc_final: 0.5652 (tmm) REVERT: B 1153 LEU cc_start: 0.7776 (mm) cc_final: 0.7167 (mm) REVERT: B 1164 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7139 (mmt90) REVERT: C 94 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7122 (mt-10) REVERT: C 96 GLU cc_start: 0.7531 (tp30) cc_final: 0.7168 (tp30) REVERT: C 221 LEU cc_start: 0.9454 (mt) cc_final: 0.9038 (mt) REVERT: C 251 MET cc_start: 0.8468 (ptp) cc_final: 0.8160 (ptp) REVERT: C 461 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8461 (mmm) REVERT: C 516 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 780 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7992 (mtm180) REVERT: C 851 LYS cc_start: 0.9454 (mttt) cc_final: 0.9185 (mtpp) REVERT: C 982 GLN cc_start: 0.7201 (tp40) cc_final: 0.6791 (tp-100) REVERT: C 1182 ASP cc_start: 0.8006 (p0) cc_final: 0.7800 (p0) REVERT: C 1294 ASP cc_start: 0.8069 (m-30) cc_final: 0.7616 (m-30) REVERT: D 335 MET cc_start: 0.8367 (ptp) cc_final: 0.7849 (mtm) REVERT: D 371 MET cc_start: 0.8823 (mtt) cc_final: 0.8608 (mtt) REVERT: D 390 MET cc_start: 0.8775 (ttp) cc_final: 0.8460 (ttp) REVERT: D 427 ASP cc_start: 0.8077 (p0) cc_final: 0.7694 (p0) REVERT: D 478 SER cc_start: 0.8663 (p) cc_final: 0.8328 (t) REVERT: E 94 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7261 (mt-10) REVERT: E 221 LEU cc_start: 0.9380 (mt) cc_final: 0.9125 (mt) REVERT: E 251 MET cc_start: 0.8688 (ptp) cc_final: 0.8371 (ptp) REVERT: E 479 MET cc_start: 0.8813 (tpp) cc_final: 0.8518 (mmm) REVERT: E 516 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: E 562 MET cc_start: 0.7600 (mtt) cc_final: 0.7309 (mtm) REVERT: E 693 MET cc_start: 0.8234 (mmm) cc_final: 0.7964 (mmm) REVERT: E 830 GLU cc_start: 0.8245 (tt0) cc_final: 0.7934 (tt0) REVERT: E 982 GLN cc_start: 0.7055 (tp40) cc_final: 0.6756 (tp-100) REVERT: E 1294 ASP cc_start: 0.8084 (m-30) cc_final: 0.7866 (m-30) REVERT: F 160 LYS cc_start: 0.8550 (tmmt) cc_final: 0.7989 (ttpt) REVERT: F 296 MET cc_start: 0.8241 (tpp) cc_final: 0.8010 (mmm) REVERT: F 389 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7104 (mm-30) REVERT: F 468 MET cc_start: 0.8739 (mtt) cc_final: 0.8325 (mtp) REVERT: F 492 TYR cc_start: 0.7991 (t80) cc_final: 0.7577 (t80) REVERT: F 858 MET cc_start: 0.7246 (mtm) cc_final: 0.6401 (mtt) REVERT: F 875 MET cc_start: 0.6812 (mmm) cc_final: 0.6589 (mmm) REVERT: F 931 LYS cc_start: 0.8459 (tttm) cc_final: 0.8182 (tttm) REVERT: F 1159 ASN cc_start: 0.8525 (m-40) cc_final: 0.8054 (t0) REVERT: G 68 ASP cc_start: 0.8273 (m-30) cc_final: 0.7997 (m-30) REVERT: J 472 LYS cc_start: 0.8076 (tmmt) cc_final: 0.7639 (tppt) outliers start: 142 outliers final: 105 residues processed: 865 average time/residue: 0.7708 time to fit residues: 1145.8067 Evaluate side-chains 830 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 721 time to evaluate : 7.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1296 VAL Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1026 ASN Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1332 THR Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1332 THR Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain E residue 1466 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1153 LEU Chi-restraints excluded: chain F residue 1256 MET Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 429 ARG Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 861 optimal weight: 2.9990 chunk 587 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 770 optimal weight: 3.9990 chunk 426 optimal weight: 5.9990 chunk 882 optimal weight: 3.9990 chunk 714 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 528 optimal weight: 5.9990 chunk 928 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN B 695 ASN C 208 HIS ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1026 ASN ** E 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 738 HIS F 868 HIS H 64 ASN H 116 HIS J 64 ASN J 116 HIS ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 84574 Z= 0.368 Angle : 0.878 82.283 114568 Z= 0.366 Chirality : 0.056 1.557 12762 Planarity : 0.004 0.051 14992 Dihedral : 5.473 161.811 11939 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.13 % Allowed : 13.66 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.08), residues: 10700 helix: 0.78 (0.09), residues: 3684 sheet: -0.68 (0.13), residues: 1562 loop : -1.75 (0.08), residues: 5454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 69 HIS 0.011 0.001 HIS A 603 PHE 0.023 0.002 PHE A 200 TYR 0.019 0.002 TYR A1367 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 737 time to evaluate : 7.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8434 (ptp) cc_final: 0.7969 (mtm) REVERT: A 390 MET cc_start: 0.8789 (ttp) cc_final: 0.8519 (ttp) REVERT: A 427 ASP cc_start: 0.8054 (p0) cc_final: 0.7756 (p0) REVERT: A 760 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 1019 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8313 (p0) REVERT: A 1214 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7851 (mmm160) REVERT: A 1294 ASP cc_start: 0.7321 (m-30) cc_final: 0.6865 (m-30) REVERT: B 160 LYS cc_start: 0.8754 (tmmt) cc_final: 0.8203 (ttmt) REVERT: B 952 MET cc_start: 0.5774 (tmm) cc_final: 0.5406 (tmm) REVERT: B 1164 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7027 (mmt90) REVERT: C 94 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 251 MET cc_start: 0.8589 (ptp) cc_final: 0.8174 (ptp) REVERT: C 354 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6609 (mtt-85) REVERT: C 461 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8478 (mmm) REVERT: C 478 SER cc_start: 0.8271 (p) cc_final: 0.7759 (t) REVERT: C 516 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: C 562 MET cc_start: 0.8129 (mtt) cc_final: 0.7818 (mtm) REVERT: C 780 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7919 (mtm180) REVERT: C 982 GLN cc_start: 0.7209 (tp40) cc_final: 0.6919 (tp-100) REVERT: C 1294 ASP cc_start: 0.8045 (m-30) cc_final: 0.7482 (m-30) REVERT: D 390 MET cc_start: 0.8759 (ttp) cc_final: 0.8471 (ttp) REVERT: D 427 ASP cc_start: 0.8077 (p0) cc_final: 0.7708 (p0) REVERT: D 711 MET cc_start: 0.8447 (ttm) cc_final: 0.8239 (ttm) REVERT: D 1186 ARG cc_start: 0.7423 (ptp-110) cc_final: 0.7090 (ptp-110) REVERT: E 94 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7294 (mt-10) REVERT: E 182 MET cc_start: 0.7706 (tpp) cc_final: 0.6867 (mmt) REVERT: E 251 MET cc_start: 0.8713 (ptp) cc_final: 0.8425 (ptp) REVERT: E 461 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8424 (mtp) REVERT: E 479 MET cc_start: 0.8806 (tpp) cc_final: 0.8501 (mmm) REVERT: E 516 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: E 562 MET cc_start: 0.7622 (mtt) cc_final: 0.7316 (mtm) REVERT: E 693 MET cc_start: 0.8285 (mmm) cc_final: 0.8043 (mmm) REVERT: E 830 GLU cc_start: 0.8271 (tt0) cc_final: 0.7904 (tt0) REVERT: E 982 GLN cc_start: 0.7150 (tp40) cc_final: 0.6914 (tp-100) REVERT: E 1294 ASP cc_start: 0.8168 (m-30) cc_final: 0.7894 (m-30) REVERT: F 160 LYS cc_start: 0.8675 (tmmt) cc_final: 0.8147 (ttpt) REVERT: F 468 MET cc_start: 0.8805 (mtt) cc_final: 0.8388 (mtp) REVERT: F 492 TYR cc_start: 0.8125 (t80) cc_final: 0.7727 (t80) REVERT: F 796 HIS cc_start: 0.7464 (t70) cc_final: 0.7217 (t-170) REVERT: F 858 MET cc_start: 0.7381 (mtm) cc_final: 0.7048 (mtt) REVERT: F 931 LYS cc_start: 0.8622 (tttm) cc_final: 0.8264 (tttm) REVERT: F 1159 ASN cc_start: 0.8660 (m-40) cc_final: 0.8123 (t0) REVERT: G 68 ASP cc_start: 0.8473 (m-30) cc_final: 0.8138 (m-30) REVERT: H 116 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8290 (m-70) REVERT: J 116 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8449 (m-70) REVERT: J 472 LYS cc_start: 0.7821 (tmmt) cc_final: 0.7563 (tppt) outliers start: 185 outliers final: 137 residues processed: 877 average time/residue: 0.7712 time to fit residues: 1166.5847 Evaluate side-chains 846 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 700 time to evaluate : 7.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 886 GLU Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1296 VAL Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1332 THR Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 1026 ASN Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1321 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1038 ILE Chi-restraints excluded: chain E residue 1057 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1242 ILE Chi-restraints excluded: chain E residue 1251 THR Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1153 LEU Chi-restraints excluded: chain F residue 1256 MET Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 429 ARG Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 418 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 347 optimal weight: 3.9990 chunk 931 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 607 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 1035 optimal weight: 0.9980 chunk 859 optimal weight: 2.9990 chunk 479 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 342 optimal weight: 7.9990 chunk 543 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 868 HIS J 64 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 84574 Z= 0.278 Angle : 0.846 82.241 114568 Z= 0.346 Chirality : 0.054 1.547 12762 Planarity : 0.004 0.055 14992 Dihedral : 5.341 162.470 11938 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.26 % Allowed : 14.45 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.08), residues: 10700 helix: 0.89 (0.09), residues: 3672 sheet: -0.57 (0.13), residues: 1562 loop : -1.60 (0.08), residues: 5466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 69 HIS 0.020 0.001 HIS H 116 PHE 0.014 0.001 PHE I 36 TYR 0.017 0.001 TYR C 207 ARG 0.005 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 733 time to evaluate : 7.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 MET cc_start: 0.8746 (ttp) cc_final: 0.8501 (ttp) REVERT: A 427 ASP cc_start: 0.8039 (p0) cc_final: 0.7748 (p0) REVERT: A 1019 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8213 (p0) REVERT: A 1214 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7793 (mmm160) REVERT: B 160 LYS cc_start: 0.8682 (tmmt) cc_final: 0.8160 (ttmt) REVERT: B 335 MET cc_start: 0.7983 (ptp) cc_final: 0.7641 (mtm) REVERT: B 860 MET cc_start: 0.6536 (ttm) cc_final: 0.5874 (mmm) REVERT: B 952 MET cc_start: 0.5780 (tmm) cc_final: 0.5403 (tmm) REVERT: B 1164 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.6958 (mmt90) REVERT: B 1322 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8881 (mm) REVERT: C 10 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7343 (p0) REVERT: C 94 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7211 (mt-10) REVERT: C 195 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8134 (mm) REVERT: C 354 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.6585 (mtt-85) REVERT: C 461 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8464 (mmm) REVERT: C 516 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 562 MET cc_start: 0.8128 (mtt) cc_final: 0.7725 (mtm) REVERT: C 780 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7833 (mtm180) REVERT: C 982 GLN cc_start: 0.7174 (tp40) cc_final: 0.6921 (tp-100) REVERT: C 1294 ASP cc_start: 0.8032 (m-30) cc_final: 0.7460 (m-30) REVERT: D 390 MET cc_start: 0.8741 (ttp) cc_final: 0.8444 (ttp) REVERT: D 427 ASP cc_start: 0.8074 (p0) cc_final: 0.7722 (p0) REVERT: D 711 MET cc_start: 0.8414 (ttm) cc_final: 0.8187 (ttm) REVERT: D 1186 ARG cc_start: 0.7455 (ptp-110) cc_final: 0.7243 (ptp-110) REVERT: E 94 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7292 (mt-10) REVERT: E 195 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8217 (mm) REVERT: E 221 LEU cc_start: 0.9393 (mt) cc_final: 0.9147 (mt) REVERT: E 251 MET cc_start: 0.8777 (ptp) cc_final: 0.8466 (ptp) REVERT: E 461 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: E 479 MET cc_start: 0.8744 (tpp) cc_final: 0.8480 (mmm) REVERT: E 516 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: E 693 MET cc_start: 0.8179 (mmm) cc_final: 0.7973 (mmm) REVERT: E 830 GLU cc_start: 0.8238 (tt0) cc_final: 0.7617 (tt0) REVERT: E 832 ARG cc_start: 0.7479 (ttm170) cc_final: 0.6897 (ttm170) REVERT: E 982 GLN cc_start: 0.7095 (tp40) cc_final: 0.6858 (tp-100) REVERT: E 1294 ASP cc_start: 0.8025 (m-30) cc_final: 0.7666 (m-30) REVERT: F 160 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8018 (ttpt) REVERT: F 335 MET cc_start: 0.7887 (ptp) cc_final: 0.7651 (mtm) REVERT: F 389 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7052 (mm-30) REVERT: F 468 MET cc_start: 0.8797 (mtt) cc_final: 0.8438 (mtp) REVERT: F 796 HIS cc_start: 0.7521 (t70) cc_final: 0.7313 (t-170) REVERT: F 858 MET cc_start: 0.7326 (mtm) cc_final: 0.7031 (mtt) REVERT: F 931 LYS cc_start: 0.8629 (tttm) cc_final: 0.8267 (tttm) REVERT: F 978 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: F 1144 GLU cc_start: 0.7997 (pt0) cc_final: 0.7796 (pp20) REVERT: F 1159 ASN cc_start: 0.8562 (m-40) cc_final: 0.8035 (t0) REVERT: F 1322 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8886 (mm) REVERT: G 68 ASP cc_start: 0.8438 (m-30) cc_final: 0.8138 (m-30) REVERT: H 116 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8527 (m170) REVERT: I 303 MET cc_start: 0.8265 (mmp) cc_final: 0.7847 (mmm) REVERT: J 116 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8519 (m170) REVERT: J 472 LYS cc_start: 0.7801 (tmmt) cc_final: 0.7550 (tppt) outliers start: 197 outliers final: 147 residues processed: 880 average time/residue: 0.8242 time to fit residues: 1265.9451 Evaluate side-chains 869 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 707 time to evaluate : 7.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1026 ASN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1296 VAL Chi-restraints excluded: chain B residue 1322 ILE Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1433 THR Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1387 MET Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 978 GLU Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1296 VAL Chi-restraints excluded: chain D residue 1311 THR Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1242 ILE Chi-restraints excluded: chain E residue 1251 THR Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 764 THR Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1153 LEU Chi-restraints excluded: chain F residue 1256 MET Chi-restraints excluded: chain F residue 1264 ILE Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1322 ILE Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1433 THR Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 36 PHE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 418 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 998 optimal weight: 9.9990 chunk 116 optimal weight: 0.3980 chunk 589 optimal weight: 10.0000 chunk 756 optimal weight: 9.9990 chunk 585 optimal weight: 0.9980 chunk 871 optimal weight: 10.0000 chunk 578 optimal weight: 0.9990 chunk 1031 optimal weight: 9.9990 chunk 645 optimal weight: 3.9990 chunk 628 optimal weight: 2.9990 chunk 476 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 497 HIS ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1026 ASN E 451 GLN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 982 GLN E1026 ASN F 422 ASN F 643 ASN F 868 HIS G 434 ASN I 434 ASN J 64 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 84574 Z= 0.214 Angle : 0.828 82.237 114568 Z= 0.333 Chirality : 0.053 1.541 12762 Planarity : 0.003 0.052 14992 Dihedral : 5.168 163.336 11936 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.03 % Allowed : 15.00 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.08), residues: 10700 helix: 1.01 (0.09), residues: 3716 sheet: -0.40 (0.13), residues: 1556 loop : -1.50 (0.08), residues: 5428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 69 HIS 0.011 0.001 HIS A 603 PHE 0.013 0.001 PHE I 36 TYR 0.017 0.001 TYR C 207 ARG 0.006 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 749 time to evaluate : 7.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8340 (ptp) cc_final: 0.8130 (mtm) REVERT: A 390 MET cc_start: 0.8703 (ttp) cc_final: 0.8376 (ttp) REVERT: A 427 ASP cc_start: 0.8036 (p0) cc_final: 0.7748 (p0) REVERT: A 1019 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8186 (p0) REVERT: A 1214 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7751 (mmm160) REVERT: B 160 LYS cc_start: 0.8496 (tmmt) cc_final: 0.8024 (ttmt) REVERT: B 479 MET cc_start: 0.7945 (tpp) cc_final: 0.7603 (mmt) REVERT: B 858 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.5757 (mmt) REVERT: B 860 MET cc_start: 0.6641 (ttm) cc_final: 0.6151 (mmm) REVERT: B 875 MET cc_start: 0.6404 (mmm) cc_final: 0.6168 (mmm) REVERT: B 952 MET cc_start: 0.5764 (tmm) cc_final: 0.5392 (tmm) REVERT: B 978 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: B 1164 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7133 (mmt90) REVERT: C 10 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7169 (p0) REVERT: C 94 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7157 (mt-10) REVERT: C 129 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8191 (tt0) REVERT: C 195 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8066 (mm) REVERT: C 227 MET cc_start: 0.8530 (ppp) cc_final: 0.7778 (ppp) REVERT: C 281 PHE cc_start: 0.8212 (t80) cc_final: 0.7797 (t80) REVERT: C 354 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6574 (mtt-85) REVERT: C 461 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8505 (mmm) REVERT: C 516 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: C 562 MET cc_start: 0.8096 (mtt) cc_final: 0.7688 (mtm) REVERT: C 780 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7847 (mtm180) REVERT: C 982 GLN cc_start: 0.7133 (tp40) cc_final: 0.6817 (tp-100) REVERT: C 1294 ASP cc_start: 0.8038 (m-30) cc_final: 0.7602 (m-30) REVERT: D 335 MET cc_start: 0.8377 (ptp) cc_final: 0.8115 (mtm) REVERT: D 390 MET cc_start: 0.8679 (ttp) cc_final: 0.8343 (ttp) REVERT: D 427 ASP cc_start: 0.8080 (p0) cc_final: 0.7738 (p0) REVERT: D 711 MET cc_start: 0.8269 (ttm) cc_final: 0.7994 (ttm) REVERT: D 1186 ARG cc_start: 0.7581 (ptp-110) cc_final: 0.7302 (ptp-110) REVERT: E 10 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6534 (p0) REVERT: E 94 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7239 (mt-10) REVERT: E 195 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8110 (mm) REVERT: E 221 LEU cc_start: 0.9395 (mt) cc_final: 0.9130 (mt) REVERT: E 227 MET cc_start: 0.8464 (ppp) cc_final: 0.8046 (ppp) REVERT: E 251 MET cc_start: 0.8728 (ptp) cc_final: 0.8414 (ptp) REVERT: E 354 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6621 (mtt-85) REVERT: E 461 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: E 479 MET cc_start: 0.8734 (tpp) cc_final: 0.8490 (mmm) REVERT: E 516 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: E 562 MET cc_start: 0.8026 (mtt) cc_final: 0.7676 (mtm) REVERT: E 830 GLU cc_start: 0.8202 (tt0) cc_final: 0.7837 (tt0) REVERT: E 832 ARG cc_start: 0.7454 (ttm170) cc_final: 0.7199 (ttm170) REVERT: E 1294 ASP cc_start: 0.7934 (m-30) cc_final: 0.7448 (m-30) REVERT: F 160 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8003 (ttpt) REVERT: F 296 MET cc_start: 0.8245 (tpp) cc_final: 0.8039 (tpp) REVERT: F 335 MET cc_start: 0.7789 (ptp) cc_final: 0.7579 (mtm) REVERT: F 389 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7142 (mm-30) REVERT: F 468 MET cc_start: 0.8773 (mtt) cc_final: 0.8397 (mtp) REVERT: F 858 MET cc_start: 0.7327 (mtm) cc_final: 0.6892 (mtt) REVERT: F 931 LYS cc_start: 0.8547 (tttm) cc_final: 0.8181 (tttm) REVERT: F 952 MET cc_start: 0.6437 (tmm) cc_final: 0.5929 (tmm) REVERT: F 978 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: F 1144 GLU cc_start: 0.7992 (pt0) cc_final: 0.7746 (pp20) REVERT: F 1159 ASN cc_start: 0.8545 (m-40) cc_final: 0.8009 (t0) REVERT: F 1322 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8928 (mm) REVERT: F 1368 MET cc_start: 0.9402 (ttt) cc_final: 0.9118 (ttm) REVERT: G 68 ASP cc_start: 0.8366 (m-30) cc_final: 0.7991 (m-30) REVERT: J 183 MET cc_start: 0.8160 (mmt) cc_final: 0.7910 (mmt) REVERT: J 472 LYS cc_start: 0.7759 (tmmt) cc_final: 0.7485 (tppt) outliers start: 177 outliers final: 134 residues processed: 888 average time/residue: 0.8197 time to fit residues: 1262.8903 Evaluate side-chains 862 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 712 time to evaluate : 7.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1019 ASP Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1433 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1387 MET Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 978 GLU Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1296 VAL Chi-restraints excluded: chain D residue 1311 THR Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1362 SER Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1264 ILE Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1322 ILE Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1433 THR Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 434 ASN Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 36 PHE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 418 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 638 optimal weight: 0.0010 chunk 411 optimal weight: 8.9990 chunk 615 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 655 optimal weight: 20.0000 chunk 702 optimal weight: 2.9990 chunk 509 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 810 optimal weight: 6.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN B 240 ASN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 972 HIS E 982 GLN F 868 HIS ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN H 116 HIS I 434 ASN J 116 HIS ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 84574 Z= 0.292 Angle : 0.853 82.325 114568 Z= 0.349 Chirality : 0.054 1.542 12762 Planarity : 0.004 0.052 14992 Dihedral : 5.277 164.352 11936 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.41 % Allowed : 15.14 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.08), residues: 10700 helix: 0.95 (0.09), residues: 3720 sheet: -0.38 (0.13), residues: 1556 loop : -1.48 (0.08), residues: 5424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 69 HIS 0.011 0.001 HIS A 603 PHE 0.019 0.001 PHE C 894 TYR 0.019 0.001 TYR B 807 ARG 0.009 0.000 ARG C1173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 720 time to evaluate : 6.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8462 (ptp) cc_final: 0.8211 (mtm) REVERT: A 390 MET cc_start: 0.8699 (ttp) cc_final: 0.8366 (ttp) REVERT: A 427 ASP cc_start: 0.8037 (p0) cc_final: 0.7747 (p0) REVERT: A 1019 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8205 (p0) REVERT: A 1214 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7770 (mmm160) REVERT: A 1368 MET cc_start: 0.9036 (ttt) cc_final: 0.8678 (ttt) REVERT: B 160 LYS cc_start: 0.8651 (tmmt) cc_final: 0.8163 (ttmt) REVERT: B 479 MET cc_start: 0.7943 (tpp) cc_final: 0.7626 (mmt) REVERT: B 860 MET cc_start: 0.6721 (ttm) cc_final: 0.6291 (mmm) REVERT: B 952 MET cc_start: 0.6033 (tmm) cc_final: 0.5606 (tmm) REVERT: B 978 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: B 1164 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.6994 (mmt90) REVERT: B 1322 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8873 (mm) REVERT: C 10 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7206 (p0) REVERT: C 94 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7198 (mt-10) REVERT: C 129 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8198 (tt0) REVERT: C 195 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8103 (mm) REVERT: C 227 MET cc_start: 0.8535 (ppp) cc_final: 0.8307 (ppp) REVERT: C 354 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6603 (mtt-85) REVERT: C 461 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8449 (mmm) REVERT: C 516 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 562 MET cc_start: 0.8112 (mtt) cc_final: 0.7735 (mtm) REVERT: C 780 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7834 (mtm180) REVERT: C 982 GLN cc_start: 0.7207 (tp40) cc_final: 0.6959 (tp-100) REVERT: D 335 MET cc_start: 0.8407 (ptp) cc_final: 0.8108 (mtm) REVERT: D 390 MET cc_start: 0.8740 (ttp) cc_final: 0.8413 (ttp) REVERT: D 427 ASP cc_start: 0.8019 (p0) cc_final: 0.7714 (p0) REVERT: D 711 MET cc_start: 0.8363 (ttm) cc_final: 0.8116 (ttm) REVERT: D 1368 MET cc_start: 0.8995 (ttt) cc_final: 0.8623 (ttt) REVERT: E 10 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6549 (p0) REVERT: E 94 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7267 (mt-10) REVERT: E 195 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8153 (mm) REVERT: E 227 MET cc_start: 0.8394 (ppp) cc_final: 0.8076 (ppp) REVERT: E 251 MET cc_start: 0.8720 (ptp) cc_final: 0.8399 (ptp) REVERT: E 354 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6664 (mtt-85) REVERT: E 461 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: E 479 MET cc_start: 0.8814 (tpp) cc_final: 0.8613 (mmm) REVERT: E 516 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: E 562 MET cc_start: 0.7996 (mtt) cc_final: 0.7700 (mtm) REVERT: E 672 GLN cc_start: 0.6995 (tt0) cc_final: 0.6710 (mt0) REVERT: E 830 GLU cc_start: 0.8219 (tt0) cc_final: 0.7863 (tt0) REVERT: E 832 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7203 (ttm170) REVERT: E 1294 ASP cc_start: 0.7962 (m-30) cc_final: 0.7497 (m-30) REVERT: F 160 LYS cc_start: 0.8654 (tmmt) cc_final: 0.8147 (ttpt) REVERT: F 335 MET cc_start: 0.7933 (ptp) cc_final: 0.7654 (mtm) REVERT: F 468 MET cc_start: 0.8796 (mtt) cc_final: 0.8389 (mtp) REVERT: F 858 MET cc_start: 0.7220 (mtm) cc_final: 0.6813 (mtt) REVERT: F 931 LYS cc_start: 0.8576 (tttm) cc_final: 0.8212 (tttm) REVERT: F 952 MET cc_start: 0.6384 (tmm) cc_final: 0.5879 (tmm) REVERT: F 978 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: F 1159 ASN cc_start: 0.8579 (m-40) cc_final: 0.8018 (t0) REVERT: F 1322 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8867 (mm) REVERT: G 68 ASP cc_start: 0.8457 (m-30) cc_final: 0.8167 (m-30) REVERT: H 116 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8550 (m-70) REVERT: J 116 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8428 (m-70) REVERT: J 472 LYS cc_start: 0.7824 (tmmt) cc_final: 0.7506 (tppt) outliers start: 210 outliers final: 173 residues processed: 885 average time/residue: 0.7627 time to fit residues: 1166.6146 Evaluate side-chains 903 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 712 time to evaluate : 7.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1019 ASP Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1296 VAL Chi-restraints excluded: chain B residue 1322 ILE Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1433 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1387 MET Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 978 GLU Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1296 VAL Chi-restraints excluded: chain D residue 1311 THR Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1057 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1242 ILE Chi-restraints excluded: chain E residue 1251 THR Chi-restraints excluded: chain E residue 1362 SER Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 764 THR Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1153 LEU Chi-restraints excluded: chain F residue 1264 ILE Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1322 ILE Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1433 THR Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 424 LEU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 36 PHE Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 418 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 938 optimal weight: 0.1980 chunk 988 optimal weight: 4.9990 chunk 901 optimal weight: 1.9990 chunk 961 optimal weight: 8.9990 chunk 987 optimal weight: 10.0000 chunk 578 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 754 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 868 optimal weight: 6.9990 chunk 908 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1026 ASN F 868 HIS H 64 ASN H 116 HIS J 64 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 84574 Z= 0.252 Angle : 0.843 82.280 114568 Z= 0.343 Chirality : 0.054 1.543 12762 Planarity : 0.004 0.053 14992 Dihedral : 5.238 164.128 11936 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.26 % Allowed : 15.35 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.08), residues: 10700 helix: 1.05 (0.09), residues: 3684 sheet: -0.33 (0.13), residues: 1556 loop : -1.41 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 69 HIS 0.012 0.001 HIS H 116 PHE 0.020 0.001 PHE E 894 TYR 0.019 0.001 TYR C 207 ARG 0.007 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 728 time to evaluate : 7.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.8387 (ptp) cc_final: 0.8182 (mtm) REVERT: A 371 MET cc_start: 0.8684 (mtt) cc_final: 0.8175 (mtt) REVERT: A 390 MET cc_start: 0.8679 (ttp) cc_final: 0.8350 (ttp) REVERT: A 427 ASP cc_start: 0.8031 (p0) cc_final: 0.7742 (p0) REVERT: A 1019 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 1214 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7763 (mmm160) REVERT: A 1368 MET cc_start: 0.8960 (ttt) cc_final: 0.8610 (ttt) REVERT: B 160 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8146 (ttmt) REVERT: B 479 MET cc_start: 0.8050 (tpp) cc_final: 0.7719 (mmt) REVERT: B 858 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.5733 (mmt) REVERT: B 860 MET cc_start: 0.6662 (ttm) cc_final: 0.6291 (mmm) REVERT: B 931 LYS cc_start: 0.8527 (tttm) cc_final: 0.8285 (tttm) REVERT: B 952 MET cc_start: 0.6012 (tmm) cc_final: 0.5594 (tmm) REVERT: B 978 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: B 1164 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.6972 (mmt90) REVERT: B 1322 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8935 (mm) REVERT: C 10 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6717 (p0) REVERT: C 94 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7191 (mt-10) REVERT: C 129 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8196 (tt0) REVERT: C 195 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8082 (mm) REVERT: C 227 MET cc_start: 0.8542 (ppp) cc_final: 0.8123 (ppp) REVERT: C 354 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6634 (mtt-85) REVERT: C 461 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8436 (mmm) REVERT: C 516 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: C 562 MET cc_start: 0.8119 (mtt) cc_final: 0.7865 (mtm) REVERT: C 780 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7789 (mtm180) REVERT: C 982 GLN cc_start: 0.7117 (tp40) cc_final: 0.6869 (tp-100) REVERT: C 1294 ASP cc_start: 0.8044 (m-30) cc_final: 0.7439 (m-30) REVERT: D 335 MET cc_start: 0.8406 (ptp) cc_final: 0.8185 (mtm) REVERT: D 371 MET cc_start: 0.8685 (mtt) cc_final: 0.8179 (mtt) REVERT: D 390 MET cc_start: 0.8695 (ttp) cc_final: 0.8359 (ttp) REVERT: D 427 ASP cc_start: 0.8017 (p0) cc_final: 0.7718 (p0) REVERT: D 711 MET cc_start: 0.8331 (ttm) cc_final: 0.8084 (ttm) REVERT: D 1368 MET cc_start: 0.8969 (ttt) cc_final: 0.8572 (ttt) REVERT: E 10 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6539 (p0) REVERT: E 94 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7260 (mt-10) REVERT: E 195 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8009 (mm) REVERT: E 227 MET cc_start: 0.8367 (ppp) cc_final: 0.8084 (ppp) REVERT: E 251 MET cc_start: 0.8706 (ptp) cc_final: 0.8337 (ptp) REVERT: E 354 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6641 (mtt-85) REVERT: E 461 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: E 479 MET cc_start: 0.8791 (tpp) cc_final: 0.8590 (mmm) REVERT: E 516 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: E 562 MET cc_start: 0.7964 (mtt) cc_final: 0.7679 (mtm) REVERT: E 672 GLN cc_start: 0.6930 (tt0) cc_final: 0.6661 (mt0) REVERT: E 830 GLU cc_start: 0.8213 (tt0) cc_final: 0.7871 (tt0) REVERT: E 832 ARG cc_start: 0.7446 (ttm170) cc_final: 0.7193 (ttm170) REVERT: E 1294 ASP cc_start: 0.7916 (m-30) cc_final: 0.7381 (m-30) REVERT: F 160 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8037 (ttpt) REVERT: F 468 MET cc_start: 0.8788 (mtt) cc_final: 0.8391 (mtp) REVERT: F 858 MET cc_start: 0.7319 (mtm) cc_final: 0.6867 (mtt) REVERT: F 860 MET cc_start: 0.6492 (ttm) cc_final: 0.5859 (mmm) REVERT: F 931 LYS cc_start: 0.8582 (tttm) cc_final: 0.8262 (tttm) REVERT: F 952 MET cc_start: 0.6390 (tmm) cc_final: 0.5894 (tmm) REVERT: F 978 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: F 1159 ASN cc_start: 0.8633 (m-40) cc_final: 0.8038 (t0) REVERT: F 1322 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8923 (mm) REVERT: G 68 ASP cc_start: 0.8415 (m-30) cc_final: 0.8112 (m-30) REVERT: J 183 MET cc_start: 0.8252 (mmt) cc_final: 0.7946 (mmt) REVERT: J 472 LYS cc_start: 0.7819 (tmmt) cc_final: 0.7503 (tppt) outliers start: 197 outliers final: 170 residues processed: 882 average time/residue: 0.7755 time to fit residues: 1184.9080 Evaluate side-chains 902 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 715 time to evaluate : 7.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1019 ASP Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1296 VAL Chi-restraints excluded: chain B residue 1322 ILE Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1433 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1387 MET Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 978 GLU Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1296 VAL Chi-restraints excluded: chain D residue 1311 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1057 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1242 ILE Chi-restraints excluded: chain E residue 1251 THR Chi-restraints excluded: chain E residue 1362 SER Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 764 THR Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1153 LEU Chi-restraints excluded: chain F residue 1264 ILE Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1322 ILE Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1433 THR Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 36 PHE Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 99 CYS Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 418 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 957 optimal weight: 9.9990 chunk 631 optimal weight: 9.9990 chunk 1016 optimal weight: 10.0000 chunk 620 optimal weight: 7.9990 chunk 482 optimal weight: 0.9990 chunk 706 optimal weight: 0.0980 chunk 1065 optimal weight: 1.9990 chunk 981 optimal weight: 1.9990 chunk 848 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 655 optimal weight: 9.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1026 ASN F 868 HIS H 64 ASN H 116 HIS J 64 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 84574 Z= 0.251 Angle : 0.845 82.324 114568 Z= 0.343 Chirality : 0.054 1.546 12762 Planarity : 0.004 0.053 14992 Dihedral : 5.228 163.944 11936 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.35 % Allowed : 15.39 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.08), residues: 10700 helix: 1.04 (0.09), residues: 3720 sheet: -0.30 (0.13), residues: 1556 loop : -1.39 (0.08), residues: 5424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 69 HIS 0.009 0.001 HIS A 603 PHE 0.018 0.001 PHE B 555 TYR 0.019 0.001 TYR C 207 ARG 0.008 0.000 ARG A 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21400 Ramachandran restraints generated. 10700 Oldfield, 0 Emsley, 10700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 727 time to evaluate : 7.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8667 (mtt) cc_final: 0.8153 (mtt) REVERT: A 390 MET cc_start: 0.8675 (ttp) cc_final: 0.8343 (ttp) REVERT: A 427 ASP cc_start: 0.8030 (p0) cc_final: 0.7740 (p0) REVERT: A 1019 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 1214 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7762 (mmm160) REVERT: B 160 LYS cc_start: 0.8603 (tmmt) cc_final: 0.8151 (ttmt) REVERT: B 479 MET cc_start: 0.8061 (tpp) cc_final: 0.7740 (mmt) REVERT: B 860 MET cc_start: 0.6632 (ttm) cc_final: 0.6325 (mmm) REVERT: B 931 LYS cc_start: 0.8524 (tttm) cc_final: 0.8270 (tttm) REVERT: B 952 MET cc_start: 0.6014 (tmm) cc_final: 0.5596 (tmm) REVERT: B 978 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: B 1164 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7046 (mmt90) REVERT: B 1322 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8922 (mm) REVERT: C 10 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6790 (p0) REVERT: C 94 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7191 (mt-10) REVERT: C 129 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8197 (tt0) REVERT: C 195 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8073 (mm) REVERT: C 227 MET cc_start: 0.8550 (ppp) cc_final: 0.8149 (ppp) REVERT: C 354 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6652 (mtt-85) REVERT: C 461 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8442 (mmm) REVERT: C 516 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: C 562 MET cc_start: 0.8169 (mtt) cc_final: 0.7883 (mtm) REVERT: C 780 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7793 (mtm180) REVERT: C 982 GLN cc_start: 0.7112 (tp40) cc_final: 0.6865 (tp-100) REVERT: C 1294 ASP cc_start: 0.8033 (m-30) cc_final: 0.7589 (m-30) REVERT: D 371 MET cc_start: 0.8610 (mtt) cc_final: 0.8130 (mtt) REVERT: D 390 MET cc_start: 0.8688 (ttp) cc_final: 0.8347 (ttp) REVERT: D 427 ASP cc_start: 0.8019 (p0) cc_final: 0.7721 (p0) REVERT: D 711 MET cc_start: 0.8328 (ttm) cc_final: 0.8084 (ttm) REVERT: E 10 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6529 (p0) REVERT: E 94 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7252 (mt-10) REVERT: E 195 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7989 (mm) REVERT: E 227 MET cc_start: 0.8351 (ppp) cc_final: 0.8074 (ppp) REVERT: E 251 MET cc_start: 0.8669 (ptp) cc_final: 0.8327 (ptp) REVERT: E 354 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6642 (mtt-85) REVERT: E 461 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: E 479 MET cc_start: 0.8775 (tpp) cc_final: 0.8512 (mmm) REVERT: E 516 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: E 562 MET cc_start: 0.7912 (mtt) cc_final: 0.7624 (mtm) REVERT: E 672 GLN cc_start: 0.6796 (tt0) cc_final: 0.6569 (mt0) REVERT: E 830 GLU cc_start: 0.8216 (tt0) cc_final: 0.7875 (tt0) REVERT: E 832 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7188 (ttm170) REVERT: E 1294 ASP cc_start: 0.7922 (m-30) cc_final: 0.7380 (m-30) REVERT: F 160 LYS cc_start: 0.8556 (tmmt) cc_final: 0.8038 (ttpt) REVERT: F 468 MET cc_start: 0.8784 (mtt) cc_final: 0.8392 (mtp) REVERT: F 858 MET cc_start: 0.7221 (mtm) cc_final: 0.6720 (mtt) REVERT: F 860 MET cc_start: 0.6480 (ttm) cc_final: 0.5887 (mmm) REVERT: F 931 LYS cc_start: 0.8576 (tttm) cc_final: 0.8255 (tttm) REVERT: F 952 MET cc_start: 0.6392 (tmm) cc_final: 0.5897 (tmm) REVERT: F 978 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: F 1159 ASN cc_start: 0.8630 (m-40) cc_final: 0.8031 (t0) REVERT: F 1322 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8922 (mm) REVERT: G 68 ASP cc_start: 0.8419 (m-30) cc_final: 0.8127 (m-30) REVERT: H 470 LYS cc_start: 0.8347 (tppt) cc_final: 0.8040 (mtpt) REVERT: J 183 MET cc_start: 0.8224 (mmt) cc_final: 0.7926 (mmt) REVERT: J 472 LYS cc_start: 0.7822 (tmmt) cc_final: 0.7502 (tppt) outliers start: 204 outliers final: 178 residues processed: 892 average time/residue: 0.7839 time to fit residues: 1213.6820 Evaluate side-chains 914 residues out of total 8698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 720 time to evaluate : 7.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1323 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 978 GLU Chi-restraints excluded: chain B residue 1008 THR Chi-restraints excluded: chain B residue 1019 ASP Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1199 CYS Chi-restraints excluded: chain B residue 1264 ILE Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1296 VAL Chi-restraints excluded: chain B residue 1322 ILE Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1433 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 780 ARG Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 997 THR Chi-restraints excluded: chain C residue 1103 ILE Chi-restraints excluded: chain C residue 1209 ASP Chi-restraints excluded: chain C residue 1242 ILE Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1387 MET Chi-restraints excluded: chain C residue 1398 ASP Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 764 THR Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 978 GLU Chi-restraints excluded: chain D residue 1050 SER Chi-restraints excluded: chain D residue 1115 VAL Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1190 VAL Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1296 VAL Chi-restraints excluded: chain D residue 1311 THR Chi-restraints excluded: chain D residue 1321 THR Chi-restraints excluded: chain D residue 1323 ILE Chi-restraints excluded: chain D residue 1369 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1057 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1209 ASP Chi-restraints excluded: chain E residue 1242 ILE Chi-restraints excluded: chain E residue 1251 THR Chi-restraints excluded: chain E residue 1362 SER Chi-restraints excluded: chain E residue 1398 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 482 ASP Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 764 THR Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1019 ASP Chi-restraints excluded: chain F residue 1023 ILE Chi-restraints excluded: chain F residue 1153 LEU Chi-restraints excluded: chain F residue 1264 ILE Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1296 VAL Chi-restraints excluded: chain F residue 1322 ILE Chi-restraints excluded: chain F residue 1323 ILE Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1433 THR Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 433 THR Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 449 SER Chi-restraints excluded: chain I residue 36 PHE Chi-restraints excluded: chain I residue 51 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 294 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 465 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 99 CYS Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 418 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain J residue 438 VAL Chi-restraints excluded: chain J residue 449 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 520 optimal weight: 3.9990 chunk 674 optimal weight: 6.9990 chunk 904 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 782 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 850 optimal weight: 0.0030 chunk 355 optimal weight: 3.9990 chunk 873 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 HIS ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 695 ASN F 868 HIS H 64 ASN H 116 HIS J 64 ASN J 116 HIS ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.088107 restraints weight = 138629.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090694 restraints weight = 76742.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092423 restraints weight = 52046.101| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 84574 Z= 0.249 Angle : 0.846 82.353 114568 Z= 0.344 Chirality : 0.054 1.543 12762 Planarity : 0.004 0.053 14992 Dihedral : 5.222 163.949 11936 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.32 % Allowed : 15.52 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.08), residues: 10700 helix: 1.05 (0.09), residues: 3720 sheet: -0.27 (0.13), residues: 1556 loop : -1.36 (0.08), residues: 5424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 69 HIS 0.009 0.001 HIS A 603 PHE 0.017 0.001 PHE B 555 TYR 0.018 0.001 TYR C 207 ARG 0.008 0.000 ARG E1220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18539.30 seconds wall clock time: 326 minutes 42.19 seconds (19602.19 seconds total)