Starting phenix.real_space_refine (version: dev) on Tue Dec 13 22:42:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/12_2022/7pmv_13541_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/12_2022/7pmv_13541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/12_2022/7pmv_13541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/12_2022/7pmv_13541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/12_2022/7pmv_13541_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/12_2022/7pmv_13541_trim.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.058 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 106": "OD1" <-> "OD2" Residue "A TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B ASP 860": "OD1" <-> "OD2" Residue "B TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1078": "OE1" <-> "OE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 681": "OE1" <-> "OE2" Residue "D TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 961": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1033": "OD1" <-> "OD2" Residue "D TYR 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 617": "OD1" <-> "OD2" Residue "E PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 1132": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 68016 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 16899 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1139, 16874 Classifications: {'peptide': 1139} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1078} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1139, 16874 Classifications: {'peptide': 1139} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1078} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 17042 Chain: "B" Number of atoms: 16916 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 16891 Classifications: {'peptide': 1141} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1080} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1141, 16891 Classifications: {'peptide': 1141} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1080} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 17059 Chain: "D" Number of atoms: 16917 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 16892 Classifications: {'peptide': 1141} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1080} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1141, 16892 Classifications: {'peptide': 1141} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1080} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 17060 Chain: "E" Number of atoms: 16899 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1139, 16874 Classifications: {'peptide': 1139} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1078} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1139, 16874 Classifications: {'peptide': 1139} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1078} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 17042 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 924 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 924 " occ=0.50 residue: pdb=" N AARG B 924 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 924 " occ=0.50 residue: pdb=" N AARG D 924 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG D 924 " occ=0.50 residue: pdb=" N AARG E 924 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG E 924 " occ=0.50 Time building chain proxies: 43.30, per 1000 atoms: 0.64 Number of scatterers: 68016 At special positions: 0 Unit cell: (217.617, 185.087, 237.809, 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) Ca 12 19.99 S 522 16.00 O 6927 8.00 N 6068 7.00 C 21814 6.00 H 32673 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=218, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 200 " distance=2.02 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 257 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 613 " distance=2.04 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 648 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 683 " distance=2.02 Simple disulfide: pdb=" SG CYS A 665 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 707 " distance=2.04 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 738 " distance=2.04 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 799 " distance=2.03 Simple disulfide: pdb=" SG CYS A 792 " - pdb=" SG CYS A 827 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 821 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 846 " - pdb=" SG CYS A 863 " distance=2.04 Simple disulfide: pdb=" SG CYS A 849 " - pdb=" SG CYS A 858 " distance=2.04 Simple disulfide: pdb=" SG CYS A 867 " - pdb=" SG CYS A 996 " distance=2.03 Simple disulfide: pdb=" SG CYS A 889 " - pdb=" SG CYS A1031 " distance=2.03 Simple disulfide: pdb=" SG CYS A 898 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 914 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1060 " - pdb=" SG CYS A1084 " distance=2.03 Simple disulfide: pdb=" SG CYS A1071 " - pdb=" SG CYS A1111 " distance=2.03 Simple disulfide: pdb=" SG CYS A1091 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS B1097 " distance=2.03 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A1130 " - pdb=" SG CYS A1173 " distance=2.04 Simple disulfide: pdb=" SG CYS A1142 " - pdb=" SG CYS B1142 " distance=2.04 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1169 " distance=2.04 Simple disulfide: pdb=" SG CYS A1153 " - pdb=" SG CYS A1165 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1196 " distance=2.04 Simple disulfide: pdb=" SG CYS A1177 " - pdb=" SG CYS A1190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 275 " distance=2.04 Simple disulfide: pdb=" SG CYS B 257 " - pdb=" SG CYS B 263 " distance=2.04 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 613 " distance=2.04 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 623 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 665 " - pdb=" SG CYS B 679 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 707 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 701 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 738 " distance=2.04 Simple disulfide: pdb=" SG CYS B 767 " - pdb=" SG CYS B 808 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 799 " distance=2.03 Simple disulfide: pdb=" SG CYS B 792 " - pdb=" SG CYS B 827 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 821 " distance=2.03 Simple disulfide: pdb=" SG CYS B 829 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 846 " - pdb=" SG CYS B 863 " distance=2.03 Simple disulfide: pdb=" SG CYS B 849 " - pdb=" SG CYS B 858 " distance=2.03 Simple disulfide: pdb=" SG CYS B 867 " - pdb=" SG CYS B 996 " distance=2.03 Simple disulfide: pdb=" SG CYS B 889 " - pdb=" SG CYS B1031 " distance=2.03 Simple disulfide: pdb=" SG CYS B 898 " - pdb=" SG CYS B 993 " distance=2.03 Simple disulfide: pdb=" SG CYS B 914 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B1046 " - pdb=" SG CYS B1089 " distance=2.03 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1084 " distance=2.03 Simple disulfide: pdb=" SG CYS B1071 " - pdb=" SG CYS B1111 " distance=2.03 Simple disulfide: pdb=" SG CYS B1091 " - pdb=" SG CYS B1099 " distance=2.03 Simple disulfide: pdb=" SG CYS B1101 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B1130 " - pdb=" SG CYS B1173 " distance=2.04 Simple disulfide: pdb=" SG CYS B1149 " - pdb=" SG CYS B1169 " distance=2.03 Simple disulfide: pdb=" SG CYS B1153 " - pdb=" SG CYS B1165 " distance=2.03 Simple disulfide: pdb=" SG CYS B1157 " - pdb=" SG CYS B1196 " distance=2.04 Simple disulfide: pdb=" SG CYS B1177 " - pdb=" SG CYS B1190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 225 " - pdb=" SG CYS D 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 275 " distance=2.04 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 263 " distance=2.03 Simple disulfide: pdb=" SG CYS D 265 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 325 " distance=2.03 Simple disulfide: pdb=" SG CYS D 308 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 312 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 342 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 372 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 384 " distance=2.03 Simple disulfide: pdb=" SG CYS D 370 " - pdb=" SG CYS D 379 " distance=2.03 Simple disulfide: pdb=" SG CYS D 388 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 410 " - pdb=" SG CYS D 559 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 440 " distance=2.03 Simple disulfide: pdb=" SG CYS D 570 " - pdb=" SG CYS D 613 " distance=2.03 Simple disulfide: pdb=" SG CYS D 584 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 633 " distance=2.03 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 621 " distance=2.03 Simple disulfide: pdb=" SG CYS D 623 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 687 " distance=2.03 Simple disulfide: pdb=" SG CYS D 661 " - pdb=" SG CYS D 683 " distance=2.03 Simple disulfide: pdb=" SG CYS D 665 " - pdb=" SG CYS D 679 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 707 " distance=2.03 Simple disulfide: pdb=" SG CYS D 689 " - pdb=" SG CYS D 701 " distance=2.03 Simple disulfide: pdb=" SG CYS D 709 " - pdb=" SG CYS D 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 729 " - pdb=" SG CYS D 738 " distance=2.03 Simple disulfide: pdb=" SG CYS D 767 " - pdb=" SG CYS D 808 " distance=2.03 Simple disulfide: pdb=" SG CYS D 776 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 799 " distance=2.03 Simple disulfide: pdb=" SG CYS D 792 " - pdb=" SG CYS D 827 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 821 " distance=2.03 Simple disulfide: pdb=" SG CYS D 829 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D 846 " - pdb=" SG CYS D 863 " distance=2.03 Simple disulfide: pdb=" SG CYS D 849 " - pdb=" SG CYS D 858 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 996 " distance=2.03 Simple disulfide: pdb=" SG CYS D 889 " - pdb=" SG CYS D1031 " distance=2.03 Simple disulfide: pdb=" SG CYS D 898 " - pdb=" SG CYS D 993 " distance=2.03 Simple disulfide: pdb=" SG CYS D 914 " - pdb=" SG CYS D 921 " distance=2.03 Simple disulfide: pdb=" SG CYS D1046 " - pdb=" SG CYS D1089 " distance=2.03 Simple disulfide: pdb=" SG CYS D1060 " - pdb=" SG CYS D1084 " distance=2.03 Simple disulfide: pdb=" SG CYS D1071 " - pdb=" SG CYS D1111 " distance=2.03 Simple disulfide: pdb=" SG CYS D1091 " - pdb=" SG CYS D1099 " distance=2.03 Simple disulfide: pdb=" SG CYS D1097 " - pdb=" SG CYS E1097 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D1130 " - pdb=" SG CYS D1173 " distance=2.04 Simple disulfide: pdb=" SG CYS D1142 " - pdb=" SG CYS E1142 " distance=2.03 Simple disulfide: pdb=" SG CYS D1149 " - pdb=" SG CYS D1169 " distance=2.03 Simple disulfide: pdb=" SG CYS D1153 " - pdb=" SG CYS D1165 " distance=2.03 Simple disulfide: pdb=" SG CYS D1157 " - pdb=" SG CYS D1196 " distance=2.05 Simple disulfide: pdb=" SG CYS D1177 " - pdb=" SG CYS D1190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.03 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.04 Simple disulfide: pdb=" SG CYS E 776 " - pdb=" SG CYS E 804 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 799 " distance=2.03 Simple disulfide: pdb=" SG CYS E 792 " - pdb=" SG CYS E 827 " distance=2.03 Simple disulfide: pdb=" SG CYS E 810 " - pdb=" SG CYS E 821 " distance=2.03 Simple disulfide: pdb=" SG CYS E 829 " - pdb=" SG CYS E 851 " distance=2.03 Simple disulfide: pdb=" SG CYS E 846 " - pdb=" SG CYS E 863 " distance=2.03 Simple disulfide: pdb=" SG CYS E 849 " - pdb=" SG CYS E 858 " distance=2.03 Simple disulfide: pdb=" SG CYS E 867 " - pdb=" SG CYS E 996 " distance=2.03 Simple disulfide: pdb=" SG CYS E 889 " - pdb=" SG CYS E1031 " distance=2.03 Simple disulfide: pdb=" SG CYS E 898 " - pdb=" SG CYS E 993 " distance=2.03 Simple disulfide: pdb=" SG CYS E 914 " - pdb=" SG CYS E 921 " distance=2.03 Simple disulfide: pdb=" SG CYS E1046 " - pdb=" SG CYS E1089 " distance=2.05 Simple disulfide: pdb=" SG CYS E1060 " - pdb=" SG CYS E1084 " distance=2.03 Simple disulfide: pdb=" SG CYS E1071 " - pdb=" SG CYS E1111 " distance=2.03 Simple disulfide: pdb=" SG CYS E1091 " - pdb=" SG CYS E1099 " distance=2.03 Simple disulfide: pdb=" SG CYS E1101 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E1130 " - pdb=" SG CYS E1173 " distance=2.03 Simple disulfide: pdb=" SG CYS E1149 " - pdb=" SG CYS E1169 " distance=2.05 Simple disulfide: pdb=" SG CYS E1153 " - pdb=" SG CYS E1165 " distance=2.03 Simple disulfide: pdb=" SG CYS E1157 " - pdb=" SG CYS E1196 " distance=2.03 Simple disulfide: pdb=" SG CYS E1177 " - pdb=" SG CYS E1190 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 156 " " NAG A1302 " - " ASN A1147 " " NAG A1303 " - " ASN A 857 " " NAG A1304 " - " ASN A 666 " " NAG B1301 " - " ASN B 156 " " NAG B1302 " - " ASN B1147 " " NAG B1303 " - " ASN B 857 " " NAG B1304 " - " ASN B 666 " " NAG C 1 " - " ASN A 99 " " NAG D1301 " - " ASN D 156 " " NAG D1302 " - " ASN D1147 " " NAG D1303 " - " ASN D 857 " " NAG D1304 " - " ASN D 666 " " NAG E1301 " - " ASN E 156 " " NAG E1302 " - " ASN E1147 " " NAG E1303 " - " ASN E 857 " " NAG E1304 " - " ASN E 666 " " NAG F 1 " - " ASN B 99 " " NAG G 1 " - " ASN D 99 " " NAG H 1 " - " ASN E 99 " Time building additional restraints: 40.86 Conformation dependent library (CDL) restraints added in 8.2 seconds 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8408 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 63 sheets defined 18.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 151 through 155 removed outlier: 4.004A pdb=" N TYR A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 155 " --> pdb=" O ASP A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 155' Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.506A pdb=" N LEU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 269 " --> pdb=" O CYS A 265 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.567A pdb=" N PHE A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.759A pdb=" N ALA A 571 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 589 through 598 removed outlier: 5.223A pdb=" N ALA A 594 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 597 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 removed outlier: 3.785A pdb=" N ARG A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 636 removed outlier: 4.230A pdb=" N CYS A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 627 " --> pdb=" O CYS A 623 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER A 628 " --> pdb=" O GLY A 624 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 1017 through 1024 removed outlier: 3.617A pdb=" N SER A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1060 Processing helix chain 'A' and resid 1061 through 1065 Processing helix chain 'A' and resid 1077 through 1086 removed outlier: 3.557A pdb=" N LEU A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1114 removed outlier: 3.559A pdb=" N CYS A1101 " --> pdb=" O CYS A1097 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR A1103 " --> pdb=" O CYS A1099 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A1104 " --> pdb=" O PHE A1100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1204 removed outlier: 3.765A pdb=" N ARG A1204 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.833A pdb=" N TYR B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.799A pdb=" N SER B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.601A pdb=" N THR B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.972A pdb=" N GLU B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 removed outlier: 4.077A pdb=" N GLU B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 545 through 551 removed outlier: 3.539A pdb=" N PHE B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.702A pdb=" N ALA B 571 " --> pdb=" O ASP B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 576 Processing helix chain 'B' and resid 577 through 584 Processing helix chain 'B' and resid 585 through 593 Proline residue: B 590 - end of helix Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.818A pdb=" N LEU B 605 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 636 removed outlier: 3.655A pdb=" N CYS B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 622 " --> pdb=" O GLY B 618 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 628 " --> pdb=" O GLY B 624 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 674 removed outlier: 3.644A pdb=" N LEU B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 827 removed outlier: 3.528A pdb=" N CYS B 827 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 953 removed outlier: 3.748A pdb=" N HIS B 952 " --> pdb=" O ASP B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1024 removed outlier: 3.624A pdb=" N ASN B1023 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B1024 " --> pdb=" O ASP B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1060 removed outlier: 3.539A pdb=" N ASP B1057 " --> pdb=" O GLN B1053 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1065 Processing helix chain 'B' and resid 1068 through 1075 removed outlier: 3.964A pdb=" N LYS B1073 " --> pdb=" O GLN B1069 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B1074 " --> pdb=" O ASP B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1086 removed outlier: 3.590A pdb=" N LEU B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1113 removed outlier: 3.795A pdb=" N ASP B1102 " --> pdb=" O ALA B1098 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR B1103 " --> pdb=" O CYS B1099 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE B1104 " --> pdb=" O PHE B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1204 removed outlier: 3.785A pdb=" N ARG B1204 " --> pdb=" O VAL B1201 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.881A pdb=" N TYR D 154 " --> pdb=" O SER D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.637A pdb=" N SER D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 237 removed outlier: 4.321A pdb=" N ARG D 236 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.858A pdb=" N GLU D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.743A pdb=" N GLU D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.587A pdb=" N PHE D 549 " --> pdb=" O ARG D 545 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 572 removed outlier: 3.714A pdb=" N ALA D 571 " --> pdb=" O ASP D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 584 Processing helix chain 'D' and resid 585 through 591 Proline residue: D 590 - end of helix Processing helix chain 'D' and resid 592 through 597 removed outlier: 4.220A pdb=" N ARG D 597 " --> pdb=" O GLU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 615 Processing helix chain 'D' and resid 617 through 636 removed outlier: 3.527A pdb=" N CYS D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 674 removed outlier: 3.836A pdb=" N LEU D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 827 removed outlier: 3.824A pdb=" N CYS D 827 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 953 removed outlier: 3.620A pdb=" N HIS D 952 " --> pdb=" O ASP D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1023 removed outlier: 3.807A pdb=" N ASN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1026 No H-bonds generated for 'chain 'D' and resid 1024 through 1026' Processing helix chain 'D' and resid 1052 through 1060 removed outlier: 3.540A pdb=" N ASP D1057 " --> pdb=" O GLN D1053 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER D1058 " --> pdb=" O THR D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1065 Processing helix chain 'D' and resid 1068 through 1075 removed outlier: 3.664A pdb=" N LYS D1073 " --> pdb=" O GLN D1069 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D1074 " --> pdb=" O ASP D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1086 Processing helix chain 'D' and resid 1097 through 1114 removed outlier: 3.608A pdb=" N CYS D1101 " --> pdb=" O CYS D1097 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP D1102 " --> pdb=" O ALA D1098 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N THR D1103 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D1104 " --> pdb=" O PHE D1100 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS D1114 " --> pdb=" O VAL D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1204 removed outlier: 3.837A pdb=" N ARG D1204 " --> pdb=" O VAL D1201 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 155 Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 232 through 238 removed outlier: 4.371A pdb=" N ARG E 236 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS E 238 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 255 Processing helix chain 'E' and resid 264 through 279 removed outlier: 3.958A pdb=" N GLU E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 348 No H-bonds generated for 'chain 'E' and resid 346 through 348' Processing helix chain 'E' and resid 448 through 452 removed outlier: 3.636A pdb=" N LEU E 451 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 517 removed outlier: 3.611A pdb=" N TYR E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 568 through 572 removed outlier: 3.739A pdb=" N ALA E 571 " --> pdb=" O ASP E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 584 removed outlier: 3.702A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 598 Proline residue: E 590 - end of helix removed outlier: 5.287A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 597 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 615 removed outlier: 3.688A pdb=" N ARG E 606 " --> pdb=" O LEU E 602 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS E 608 " --> pdb=" O TYR E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 636 removed outlier: 3.585A pdb=" N CYS E 621 " --> pdb=" O ASP E 617 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS E 623 " --> pdb=" O ARG E 619 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 Processing helix chain 'E' and resid 823 through 827 Processing helix chain 'E' and resid 949 through 953 Processing helix chain 'E' and resid 985 through 989 removed outlier: 3.694A pdb=" N TYR E 988 " --> pdb=" O LYS E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 1017 through 1023 Processing helix chain 'E' and resid 1024 through 1026 No H-bonds generated for 'chain 'E' and resid 1024 through 1026' Processing helix chain 'E' and resid 1054 through 1060 removed outlier: 3.526A pdb=" N CYS E1060 " --> pdb=" O VAL E1056 " (cutoff:3.500A) Processing helix chain 'E' and resid 1061 through 1065 Processing helix chain 'E' and resid 1070 through 1075 removed outlier: 3.952A pdb=" N LEU E1074 " --> pdb=" O ASP E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1086 removed outlier: 3.790A pdb=" N LEU E1081 " --> pdb=" O PRO E1077 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP E1082 " --> pdb=" O GLU E1078 " (cutoff:3.500A) Processing helix chain 'E' and resid 1097 through 1114 removed outlier: 4.111A pdb=" N CYS E1101 " --> pdb=" O CYS E1097 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR E1103 " --> pdb=" O CYS E1099 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE E1104 " --> pdb=" O PHE E1100 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS E1114 " --> pdb=" O VAL E1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1204 removed outlier: 3.708A pdb=" N ARG E1204 " --> pdb=" O VAL E1201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.645A pdb=" N ILE A 72 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER A 83 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.669A pdb=" N SER A 130 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 128 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 404 removed outlier: 5.683A pdb=" N LEU A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 494 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 412 through 416 removed outlier: 6.926A pdb=" N ILE A 425 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 443 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 430 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 441 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL A 464 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 774 Processing sheet with id=AB1, first strand: chain 'A' and resid 841 through 844 removed outlier: 3.684A pdb=" N ASN A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB3, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AB4, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.963A pdb=" N VAL A 894 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 911 through 912 removed outlier: 3.792A pdb=" N LYS A 922 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1144 through 1147 Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.826A pdb=" N LYS B 128 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 130 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.534A pdb=" N TYR B 59 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 72 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER B 83 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 77 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 302 through 305 removed outlier: 4.033A pdb=" N CYS B 304 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 326 " --> pdb=" O CYS B 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AC3, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AC4, first strand: chain 'B' and resid 363 through 364 removed outlier: 4.412A pdb=" N ILE B 371 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 378 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 386 through 387 removed outlier: 3.584A pdb=" N GLY B 386 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 499 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP B 502 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 483 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 390 through 391 removed outlier: 3.514A pdb=" N PHE B 404 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 411 through 416 removed outlier: 5.726A pdb=" N GLN B 411 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 429 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU B 413 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 427 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER B 424 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 446 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 426 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 444 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 428 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 454 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 709 through 710 Processing sheet with id=AC9, first strand: chain 'B' and resid 728 through 730 removed outlier: 3.935A pdb=" N GLN D 431 " --> pdb=" O SER B 723 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 415 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE D 427 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU D 413 " --> pdb=" O ILE D 427 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR D 429 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN D 411 " --> pdb=" O THR D 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 728 through 730 removed outlier: 3.935A pdb=" N GLN D 431 " --> pdb=" O SER B 723 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER D 424 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL D 446 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 426 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL D 444 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU D 428 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 841 through 844 Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 868 Processing sheet with id=AD4, first strand: chain 'B' and resid 874 through 876 Processing sheet with id=AD5, first strand: chain 'B' and resid 892 through 895 removed outlier: 7.071A pdb=" N ILE B 907 " --> pdb=" O LEU B 893 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 911 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1145 through 1147 removed outlier: 4.029A pdb=" N GLY B1172 " --> pdb=" O ASN B1147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.654A pdb=" N SER D 130 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AE1, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.607A pdb=" N ILE D 72 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 75 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER D 83 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN D 77 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AE3, first strand: chain 'D' and resid 350 through 352 Processing sheet with id=AE4, first strand: chain 'D' and resid 363 through 364 removed outlier: 3.620A pdb=" N LEU D 363 " --> pdb=" O CYS D 370 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS D 370 " --> pdb=" O LEU D 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 372 through 373 removed outlier: 3.630A pdb=" N GLN D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AE7, first strand: chain 'D' and resid 709 through 710 Processing sheet with id=AE8, first strand: chain 'D' and resid 841 through 844 Processing sheet with id=AE9, first strand: chain 'D' and resid 882 through 884 removed outlier: 3.856A pdb=" N LEU D 984 " --> pdb=" O ALA D 865 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 869 " --> pdb=" O ILE D 980 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE D 980 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 954 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 892 through 895 removed outlier: 7.035A pdb=" N ILE D 907 " --> pdb=" O LEU D 893 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 911 through 912 removed outlier: 3.560A pdb=" N LYS D 922 " --> pdb=" O LYS D 912 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1144 through 1147 removed outlier: 4.149A pdb=" N GLY D1172 " --> pdb=" O ASN D1147 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 51 through 52 removed outlier: 3.534A pdb=" N PHE E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.693A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 335 through 337 Processing sheet with id=AF7, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AF8, first strand: chain 'E' and resid 363 through 364 Processing sheet with id=AF9, first strand: chain 'E' and resid 403 through 404 removed outlier: 3.623A pdb=" N PHE E 404 " --> pdb=" O PHE E 396 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 391 " --> pdb=" O HIS E 395 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 389 " --> pdb=" O LYS E 397 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 386 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG E 491 " --> pdb=" O GLN E 483 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN E 483 " --> pdb=" O ARG E 491 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.789A pdb=" N VAL E 444 " --> pdb=" O LEU E 458 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU E 428 " --> pdb=" O ARG E 442 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL E 444 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 426 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL E 446 " --> pdb=" O SER E 424 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER E 424 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE E 425 " --> pdb=" O LEU E 414 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 773 through 774 removed outlier: 3.648A pdb=" N GLY E 807 " --> pdb=" O LEU E 774 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 815 through 816 removed outlier: 3.943A pdb=" N VAL E 815 " --> pdb=" O VAL E 822 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 829 through 831 removed outlier: 3.767A pdb=" N HIS E 831 " --> pdb=" O LYS E 834 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS E 834 " --> pdb=" O HIS E 831 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 841 through 844 removed outlier: 3.702A pdb=" N ASN E 847 " --> pdb=" O ILE E 844 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 865 through 868 removed outlier: 3.535A pdb=" N GLU E 954 " --> pdb=" O LEU E 965 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 874 through 876 removed outlier: 3.547A pdb=" N TYR E 875 " --> pdb=" O TYR E 883 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 883 " --> pdb=" O TYR E 875 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'E' and resid 892 through 895 removed outlier: 4.053A pdb=" N VAL E 894 " --> pdb=" O ILE E 907 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 1144 through 1146 805 hydrogen bonds defined for protein. 1894 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: 25.78 Time building geometry restraints manager: 43.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 32667 1.04 - 1.25: 4956 1.25 - 1.45: 10880 1.45 - 1.65: 19675 1.65 - 1.86: 602 Bond restraints: 68780 Sorted by residual: bond pdb=" CA CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.30e-02 5.92e+03 4.79e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.426 1.476 -0.050 3.20e-02 9.77e+02 2.47e+00 bond pdb=" CB CYS A1149 " pdb=" SG CYS A1149 " ideal model delta sigma weight residual 1.808 1.856 -0.048 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB PRO D 332 " pdb=" CG PRO D 332 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" CB CYS E1149 " pdb=" SG CYS E1149 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 68775 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 1196 106.50 - 113.39: 78810 113.39 - 120.28: 22557 120.28 - 127.16: 20748 127.16 - 134.05: 412 Bond angle restraints: 123723 Sorted by residual: angle pdb=" C ARG A 826 " pdb=" N CYS A 827 " pdb=" CA CYS A 827 " ideal model delta sigma weight residual 120.67 113.30 7.37 1.34e+00 5.57e-01 3.03e+01 angle pdb=" N ILE D 934 " pdb=" CA ILE D 934 " pdb=" C ILE D 934 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" N CYS E 418 " pdb=" CA CYS E 418 " pdb=" CB CYS E 418 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" CB MET A 320 " pdb=" CG MET A 320 " pdb=" SD MET A 320 " ideal model delta sigma weight residual 112.70 123.86 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C MET A 736 " pdb=" N HIS A 737 " pdb=" CA HIS A 737 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 ... (remaining 123718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 26605 22.88 - 45.76: 1409 45.76 - 68.64: 215 68.64 - 91.52: 71 91.52 - 114.40: 8 Dihedral angle restraints: 28308 sinusoidal: 13028 harmonic: 15280 Sorted by residual: dihedral pdb=" CB CYS E 729 " pdb=" SG CYS E 729 " pdb=" SG CYS E 738 " pdb=" CB CYS E 738 " ideal model delta sinusoidal sigma weight residual -86.00 -176.19 90.19 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 846 " pdb=" SG CYS A 846 " pdb=" SG CYS A 863 " pdb=" CB CYS A 863 " ideal model delta sinusoidal sigma weight residual -86.00 -175.54 89.54 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS D 846 " pdb=" SG CYS D 846 " pdb=" SG CYS D 863 " pdb=" CB CYS D 863 " ideal model delta sinusoidal sigma weight residual -86.00 -174.54 88.54 1 1.00e+01 1.00e-02 9.36e+01 ... (remaining 28305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5045 0.091 - 0.182: 316 0.182 - 0.272: 4 0.272 - 0.363: 1 0.363 - 0.454: 1 Chirality restraints: 5367 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 99 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA HIS A 737 " pdb=" N HIS A 737 " pdb=" C HIS A 737 " pdb=" CB HIS A 737 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 5364 not shown) Planarity restraints: 10815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1150 " 0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO D1151 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO D1151 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D1151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1150 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO B1151 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B1151 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B1151 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 906 " 0.279 9.50e-02 1.11e+02 9.32e-02 9.71e+00 pdb=" NE ARG A 906 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 906 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 906 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 906 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 906 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 906 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 906 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 906 " 0.000 2.00e-02 2.50e+03 ... (remaining 10812 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 488 1.97 - 2.63: 81523 2.63 - 3.28: 185106 3.28 - 3.94: 225764 3.94 - 4.60: 351686 Nonbonded interactions: 844567 Sorted by model distance: nonbonded pdb=" OD1 ASN B 780 " pdb="HH11 ARG B 782 " model vdw 1.311 1.850 nonbonded pdb=" O CYS E1046 " pdb=" HD1 HIS E1047 " model vdw 1.491 1.850 nonbonded pdb=" H ASP D 696 " pdb=" O ASP D 700 " model vdw 1.542 1.850 nonbonded pdb=" OE1 GLU A 677 " pdb=" H GLU A 677 " model vdw 1.551 1.850 nonbonded pdb=" OD1 ASN D 780 " pdb="HH11 ARG D 782 " model vdw 1.555 1.850 ... (remaining 844562 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' and (resid 31 through 542 or (resid 543 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 544 through 807 or \ (resid 808 and (name N or name CA or name C or name O or name CB or name SG or n \ ame H or name HA or name HB2 or name HB3)) or resid 809 through 923 or resid 926 \ through 1207 or resid 1301 through 1307)) selection = (chain 'B' and (resid 31 through 739 or (resid 768 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 769 through 923 or resid 926 through 1207 or resid 1301 through 1307)) \ selection = (chain 'D' and (resid 31 through 542 or (resid 543 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 544 through 739 or \ (resid 768 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or n \ ame HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12 or name HH21 or name HH22)) or resid 769 through 923 or resid 926 t \ hrough 1207 or resid 1301 through 1307)) selection = (chain 'E' and (resid 31 through 542 or (resid 543 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 544 through 807 or \ (resid 808 and (name N or name CA or name C or name O or name CB or name SG or n \ ame H or name HA or name HB2 or name HB3)) or resid 809 through 923 or resid 926 \ through 1207 or resid 1301 through 1307)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 S 522 5.16 5 C 21814 2.51 5 N 6068 2.21 5 O 6927 1.98 5 H 32673 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.010 Normalize map: mean=0, sd=1: 0.850 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: 0.790 Extract box with map and model: 7.880 Check model and map are aligned: 0.760 Convert atoms to be neutral: 0.440 Process input model: 190.290 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 36107 Z= 0.197 Angle : 0.663 11.161 48971 Z= 0.375 Chirality : 0.043 0.454 5367 Planarity : 0.005 0.125 6480 Dihedral : 13.833 114.403 13252 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.70 % Favored : 85.03 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % 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: -2.65 (0.12), residues: 4548 helix: -0.10 (0.23), residues: 536 sheet: -0.34 (0.22), residues: 678 loop : -2.58 (0.10), residues: 3334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 684 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 683 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 683 average time/residue: 0.8726 time to fit residues: 931.6251 Evaluate side-chains 525 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 3.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 383 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 chunk 412 optimal weight: 50.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN E 147 GLN E 596 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 36107 Z= 0.357 Angle : 0.701 7.224 48971 Z= 0.374 Chirality : 0.046 0.410 5367 Planarity : 0.006 0.088 6480 Dihedral : 7.516 114.585 5126 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.23 % Favored : 83.40 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.07 % 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: -2.87 (0.12), residues: 4548 helix: -0.50 (0.22), residues: 554 sheet: -0.48 (0.22), residues: 690 loop : -2.71 (0.10), residues: 3304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 576 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 538 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 34 residues processed: 558 average time/residue: 0.8618 time to fit residues: 762.0878 Evaluate side-chains 532 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 498 time to evaluate : 3.997 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5541 time to fit residues: 40.8421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 229 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 413 optimal weight: 10.0000 chunk 446 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 409 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 565 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN B 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 36107 Z= 0.260 Angle : 0.648 7.031 48971 Z= 0.345 Chirality : 0.044 0.404 5367 Planarity : 0.005 0.076 6480 Dihedral : 7.463 114.475 5126 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.59 % Favored : 84.08 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.85 (0.12), residues: 4548 helix: -0.59 (0.22), residues: 566 sheet: -0.39 (0.22), residues: 694 loop : -2.70 (0.10), residues: 3288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 534 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 516 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 524 average time/residue: 0.9112 time to fit residues: 755.0239 Evaluate side-chains 510 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 495 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5562 time to fit residues: 21.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 408 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 438 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 392 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 998 ASN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN E 596 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 36107 Z= 0.229 Angle : 0.629 8.242 48971 Z= 0.332 Chirality : 0.043 0.390 5367 Planarity : 0.005 0.074 6480 Dihedral : 7.396 114.247 5126 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.37 % Favored : 84.28 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.78 (0.12), residues: 4548 helix: -0.49 (0.22), residues: 558 sheet: -0.35 (0.22), residues: 694 loop : -2.65 (0.10), residues: 3296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 511 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 517 average time/residue: 0.8806 time to fit residues: 715.4059 Evaluate side-chains 500 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 493 time to evaluate : 3.905 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5441 time to fit residues: 12.5875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 365 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 326 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 374 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN B 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 36107 Z= 0.244 Angle : 0.630 7.634 48971 Z= 0.332 Chirality : 0.043 0.379 5367 Planarity : 0.005 0.071 6480 Dihedral : 7.393 114.549 5126 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.74 % Favored : 83.97 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.77 (0.12), residues: 4548 helix: -0.56 (0.22), residues: 568 sheet: -0.34 (0.21), residues: 722 loop : -2.65 (0.10), residues: 3258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 541 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 512 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 24 residues processed: 527 average time/residue: 0.8873 time to fit residues: 743.0029 Evaluate side-chains 525 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 501 time to evaluate : 3.964 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.5742 time to fit residues: 31.4223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 147 optimal weight: 3.9990 chunk 395 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 257 optimal weight: 30.0000 chunk 108 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 364 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 36107 Z= 0.267 Angle : 0.642 8.203 48971 Z= 0.339 Chirality : 0.044 0.367 5367 Planarity : 0.005 0.070 6480 Dihedral : 7.456 114.423 5126 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.78 % Favored : 83.88 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.05 % 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: -2.79 (0.12), residues: 4548 helix: -0.44 (0.22), residues: 546 sheet: -0.44 (0.21), residues: 732 loop : -2.66 (0.10), residues: 3270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 528 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 507 time to evaluate : 5.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 520 average time/residue: 0.8693 time to fit residues: 718.3646 Evaluate side-chains 510 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 495 time to evaluate : 3.927 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.5569 time to fit residues: 20.9032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 423 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 369 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 437 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN B 725 HIS B 998 ASN D 832 GLN ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 36107 Z= 0.403 Angle : 0.714 10.506 48971 Z= 0.380 Chirality : 0.046 0.344 5367 Planarity : 0.005 0.068 6480 Dihedral : 7.704 115.036 5126 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.37 % Allowed : 17.44 % Favored : 82.19 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.07 % 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: -2.99 (0.12), residues: 4548 helix: -0.76 (0.21), residues: 560 sheet: -0.48 (0.21), residues: 714 loop : -2.80 (0.10), residues: 3274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 550 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 516 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 529 average time/residue: 0.8937 time to fit residues: 748.2306 Evaluate side-chains 530 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 504 time to evaluate : 3.956 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 26 average time/residue: 0.6097 time to fit residues: 34.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 270 optimal weight: 2.9990 chunk 174 optimal weight: 0.0670 chunk 261 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 298 optimal weight: 50.0000 chunk 216 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 343 optimal weight: 6.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 36107 Z= 0.188 Angle : 0.632 7.886 48971 Z= 0.333 Chirality : 0.043 0.349 5367 Planarity : 0.005 0.066 6480 Dihedral : 7.454 113.971 5126 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.51 % Favored : 85.19 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.78 (0.12), residues: 4548 helix: -0.43 (0.22), residues: 546 sheet: -0.19 (0.22), residues: 668 loop : -2.68 (0.10), residues: 3334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 519 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 524 average time/residue: 0.8981 time to fit residues: 750.5234 Evaluate side-chains 503 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 497 time to evaluate : 3.952 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.6706 time to fit residues: 12.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 398 optimal weight: 3.9990 chunk 419 optimal weight: 8.9990 chunk 382 optimal weight: 9.9990 chunk 407 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 368 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 406 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.067 36107 Z= 0.495 Angle : 0.746 8.574 48971 Z= 0.399 Chirality : 0.048 0.338 5367 Planarity : 0.006 0.067 6480 Dihedral : 7.798 115.316 5126 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 18.45 % Favored : 81.19 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.07 % 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: -3.07 (0.12), residues: 4548 helix: -0.89 (0.21), residues: 564 sheet: -0.62 (0.21), residues: 734 loop : -2.83 (0.10), residues: 3250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 510 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 517 average time/residue: 0.8929 time to fit residues: 733.0576 Evaluate side-chains 510 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 499 time to evaluate : 3.927 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 11 average time/residue: 0.6037 time to fit residues: 17.4796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 267 optimal weight: 2.9990 chunk 431 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 452 optimal weight: 0.0570 chunk 416 optimal weight: 9.9990 chunk 360 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 36107 Z= 0.191 Angle : 0.640 12.349 48971 Z= 0.337 Chirality : 0.044 0.369 5367 Planarity : 0.005 0.068 6480 Dihedral : 7.509 114.066 5126 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.40 % Favored : 85.30 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.80 (0.12), residues: 4548 helix: -0.44 (0.22), residues: 534 sheet: -0.22 (0.22), residues: 670 loop : -2.69 (0.10), residues: 3344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 221 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 740 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 519 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 521 average time/residue: 0.9090 time to fit residues: 756.3829 Evaluate side-chains 506 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 502 time to evaluate : 3.964 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.7583 time to fit residues: 10.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 286 optimal weight: 1.9990 chunk 383 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 370 optimal weight: 20.0000 chunk 45 optimal weight: 0.0000 chunk 66 optimal weight: 9.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.215104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.178194 restraints weight = 161185.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.167532 restraints weight = 161080.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.161618 restraints weight = 103162.990| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 36107 Z= 0.204 Angle : 0.627 10.908 48971 Z= 0.330 Chirality : 0.043 0.337 5367 Planarity : 0.005 0.068 6480 Dihedral : 7.419 114.895 5126 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.70 % Favored : 84.02 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % 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: -2.73 (0.12), residues: 4548 helix: -0.39 (0.22), residues: 550 sheet: -0.22 (0.22), residues: 702 loop : -2.66 (0.10), residues: 3296 =============================================================================== Job complete usr+sys time: 12506.18 seconds wall clock time: 216 minutes 58.82 seconds (13018.82 seconds total)