Starting phenix.real_space_refine on Fri Feb 16 21:17:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/02_2024/7pmv_13541_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/02_2024/7pmv_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_13541/02_2024/7pmv_13541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/02_2024/7pmv_13541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/02_2024/7pmv_13541_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmv_13541/02_2024/7pmv_13541_trim.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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-5238/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: 9 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: 9 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: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 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: 41.41, per 1000 atoms: 0.61 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: 44.87 Conformation dependent library (CDL) restraints added in 10.6 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: 4.60 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: 26.78 Time building geometry restraints manager: 47.50 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=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.19e+00 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 E1304 " pdb=" O5 NAG E1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+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 - 25.47: 31682 25.47 - 50.95: 1777 50.95 - 76.42: 311 76.42 - 101.89: 60 101.89 - 127.36: 30 Dihedral angle restraints: 33860 sinusoidal: 18580 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 33857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5025 0.091 - 0.182: 333 0.182 - 0.272: 6 0.272 - 0.363: 2 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=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (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 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: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.000 Extract box with map and model: 6.140 Check model and map are aligned: 0.740 Set scattering table: 0.500 Process input model: 198.340 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 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 0.070 36107 Z= 0.216 Angle : 0.683 11.161 48971 Z= 0.378 Chirality : 0.044 0.454 5367 Planarity : 0.005 0.125 6480 Dihedral : 15.113 127.363 13639 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.70 % Favored : 85.03 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 642 HIS 0.009 0.001 HIS E 737 PHE 0.012 0.001 PHE A 716 TYR 0.018 0.001 TYR A 59 ARG 0.007 0.000 ARG B1035 *********************** 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 : 3.964 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 REVERT: A 80 LYS cc_start: 0.6588 (mmmm) cc_final: 0.6339 (mmmm) REVERT: A 108 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7539 (ttm110) REVERT: A 280 MET cc_start: 0.6801 (tmm) cc_final: 0.6513 (ppp) REVERT: A 420 ASP cc_start: 0.5778 (t0) cc_final: 0.5086 (t0) REVERT: A 447 ARG cc_start: 0.7189 (ttt-90) cc_final: 0.6412 (ttm-80) REVERT: A 466 MET cc_start: 0.7210 (tpt) cc_final: 0.6789 (tpt) REVERT: A 503 ASP cc_start: 0.7162 (p0) cc_final: 0.6916 (p0) REVERT: A 523 LEU cc_start: 0.7826 (tp) cc_final: 0.7606 (tp) REVERT: A 600 SER cc_start: 0.8463 (t) cc_final: 0.8223 (p) REVERT: A 687 CYS cc_start: 0.4869 (m) cc_final: 0.4534 (m) REVERT: A 814 MET cc_start: 0.7105 (tpp) cc_final: 0.6820 (tpp) REVERT: A 861 HIS cc_start: 0.7732 (m90) cc_final: 0.7421 (m90) REVERT: A 872 MET cc_start: 0.7557 (ppp) cc_final: 0.7260 (ptp) REVERT: A 938 ASP cc_start: 0.7264 (m-30) cc_final: 0.7017 (m-30) REVERT: A 945 ARG cc_start: 0.6199 (mtt180) cc_final: 0.5925 (mtm180) REVERT: A 947 MET cc_start: 0.6118 (tpp) cc_final: 0.5558 (ttm) REVERT: A 968 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7112 (mmmm) REVERT: A 1145 ARG cc_start: 0.6785 (mtt90) cc_final: 0.6527 (mtt-85) REVERT: A 1146 TYR cc_start: 0.7331 (t80) cc_final: 0.7060 (t80) REVERT: B 280 MET cc_start: 0.5199 (ppp) cc_final: 0.4896 (ppp) REVERT: B 338 ASP cc_start: 0.7167 (t0) cc_final: 0.6792 (t70) REVERT: B 564 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7192 (tptt) REVERT: B 609 ARG cc_start: 0.6371 (ttm-80) cc_final: 0.5905 (mtp-110) REVERT: B 684 LEU cc_start: 0.7454 (mt) cc_final: 0.7209 (mt) REVERT: B 728 MET cc_start: 0.6937 (ttp) cc_final: 0.6628 (ttm) REVERT: B 816 ARG cc_start: 0.6447 (ttt180) cc_final: 0.5853 (ttt180) REVERT: B 990 GLU cc_start: 0.7417 (tp30) cc_final: 0.7173 (mt-10) REVERT: B 1055 MET cc_start: 0.7042 (mtt) cc_final: 0.6677 (mtp) REVERT: B 1076 ASP cc_start: 0.8022 (p0) cc_final: 0.7642 (p0) REVERT: B 1092 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7474 (mm-30) REVERT: D 66 GLN cc_start: 0.8010 (mm110) cc_final: 0.7770 (mm110) REVERT: D 113 TYR cc_start: 0.7102 (t80) cc_final: 0.6769 (t80) REVERT: D 139 ARG cc_start: 0.4845 (mtp85) cc_final: 0.4039 (mtm-85) REVERT: D 153 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.7364 (ptt90) REVERT: D 174 MET cc_start: 0.5063 (ttp) cc_final: 0.4688 (ptm) REVERT: D 491 ARG cc_start: 0.6641 (ttp-170) cc_final: 0.6414 (ttp-170) REVERT: D 564 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7590 (tmtt) REVERT: D 597 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6913 (ppt170) REVERT: D 605 LEU cc_start: 0.7604 (tp) cc_final: 0.7387 (mt) REVERT: D 814 MET cc_start: 0.4408 (tpt) cc_final: 0.4197 (tpt) REVERT: D 830 PHE cc_start: 0.7532 (m-80) cc_final: 0.6964 (m-80) REVERT: D 947 MET cc_start: 0.4729 (tpp) cc_final: 0.1894 (ttm) REVERT: D 1071 CYS cc_start: 0.5369 (m) cc_final: 0.5119 (m) REVERT: D 1174 HIS cc_start: 0.7216 (t-90) cc_final: 0.6628 (t-90) REVERT: E 147 GLN cc_start: 0.6470 (pt0) cc_final: 0.6122 (pt0) REVERT: E 198 GLN cc_start: 0.5623 (tp40) cc_final: 0.4643 (tt0) REVERT: E 201 GLU cc_start: 0.7472 (pm20) cc_final: 0.6948 (mt-10) REVERT: E 280 MET cc_start: 0.3729 (tmm) cc_final: 0.3017 (tmm) REVERT: E 302 ARG cc_start: 0.6364 (ptt90) cc_final: 0.6107 (ptt-90) REVERT: E 436 ARG cc_start: 0.6379 (tpt90) cc_final: 0.6087 (ttm-80) REVERT: E 505 ARG cc_start: 0.4221 (mmm160) cc_final: 0.3913 (tpt170) REVERT: E 554 LYS cc_start: 0.5346 (mtmt) cc_final: 0.5112 (mttp) REVERT: E 800 MET cc_start: 0.4336 (tmm) cc_final: 0.4086 (tmm) REVERT: E 864 ASP cc_start: 0.5786 (p0) cc_final: 0.5443 (p0) REVERT: E 872 MET cc_start: 0.7410 (ppp) cc_final: 0.7185 (tmm) REVERT: E 964 LEU cc_start: 0.6176 (tt) cc_final: 0.5856 (tt) REVERT: E 977 HIS cc_start: 0.7840 (t-90) cc_final: 0.7553 (t-90) outliers start: 1 outliers final: 0 residues processed: 683 average time/residue: 0.9377 time to fit residues: 996.3243 Evaluate side-chains 537 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 4.006 ------------------------------------------------------------------------------- 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: 4.9990 chunk 344 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 355 optimal weight: 4.9990 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: 4.1588 ------------------------------------------------------------------------------- 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 794 ASN ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.1547 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= 0.447 Angle : 0.751 8.801 48971 Z= 0.399 Chirality : 0.048 0.254 5367 Planarity : 0.006 0.090 6480 Dihedral : 10.154 117.643 5513 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.95 % Favored : 82.67 % Rotamer: Outliers : 1.17 % Allowed : 6.06 % Favored : 92.77 % 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: -0.68 (0.21), residues: 556 sheet: -0.60 (0.21), residues: 714 loop : -2.78 (0.10), residues: 3278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 502 HIS 0.008 0.002 HIS D 831 PHE 0.025 0.002 PHE A 404 TYR 0.032 0.002 TYR A 185 ARG 0.009 0.001 ARG D 578 *********************** 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 586 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 540 time to evaluate : 3.985 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: A 80 LYS cc_start: 0.6859 (mmmm) cc_final: 0.6619 (mmmm) REVERT: A 280 MET cc_start: 0.7227 (tmm) cc_final: 0.6921 (ppp) REVERT: A 333 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7486 (tm-30) REVERT: A 420 ASP cc_start: 0.6095 (t0) cc_final: 0.5780 (t0) REVERT: A 428 GLU cc_start: 0.6219 (tt0) cc_final: 0.5109 (mt-10) REVERT: A 447 ARG cc_start: 0.7166 (ttt-90) cc_final: 0.6401 (ttm-80) REVERT: A 466 MET cc_start: 0.6640 (tpt) cc_final: 0.6274 (tpt) REVERT: A 687 CYS cc_start: 0.5059 (m) cc_final: 0.4620 (m) REVERT: A 814 MET cc_start: 0.7226 (tpp) cc_final: 0.6853 (tpp) REVERT: A 861 HIS cc_start: 0.7693 (m90) cc_final: 0.7384 (m90) REVERT: A 893 LEU cc_start: 0.7907 (tp) cc_final: 0.7581 (tp) REVERT: A 920 LYS cc_start: 0.4202 (mtmm) cc_final: 0.3849 (mmmm) REVERT: A 945 ARG cc_start: 0.6310 (mtt180) cc_final: 0.6085 (mtt180) REVERT: A 947 MET cc_start: 0.6102 (tpp) cc_final: 0.5605 (ttm) REVERT: A 968 LYS cc_start: 0.7553 (mmmt) cc_final: 0.7232 (mmmm) REVERT: A 1145 ARG cc_start: 0.6811 (mtt90) cc_final: 0.6523 (mtt-85) REVERT: A 1146 TYR cc_start: 0.7254 (t80) cc_final: 0.7051 (t80) REVERT: B 226 GLN cc_start: 0.7132 (mp10) cc_final: 0.6522 (mp10) REVERT: B 280 MET cc_start: 0.5153 (ppp) cc_final: 0.4668 (ppp) REVERT: B 338 ASP cc_start: 0.7360 (t0) cc_final: 0.7002 (t70) REVERT: B 425 ILE cc_start: 0.7212 (mt) cc_final: 0.6915 (mm) REVERT: B 564 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7482 (tptp) REVERT: B 609 ARG cc_start: 0.6594 (ttm-80) cc_final: 0.5879 (mtp-110) REVERT: B 706 GLN cc_start: 0.7574 (pt0) cc_final: 0.7284 (pt0) REVERT: B 728 MET cc_start: 0.7054 (ttp) cc_final: 0.6676 (ttm) REVERT: B 771 MET cc_start: 0.6720 (pmm) cc_final: 0.4706 (pmm) REVERT: B 816 ARG cc_start: 0.6469 (ttt180) cc_final: 0.5936 (ttt180) REVERT: B 872 MET cc_start: 0.8316 (ppp) cc_final: 0.8082 (ptt) REVERT: B 990 GLU cc_start: 0.7570 (tp30) cc_final: 0.7287 (tt0) REVERT: B 1055 MET cc_start: 0.6848 (mtt) cc_final: 0.6477 (mtp) REVERT: B 1092 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7313 (mm-30) REVERT: B 1131 GLU cc_start: 0.8124 (pp20) cc_final: 0.7372 (pp20) REVERT: D 113 TYR cc_start: 0.7238 (t80) cc_final: 0.6636 (t80) REVERT: D 139 ARG cc_start: 0.5002 (mtp85) cc_final: 0.4124 (mtm-85) REVERT: D 174 MET cc_start: 0.5064 (ttp) cc_final: 0.4689 (ptm) REVERT: D 271 TYR cc_start: 0.6473 (t80) cc_final: 0.6074 (t80) REVERT: D 419 GLN cc_start: 0.6509 (tm-30) cc_final: 0.5748 (tm-30) REVERT: D 578 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6629 (mmm160) REVERT: D 830 PHE cc_start: 0.7631 (m-80) cc_final: 0.7033 (m-80) REVERT: D 945 ARG cc_start: 0.5902 (mtm-85) cc_final: 0.5398 (mtm-85) REVERT: D 947 MET cc_start: 0.4866 (tpp) cc_final: 0.1871 (ttm) REVERT: D 1174 HIS cc_start: 0.7323 (t-90) cc_final: 0.6674 (t-90) REVERT: E 139 ARG cc_start: 0.5265 (mtm180) cc_final: 0.4916 (mtp180) REVERT: E 198 GLN cc_start: 0.5766 (tp40) cc_final: 0.4756 (tt0) REVERT: E 201 GLU cc_start: 0.7430 (pm20) cc_final: 0.6843 (mt-10) REVERT: E 436 ARG cc_start: 0.6353 (tpt90) cc_final: 0.6084 (ttm-80) REVERT: E 498 LEU cc_start: 0.7870 (tp) cc_final: 0.7622 (mp) REVERT: E 505 ARG cc_start: 0.4378 (mmm160) cc_final: 0.4030 (tpt170) REVERT: E 573 ASN cc_start: 0.6737 (t0) cc_final: 0.6501 (t0) REVERT: E 977 HIS cc_start: 0.7770 (t-90) cc_final: 0.7387 (t-90) REVERT: E 988 TYR cc_start: 0.6251 (m-80) cc_final: 0.5903 (m-80) outliers start: 46 outliers final: 40 residues processed: 566 average time/residue: 0.9276 time to fit residues: 820.3704 Evaluate side-chains 552 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 512 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 841 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1110 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 596 HIS Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 1124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 229 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 413 optimal weight: 20.0000 chunk 446 optimal weight: 2.9990 chunk 367 optimal weight: 0.9990 chunk 409 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36107 Z= 0.260 Angle : 0.659 8.438 48971 Z= 0.347 Chirality : 0.044 0.278 5367 Planarity : 0.005 0.073 6480 Dihedral : 9.038 116.465 5513 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.08 % Favored : 84.57 % Rotamer: Outliers : 0.99 % Allowed : 8.02 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.95 (0.12), residues: 4548 helix: -0.71 (0.21), residues: 570 sheet: -0.46 (0.22), residues: 688 loop : -2.76 (0.10), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 502 HIS 0.009 0.001 HIS E 596 PHE 0.017 0.001 PHE D 165 TYR 0.022 0.001 TYR A 59 ARG 0.005 0.000 ARG D 906 *********************** 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 565 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 526 time to evaluate : 4.543 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: A 80 LYS cc_start: 0.6654 (mmmm) cc_final: 0.6416 (mmmm) REVERT: A 280 MET cc_start: 0.7184 (tmm) cc_final: 0.6868 (ppp) REVERT: A 420 ASP cc_start: 0.5915 (t0) cc_final: 0.5511 (t0) REVERT: A 428 GLU cc_start: 0.6197 (tt0) cc_final: 0.4963 (mt-10) REVERT: A 447 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6288 (ttm-80) REVERT: A 466 MET cc_start: 0.6616 (tpt) cc_final: 0.6268 (tpt) REVERT: A 687 CYS cc_start: 0.5192 (m) cc_final: 0.4737 (m) REVERT: A 814 MET cc_start: 0.7265 (tpp) cc_final: 0.6898 (tpp) REVERT: A 861 HIS cc_start: 0.7767 (m90) cc_final: 0.7430 (m90) REVERT: A 893 LEU cc_start: 0.7757 (tp) cc_final: 0.7424 (tp) REVERT: A 920 LYS cc_start: 0.3995 (mtmm) cc_final: 0.3674 (mmmm) REVERT: A 938 ASP cc_start: 0.7687 (m-30) cc_final: 0.7392 (m-30) REVERT: A 945 ARG cc_start: 0.6184 (mtt180) cc_final: 0.5982 (mtt180) REVERT: A 947 MET cc_start: 0.6098 (tpp) cc_final: 0.5555 (ttm) REVERT: A 968 LYS cc_start: 0.7532 (mmmt) cc_final: 0.7209 (mmmm) REVERT: A 1145 ARG cc_start: 0.6742 (mtt90) cc_final: 0.6447 (mtt-85) REVERT: A 1146 TYR cc_start: 0.7236 (t80) cc_final: 0.7021 (t80) REVERT: B 226 GLN cc_start: 0.7139 (mp10) cc_final: 0.6512 (mp10) REVERT: B 280 MET cc_start: 0.5097 (ppp) cc_final: 0.4521 (ppp) REVERT: B 338 ASP cc_start: 0.7527 (t0) cc_final: 0.7076 (t70) REVERT: B 425 ILE cc_start: 0.7178 (mt) cc_final: 0.6932 (mm) REVERT: B 564 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7512 (tptt) REVERT: B 609 ARG cc_start: 0.6629 (ttm-80) cc_final: 0.6004 (mtp-110) REVERT: B 728 MET cc_start: 0.7212 (ttp) cc_final: 0.7000 (tmm) REVERT: B 816 ARG cc_start: 0.6521 (ttt180) cc_final: 0.5997 (ttt180) REVERT: B 872 MET cc_start: 0.8299 (ppp) cc_final: 0.8043 (ptt) REVERT: B 990 GLU cc_start: 0.7511 (tp30) cc_final: 0.7131 (tt0) REVERT: B 1055 MET cc_start: 0.6840 (mtt) cc_final: 0.6351 (mtp) REVERT: B 1131 GLU cc_start: 0.8156 (pp20) cc_final: 0.7445 (pp20) REVERT: D 113 TYR cc_start: 0.7235 (t80) cc_final: 0.6541 (t80) REVERT: D 139 ARG cc_start: 0.5037 (mtp85) cc_final: 0.4167 (mtm-85) REVERT: D 174 MET cc_start: 0.5023 (ttp) cc_final: 0.4657 (ptm) REVERT: D 419 GLN cc_start: 0.6519 (tm-30) cc_final: 0.5953 (tm-30) REVERT: D 500 MET cc_start: 0.8299 (mtp) cc_final: 0.8034 (mtp) REVERT: D 578 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6606 (mmm160) REVERT: D 830 PHE cc_start: 0.7618 (m-80) cc_final: 0.6997 (m-80) REVERT: D 945 ARG cc_start: 0.5884 (mtm-85) cc_final: 0.5399 (mtm-85) REVERT: D 947 MET cc_start: 0.4884 (tpp) cc_final: 0.1857 (ttm) REVERT: D 1174 HIS cc_start: 0.7322 (t-90) cc_final: 0.6676 (t-90) REVERT: E 66 GLN cc_start: 0.6207 (mp10) cc_final: 0.5940 (mp10) REVERT: E 111 MET cc_start: 0.4756 (tmm) cc_final: 0.4148 (tmm) REVERT: E 139 ARG cc_start: 0.5142 (mtm180) cc_final: 0.4492 (ttm110) REVERT: E 198 GLN cc_start: 0.5773 (tp40) cc_final: 0.4761 (tt0) REVERT: E 436 ARG cc_start: 0.6339 (tpt90) cc_final: 0.6079 (ttm-80) REVERT: E 498 LEU cc_start: 0.7865 (tp) cc_final: 0.7617 (mp) REVERT: E 505 ARG cc_start: 0.4455 (mmm160) cc_final: 0.3981 (tpt170) REVERT: E 573 ASN cc_start: 0.6595 (t0) cc_final: 0.6384 (t0) REVERT: E 800 MET cc_start: 0.3903 (tmm) cc_final: 0.3629 (tpp) outliers start: 39 outliers final: 36 residues processed: 546 average time/residue: 0.9504 time to fit residues: 811.5032 Evaluate side-chains 542 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 506 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 596 HIS Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1124 THR 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: 4.9990 chunk 214 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 438 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 977 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36107 Z= 0.281 Angle : 0.656 8.636 48971 Z= 0.346 Chirality : 0.044 0.282 5367 Planarity : 0.005 0.066 6480 Dihedral : 8.576 115.037 5513 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.18 % Favored : 83.47 % Rotamer: Outliers : 1.32 % Allowed : 8.73 % Favored : 89.95 % 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: -2.93 (0.12), residues: 4548 helix: -0.62 (0.22), residues: 558 sheet: -0.50 (0.21), residues: 718 loop : -2.76 (0.10), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 642 HIS 0.019 0.001 HIS E 596 PHE 0.019 0.001 PHE D 165 TYR 0.025 0.001 TYR D 527 ARG 0.009 0.000 ARG A 108 *********************** 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 571 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 519 time to evaluate : 3.941 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: A 80 LYS cc_start: 0.6804 (mmmm) cc_final: 0.6560 (mmmm) REVERT: A 280 MET cc_start: 0.7315 (tmm) cc_final: 0.6984 (ppp) REVERT: A 333 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 420 ASP cc_start: 0.5952 (t0) cc_final: 0.5559 (t0) REVERT: A 428 GLU cc_start: 0.6155 (tt0) cc_final: 0.4905 (mt-10) REVERT: A 447 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6290 (ttm-80) REVERT: A 466 MET cc_start: 0.6608 (tpt) cc_final: 0.6253 (tpt) REVERT: A 687 CYS cc_start: 0.5150 (m) cc_final: 0.4717 (m) REVERT: A 814 MET cc_start: 0.7294 (tpp) cc_final: 0.6900 (tpp) REVERT: A 861 HIS cc_start: 0.7723 (m90) cc_final: 0.7415 (m90) REVERT: A 893 LEU cc_start: 0.7832 (tp) cc_final: 0.7494 (tp) REVERT: A 920 LYS cc_start: 0.4091 (mtmm) cc_final: 0.3768 (mmmm) REVERT: A 947 MET cc_start: 0.6293 (tpp) cc_final: 0.5695 (ttm) REVERT: A 968 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7229 (mmmm) REVERT: A 1145 ARG cc_start: 0.6762 (mtt90) cc_final: 0.6475 (mtt-85) REVERT: A 1146 TYR cc_start: 0.7261 (t80) cc_final: 0.7047 (t80) REVERT: B 226 GLN cc_start: 0.7175 (mp10) cc_final: 0.6574 (mp10) REVERT: B 280 MET cc_start: 0.5113 (ppp) cc_final: 0.4535 (ppp) REVERT: B 338 ASP cc_start: 0.7534 (t0) cc_final: 0.7057 (t70) REVERT: B 425 ILE cc_start: 0.7174 (mt) cc_final: 0.6934 (mm) REVERT: B 564 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7561 (tptt) REVERT: B 609 ARG cc_start: 0.6642 (ttm-80) cc_final: 0.6019 (mtp-110) REVERT: B 728 MET cc_start: 0.7139 (ttp) cc_final: 0.6906 (tmm) REVERT: B 816 ARG cc_start: 0.6540 (ttt180) cc_final: 0.6201 (ttt180) REVERT: B 990 GLU cc_start: 0.7495 (tp30) cc_final: 0.7149 (tt0) REVERT: B 1131 GLU cc_start: 0.8162 (pp20) cc_final: 0.7480 (pp20) REVERT: D 113 TYR cc_start: 0.7259 (t80) cc_final: 0.6579 (t80) REVERT: D 139 ARG cc_start: 0.5124 (mtp85) cc_final: 0.4191 (mtm-85) REVERT: D 174 MET cc_start: 0.5024 (ttp) cc_final: 0.4646 (ptm) REVERT: D 419 GLN cc_start: 0.6601 (tm-30) cc_final: 0.6000 (tm-30) REVERT: D 830 PHE cc_start: 0.7633 (m-80) cc_final: 0.7022 (m-80) REVERT: D 945 ARG cc_start: 0.5883 (mtm-85) cc_final: 0.5415 (mtm-85) REVERT: D 947 MET cc_start: 0.4842 (tpp) cc_final: 0.1416 (ttp) REVERT: D 1174 HIS cc_start: 0.7293 (t-90) cc_final: 0.6666 (t-90) REVERT: E 66 GLN cc_start: 0.6219 (mp10) cc_final: 0.5971 (mp10) REVERT: E 111 MET cc_start: 0.4574 (tmm) cc_final: 0.4044 (tmm) REVERT: E 139 ARG cc_start: 0.5176 (mtm180) cc_final: 0.4533 (ttm110) REVERT: E 198 GLN cc_start: 0.5738 (tp40) cc_final: 0.4808 (tt0) REVERT: E 436 ARG cc_start: 0.6349 (tpt90) cc_final: 0.6081 (ttm-80) REVERT: E 505 ARG cc_start: 0.4295 (mmm160) cc_final: 0.3908 (tpt170) REVERT: E 573 ASN cc_start: 0.6582 (t0) cc_final: 0.6316 (t0) REVERT: E 793 GLN cc_start: 0.7080 (pm20) cc_final: 0.6777 (pm20) REVERT: E 800 MET cc_start: 0.3929 (tmm) cc_final: 0.3647 (tpp) outliers start: 52 outliers final: 48 residues processed: 546 average time/residue: 0.9664 time to fit residues: 828.2379 Evaluate side-chains 556 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 508 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 981 SER Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain D residue 732 GLU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 841 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1122 THR Chi-restraints excluded: chain E residue 1124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 365 optimal weight: 20.0000 chunk 249 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 326 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 374 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36107 Z= 0.327 Angle : 0.672 8.738 48971 Z= 0.355 Chirality : 0.045 0.290 5367 Planarity : 0.005 0.072 6480 Dihedral : 8.376 115.505 5513 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.67 % Favored : 83.05 % Rotamer: Outliers : 1.76 % Allowed : 9.36 % Favored : 88.88 % 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: -2.98 (0.12), residues: 4548 helix: -0.75 (0.21), residues: 558 sheet: -0.57 (0.21), residues: 718 loop : -2.77 (0.10), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 502 HIS 0.006 0.001 HIS B 725 PHE 0.023 0.002 PHE D 165 TYR 0.028 0.002 TYR A 59 ARG 0.008 0.000 ARG D 578 *********************** 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 592 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 523 time to evaluate : 4.059 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: A 80 LYS cc_start: 0.6841 (mmmm) cc_final: 0.6594 (mmmm) REVERT: A 154 TYR cc_start: 0.8093 (m-80) cc_final: 0.7828 (m-80) REVERT: A 174 MET cc_start: 0.7528 (mtm) cc_final: 0.7228 (mtp) REVERT: A 280 MET cc_start: 0.7315 (tmm) cc_final: 0.6968 (ppp) REVERT: A 333 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 420 ASP cc_start: 0.5990 (t0) cc_final: 0.5565 (t0) REVERT: A 428 GLU cc_start: 0.6146 (tt0) cc_final: 0.4894 (mt-10) REVERT: A 447 ARG cc_start: 0.7116 (ttt-90) cc_final: 0.6281 (ttm-80) REVERT: A 466 MET cc_start: 0.6554 (tpt) cc_final: 0.6197 (tpt) REVERT: A 814 MET cc_start: 0.7199 (tpp) cc_final: 0.6753 (tpp) REVERT: A 861 HIS cc_start: 0.7765 (m90) cc_final: 0.7457 (m90) REVERT: A 893 LEU cc_start: 0.7862 (tp) cc_final: 0.7547 (tp) REVERT: A 920 LYS cc_start: 0.4270 (mtmm) cc_final: 0.3914 (mmmm) REVERT: A 947 MET cc_start: 0.6012 (tpp) cc_final: 0.5350 (ttm) REVERT: A 968 LYS cc_start: 0.7575 (mmmt) cc_final: 0.7242 (mmmm) REVERT: A 1145 ARG cc_start: 0.6795 (mtt90) cc_final: 0.6507 (mtt-85) REVERT: B 226 GLN cc_start: 0.7126 (mp10) cc_final: 0.6508 (mp10) REVERT: B 280 MET cc_start: 0.5120 (ppp) cc_final: 0.4454 (ppp) REVERT: B 338 ASP cc_start: 0.7432 (t0) cc_final: 0.7044 (t70) REVERT: B 425 ILE cc_start: 0.7158 (mt) cc_final: 0.6922 (mm) REVERT: B 564 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7546 (tptt) REVERT: B 609 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.6035 (mtp-110) REVERT: B 728 MET cc_start: 0.7236 (ttp) cc_final: 0.7020 (tmm) REVERT: B 816 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6233 (ttt180) REVERT: B 990 GLU cc_start: 0.7588 (tp30) cc_final: 0.7138 (tt0) REVERT: B 1051 MET cc_start: 0.6530 (tmm) cc_final: 0.6135 (tmm) REVERT: D 108 ARG cc_start: 0.7067 (mmm160) cc_final: 0.6681 (mmm160) REVERT: D 113 TYR cc_start: 0.7284 (t80) cc_final: 0.6530 (t80) REVERT: D 139 ARG cc_start: 0.5057 (mtp85) cc_final: 0.4189 (mtm-85) REVERT: D 174 MET cc_start: 0.4911 (ttp) cc_final: 0.4468 (ptm) REVERT: D 271 TYR cc_start: 0.6480 (t80) cc_final: 0.6173 (t80) REVERT: D 419 GLN cc_start: 0.6614 (tm-30) cc_final: 0.6022 (tm-30) REVERT: D 578 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6559 (mmm160) REVERT: D 830 PHE cc_start: 0.7665 (m-80) cc_final: 0.7058 (m-80) REVERT: D 1174 HIS cc_start: 0.7300 (t-90) cc_final: 0.6677 (t-90) REVERT: E 66 GLN cc_start: 0.6373 (mp10) cc_final: 0.6144 (mp10) REVERT: E 111 MET cc_start: 0.4605 (tmm) cc_final: 0.4152 (tmm) REVERT: E 139 ARG cc_start: 0.5210 (mtm180) cc_final: 0.4576 (ttm110) REVERT: E 198 GLN cc_start: 0.5666 (tp40) cc_final: 0.4684 (tt0) REVERT: E 436 ARG cc_start: 0.6319 (tpt90) cc_final: 0.6037 (ttm-80) REVERT: E 505 ARG cc_start: 0.4312 (mmm160) cc_final: 0.3908 (tpt170) REVERT: E 573 ASN cc_start: 0.6746 (t0) cc_final: 0.6502 (t0) REVERT: E 793 GLN cc_start: 0.7057 (pm20) cc_final: 0.6743 (pm20) REVERT: E 800 MET cc_start: 0.3939 (tmm) cc_final: 0.3668 (tpp) REVERT: E 964 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5702 (tt) outliers start: 69 outliers final: 61 residues processed: 558 average time/residue: 0.9362 time to fit residues: 817.7442 Evaluate side-chains 570 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 508 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 981 SER Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain D residue 732 GLU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 841 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 896 ASP Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1122 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1149 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 147 optimal weight: 0.8980 chunk 395 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 257 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 chunk 439 optimal weight: 0.0570 chunk 364 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36107 Z= 0.223 Angle : 0.641 10.273 48971 Z= 0.336 Chirality : 0.043 0.290 5367 Planarity : 0.005 0.067 6480 Dihedral : 8.119 113.987 5513 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.61 % Favored : 84.08 % Rotamer: Outliers : 1.70 % Allowed : 10.08 % Favored : 88.22 % 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: -2.86 (0.12), residues: 4548 helix: -0.53 (0.22), residues: 544 sheet: -0.44 (0.21), residues: 708 loop : -2.71 (0.10), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 285 HIS 0.005 0.001 HIS D 831 PHE 0.020 0.001 PHE D 165 TYR 0.023 0.001 TYR D 527 ARG 0.009 0.000 ARG A 108 *********************** 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 589 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 522 time to evaluate : 4.036 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: A 80 LYS cc_start: 0.6793 (mmmm) cc_final: 0.6548 (mmmm) REVERT: A 174 MET cc_start: 0.7525 (mtm) cc_final: 0.7226 (mtp) REVERT: A 280 MET cc_start: 0.7286 (tmm) cc_final: 0.6941 (ppp) REVERT: A 333 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 420 ASP cc_start: 0.5868 (t0) cc_final: 0.5461 (t0) REVERT: A 447 ARG cc_start: 0.7098 (ttt-90) cc_final: 0.6266 (ttm-80) REVERT: A 466 MET cc_start: 0.6513 (tpt) cc_final: 0.6169 (tpt) REVERT: A 560 GLN cc_start: 0.8471 (pm20) cc_final: 0.8123 (mt0) REVERT: A 687 CYS cc_start: 0.5219 (m) cc_final: 0.4784 (m) REVERT: A 814 MET cc_start: 0.7212 (tpp) cc_final: 0.6769 (tpp) REVERT: A 855 LYS cc_start: 0.5014 (mtpp) cc_final: 0.4804 (mttp) REVERT: A 861 HIS cc_start: 0.7773 (m90) cc_final: 0.7452 (m90) REVERT: A 920 LYS cc_start: 0.4261 (mtmm) cc_final: 0.3897 (mmmm) REVERT: A 947 MET cc_start: 0.6063 (tpp) cc_final: 0.5329 (ttm) REVERT: A 1145 ARG cc_start: 0.6792 (mtt90) cc_final: 0.6469 (mtt-85) REVERT: B 109 VAL cc_start: 0.8888 (m) cc_final: 0.8653 (p) REVERT: B 226 GLN cc_start: 0.7126 (mp10) cc_final: 0.6504 (mp10) REVERT: B 338 ASP cc_start: 0.7533 (t0) cc_final: 0.7040 (t70) REVERT: B 425 ILE cc_start: 0.7128 (mt) cc_final: 0.6890 (mm) REVERT: B 564 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7553 (tptt) REVERT: B 609 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6020 (mtp-110) REVERT: B 728 MET cc_start: 0.7234 (ttp) cc_final: 0.6984 (tmm) REVERT: B 816 ARG cc_start: 0.6570 (ttt180) cc_final: 0.6025 (ttt180) REVERT: B 990 GLU cc_start: 0.7567 (tp30) cc_final: 0.7148 (tt0) REVERT: B 1051 MET cc_start: 0.6561 (tmm) cc_final: 0.6154 (tmm) REVERT: D 113 TYR cc_start: 0.7267 (t80) cc_final: 0.6514 (t80) REVERT: D 139 ARG cc_start: 0.5004 (mtp85) cc_final: 0.4049 (mtm-85) REVERT: D 174 MET cc_start: 0.4911 (ttp) cc_final: 0.4462 (ptm) REVERT: D 419 GLN cc_start: 0.6613 (tm-30) cc_final: 0.6010 (tm-30) REVERT: D 578 ARG cc_start: 0.6907 (mtm110) cc_final: 0.6540 (mmm160) REVERT: D 639 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7751 (mmm-85) REVERT: D 830 PHE cc_start: 0.7638 (m-80) cc_final: 0.7030 (m-80) REVERT: D 849 CYS cc_start: 0.7275 (m) cc_final: 0.7021 (t) REVERT: D 945 ARG cc_start: 0.5862 (mtp180) cc_final: 0.5307 (mtm-85) REVERT: D 1174 HIS cc_start: 0.7298 (t-90) cc_final: 0.6692 (t-90) REVERT: E 111 MET cc_start: 0.4553 (tmm) cc_final: 0.4103 (tmm) REVERT: E 139 ARG cc_start: 0.5166 (mtm180) cc_final: 0.4565 (ttm110) REVERT: E 198 GLN cc_start: 0.5677 (tp40) cc_final: 0.4695 (tt0) REVERT: E 436 ARG cc_start: 0.6347 (tpt90) cc_final: 0.6081 (ttm-80) REVERT: E 505 ARG cc_start: 0.4308 (mmm160) cc_final: 0.3907 (tpt170) REVERT: E 573 ASN cc_start: 0.6670 (t0) cc_final: 0.6429 (t0) REVERT: E 800 MET cc_start: 0.3943 (tmm) cc_final: 0.3669 (tpp) REVERT: E 964 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5596 (tt) REVERT: E 993 CYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5717 (t) outliers start: 67 outliers final: 60 residues processed: 561 average time/residue: 0.9324 time to fit residues: 822.2751 Evaluate side-chains 571 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 509 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 981 SER Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 896 ASP Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 993 CYS Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1122 THR Chi-restraints excluded: chain E residue 1124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 423 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 369 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 437 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 565 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN B 998 ASN D 832 GLN E 303 GLN E 411 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 36107 Z= 0.375 Angle : 0.698 9.018 48971 Z= 0.369 Chirality : 0.046 0.294 5367 Planarity : 0.005 0.067 6480 Dihedral : 8.120 115.428 5513 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 17.81 % Favored : 81.83 % Rotamer: Outliers : 2.04 % Allowed : 10.38 % Favored : 87.58 % 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: -3.02 (0.12), residues: 4548 helix: -0.80 (0.21), residues: 562 sheet: -0.58 (0.21), residues: 730 loop : -2.80 (0.10), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 642 HIS 0.007 0.001 HIS A 395 PHE 0.027 0.002 PHE D 165 TYR 0.031 0.002 TYR A 59 ARG 0.006 0.001 ARG D 578 *********************** 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 603 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 523 time to evaluate : 3.927 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: A 80 LYS cc_start: 0.6914 (mmmm) cc_final: 0.6660 (mmmm) REVERT: A 185 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.5783 (t80) REVERT: A 280 MET cc_start: 0.7331 (tmm) cc_final: 0.6963 (ppp) REVERT: A 299 MET cc_start: 0.6212 (mtp) cc_final: 0.5997 (mtp) REVERT: A 333 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 420 ASP cc_start: 0.5978 (t0) cc_final: 0.5547 (t0) REVERT: A 428 GLU cc_start: 0.6156 (tt0) cc_final: 0.4890 (mt-10) REVERT: A 447 ARG cc_start: 0.7159 (ttt-90) cc_final: 0.6320 (ttm-80) REVERT: A 466 MET cc_start: 0.6544 (tpt) cc_final: 0.6189 (tpt) REVERT: A 560 GLN cc_start: 0.8521 (pm20) cc_final: 0.8130 (mt0) REVERT: A 565 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7066 (tp40) REVERT: A 814 MET cc_start: 0.7281 (tpp) cc_final: 0.6859 (tpp) REVERT: A 861 HIS cc_start: 0.7745 (m90) cc_final: 0.7426 (m90) REVERT: A 920 LYS cc_start: 0.4371 (mtmm) cc_final: 0.3947 (mmmm) REVERT: A 947 MET cc_start: 0.6233 (tpp) cc_final: 0.5293 (ttm) REVERT: A 968 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7324 (mmmm) REVERT: A 1145 ARG cc_start: 0.6834 (mtt90) cc_final: 0.6502 (mtt-85) REVERT: B 226 GLN cc_start: 0.7219 (mp10) cc_final: 0.6633 (mp10) REVERT: B 338 ASP cc_start: 0.7490 (t0) cc_final: 0.7090 (t70) REVERT: B 425 ILE cc_start: 0.7161 (mt) cc_final: 0.6923 (mm) REVERT: B 564 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7580 (tptt) REVERT: B 609 ARG cc_start: 0.6713 (ttm-80) cc_final: 0.6070 (mtp-110) REVERT: B 728 MET cc_start: 0.7231 (ttp) cc_final: 0.7027 (tmm) REVERT: B 816 ARG cc_start: 0.6595 (ttt180) cc_final: 0.6252 (ttt180) REVERT: B 990 GLU cc_start: 0.7599 (tp30) cc_final: 0.7201 (tt0) REVERT: B 1051 MET cc_start: 0.6688 (tmm) cc_final: 0.6339 (tmm) REVERT: D 113 TYR cc_start: 0.7328 (t80) cc_final: 0.6569 (t80) REVERT: D 139 ARG cc_start: 0.5126 (mtp85) cc_final: 0.4193 (mtm-85) REVERT: D 174 MET cc_start: 0.4937 (ttp) cc_final: 0.4451 (ptm) REVERT: D 419 GLN cc_start: 0.6624 (tm-30) cc_final: 0.6023 (tm-30) REVERT: D 578 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6575 (mmm160) REVERT: D 639 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7799 (mmm-85) REVERT: D 830 PHE cc_start: 0.7663 (m-80) cc_final: 0.7068 (m-80) REVERT: D 945 ARG cc_start: 0.5851 (mtp180) cc_final: 0.5321 (mtm-85) REVERT: D 1174 HIS cc_start: 0.7324 (t-90) cc_final: 0.6727 (t-90) REVERT: E 111 MET cc_start: 0.4603 (tmm) cc_final: 0.4109 (tpt) REVERT: E 139 ARG cc_start: 0.5195 (mtm180) cc_final: 0.4583 (ttm110) REVERT: E 198 GLN cc_start: 0.5737 (tp40) cc_final: 0.4760 (tt0) REVERT: E 324 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6631 (mtp-110) REVERT: E 436 ARG cc_start: 0.6603 (tpt90) cc_final: 0.6278 (ttm-80) REVERT: E 505 ARG cc_start: 0.4438 (mmm160) cc_final: 0.3919 (tpt170) REVERT: E 573 ASN cc_start: 0.6772 (t0) cc_final: 0.6531 (t0) REVERT: E 800 MET cc_start: 0.3941 (tmm) cc_final: 0.3681 (tpp) REVERT: E 964 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5608 (tt) REVERT: E 993 CYS cc_start: 0.6359 (OUTLIER) cc_final: 0.6086 (t) outliers start: 80 outliers final: 68 residues processed: 570 average time/residue: 0.9279 time to fit residues: 831.5793 Evaluate side-chains 589 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 517 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 916 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 981 SER Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 841 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 896 ASP Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 993 CYS Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1110 VAL Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1122 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1149 CYS 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: 5.9990 chunk 261 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 343 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN E 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36107 Z= 0.182 Angle : 0.637 8.837 48971 Z= 0.333 Chirality : 0.043 0.275 5367 Planarity : 0.005 0.068 6480 Dihedral : 7.745 116.203 5513 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.64 % Favored : 85.05 % Rotamer: Outliers : 1.25 % Allowed : 11.45 % Favored : 87.30 % 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: -2.82 (0.12), residues: 4548 helix: -0.47 (0.22), residues: 546 sheet: -0.20 (0.22), residues: 654 loop : -2.70 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 285 HIS 0.005 0.001 HIS A 421 PHE 0.021 0.001 PHE D 165 TYR 0.022 0.001 TYR D 527 ARG 0.011 0.000 ARG A 108 *********************** 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 569 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 520 time to evaluate : 3.950 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: A 80 LYS cc_start: 0.6784 (mmmm) cc_final: 0.6546 (mmmm) REVERT: A 185 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.5696 (t80) REVERT: A 280 MET cc_start: 0.7297 (tmm) cc_final: 0.6977 (ppp) REVERT: A 299 MET cc_start: 0.5915 (mtp) cc_final: 0.5708 (mtp) REVERT: A 333 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 420 ASP cc_start: 0.5840 (t0) cc_final: 0.5449 (t0) REVERT: A 447 ARG cc_start: 0.7075 (ttt-90) cc_final: 0.6227 (ttm-80) REVERT: A 466 MET cc_start: 0.6482 (tpt) cc_final: 0.6139 (tpt) REVERT: A 467 ASP cc_start: 0.7426 (t0) cc_final: 0.7108 (t0) REVERT: A 560 GLN cc_start: 0.8518 (pm20) cc_final: 0.8126 (mt0) REVERT: A 814 MET cc_start: 0.7257 (tpp) cc_final: 0.6777 (tpp) REVERT: A 855 LYS cc_start: 0.5015 (mtpp) cc_final: 0.4790 (mttp) REVERT: A 920 LYS cc_start: 0.4204 (mtmm) cc_final: 0.3818 (mmmm) REVERT: A 947 MET cc_start: 0.6280 (tpp) cc_final: 0.5263 (ttm) REVERT: A 1145 ARG cc_start: 0.6785 (mtt90) cc_final: 0.6464 (mtt-85) REVERT: B 109 VAL cc_start: 0.8893 (m) cc_final: 0.8669 (p) REVERT: B 226 GLN cc_start: 0.7140 (mp10) cc_final: 0.6563 (mp10) REVERT: B 338 ASP cc_start: 0.7498 (t0) cc_final: 0.7004 (t70) REVERT: B 564 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7515 (tptt) REVERT: B 609 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6011 (mtp-110) REVERT: B 728 MET cc_start: 0.7185 (ttp) cc_final: 0.6907 (tmm) REVERT: B 816 ARG cc_start: 0.6588 (ttt180) cc_final: 0.6056 (ttt180) REVERT: B 990 GLU cc_start: 0.7541 (tp30) cc_final: 0.7207 (tt0) REVERT: B 1051 MET cc_start: 0.6643 (tmm) cc_final: 0.6284 (tmm) REVERT: D 113 TYR cc_start: 0.7268 (t80) cc_final: 0.6550 (t80) REVERT: D 139 ARG cc_start: 0.4992 (mtp85) cc_final: 0.4004 (mtm-85) REVERT: D 174 MET cc_start: 0.4998 (ttp) cc_final: 0.4502 (ptm) REVERT: D 280 MET cc_start: 0.4711 (tmm) cc_final: 0.4261 (tmm) REVERT: D 419 GLN cc_start: 0.6597 (tm-30) cc_final: 0.6029 (tm-30) REVERT: D 578 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6548 (mmm160) REVERT: D 639 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7786 (mmm-85) REVERT: D 830 PHE cc_start: 0.7626 (m-80) cc_final: 0.7021 (m-80) REVERT: D 1174 HIS cc_start: 0.7308 (t-90) cc_final: 0.6706 (t-90) REVERT: E 111 MET cc_start: 0.4463 (tmm) cc_final: 0.3986 (tpt) REVERT: E 139 ARG cc_start: 0.5118 (mtm180) cc_final: 0.4515 (ttm110) REVERT: E 198 GLN cc_start: 0.5731 (tp40) cc_final: 0.4759 (tt0) REVERT: E 324 ARG cc_start: 0.7062 (mtp180) cc_final: 0.6623 (mtp-110) REVERT: E 436 ARG cc_start: 0.6351 (tpt90) cc_final: 0.6065 (ttm-80) REVERT: E 505 ARG cc_start: 0.4284 (mmm160) cc_final: 0.3915 (tpt170) REVERT: E 573 ASN cc_start: 0.6600 (t0) cc_final: 0.6374 (t0) REVERT: E 800 MET cc_start: 0.3944 (tmm) cc_final: 0.3684 (tpp) REVERT: E 864 ASP cc_start: 0.6971 (p0) cc_final: 0.6688 (p0) REVERT: E 964 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5584 (tt) REVERT: E 993 CYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5738 (t) outliers start: 49 outliers final: 42 residues processed: 548 average time/residue: 0.9528 time to fit residues: 820.3043 Evaluate side-chains 555 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 510 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 916 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 896 ASP Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 993 CYS Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1149 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 398 optimal weight: 4.9990 chunk 419 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 368 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 406 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 563 GLN A 861 HIS ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 36107 Z= 0.378 Angle : 0.696 8.364 48971 Z= 0.368 Chirality : 0.046 0.275 5367 Planarity : 0.005 0.069 6480 Dihedral : 7.761 119.907 5513 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 17.77 % Favored : 81.88 % Rotamer: Outliers : 1.55 % Allowed : 11.48 % Favored : 86.97 % 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: -2.96 (0.12), residues: 4548 helix: -0.72 (0.21), residues: 560 sheet: -0.50 (0.21), residues: 730 loop : -2.78 (0.10), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 642 HIS 0.007 0.001 HIS A 395 PHE 0.028 0.002 PHE D 165 TYR 0.032 0.002 TYR A 59 ARG 0.006 0.001 ARG E 34 *********************** 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 569 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 508 time to evaluate : 4.034 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: A 80 LYS cc_start: 0.6911 (mmmm) cc_final: 0.6653 (mmmm) REVERT: A 185 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.5762 (t80) REVERT: A 280 MET cc_start: 0.7341 (tmm) cc_final: 0.7077 (ttm) REVERT: A 333 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 420 ASP cc_start: 0.6025 (t0) cc_final: 0.5598 (t0) REVERT: A 428 GLU cc_start: 0.5923 (tt0) cc_final: 0.4619 (mt-10) REVERT: A 447 ARG cc_start: 0.7143 (ttt-90) cc_final: 0.6293 (ttm-80) REVERT: A 466 MET cc_start: 0.6543 (tpt) cc_final: 0.6188 (tpt) REVERT: A 560 GLN cc_start: 0.8539 (pm20) cc_final: 0.8137 (mt0) REVERT: A 893 LEU cc_start: 0.7874 (tp) cc_final: 0.7340 (tp) REVERT: A 920 LYS cc_start: 0.4345 (mtmm) cc_final: 0.3911 (mmmm) REVERT: A 947 MET cc_start: 0.6338 (tpp) cc_final: 0.5376 (ttm) REVERT: A 968 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7329 (mmmm) REVERT: A 1145 ARG cc_start: 0.6838 (mtt90) cc_final: 0.6492 (mtt-85) REVERT: B 226 GLN cc_start: 0.7217 (mp10) cc_final: 0.6609 (mp10) REVERT: B 338 ASP cc_start: 0.7497 (t0) cc_final: 0.7100 (t70) REVERT: B 564 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7575 (tptt) REVERT: B 609 ARG cc_start: 0.6727 (ttm-80) cc_final: 0.6076 (mtp-110) REVERT: B 736 MET cc_start: 0.3866 (mmt) cc_final: 0.3456 (mmt) REVERT: B 816 ARG cc_start: 0.6617 (ttt180) cc_final: 0.6062 (ttt180) REVERT: B 990 GLU cc_start: 0.7555 (tp30) cc_final: 0.7225 (tt0) REVERT: B 1131 GLU cc_start: 0.8241 (pp20) cc_final: 0.7569 (pp20) REVERT: D 113 TYR cc_start: 0.7330 (t80) cc_final: 0.6597 (t80) REVERT: D 139 ARG cc_start: 0.5098 (mtp85) cc_final: 0.4007 (mtm-85) REVERT: D 174 MET cc_start: 0.4951 (ttp) cc_final: 0.4402 (ptm) REVERT: D 419 GLN cc_start: 0.6577 (tm-30) cc_final: 0.5996 (tm-30) REVERT: D 578 ARG cc_start: 0.6974 (mtm110) cc_final: 0.6587 (mmm160) REVERT: D 639 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7813 (mmm-85) REVERT: D 830 PHE cc_start: 0.7658 (m-80) cc_final: 0.7056 (m-80) REVERT: D 945 ARG cc_start: 0.5915 (mtp180) cc_final: 0.5381 (mtm-85) REVERT: D 1174 HIS cc_start: 0.7345 (t-90) cc_final: 0.6750 (t-90) REVERT: E 111 MET cc_start: 0.4598 (tmm) cc_final: 0.4325 (tpt) REVERT: E 139 ARG cc_start: 0.5134 (mtm180) cc_final: 0.4583 (ttm110) REVERT: E 198 GLN cc_start: 0.5748 (tp40) cc_final: 0.4769 (tt0) REVERT: E 324 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6628 (mtp-110) REVERT: E 436 ARG cc_start: 0.6608 (tpt90) cc_final: 0.6279 (ttm-80) REVERT: E 505 ARG cc_start: 0.4437 (mmm160) cc_final: 0.3903 (tpt170) REVERT: E 573 ASN cc_start: 0.6753 (t0) cc_final: 0.6517 (t0) REVERT: E 800 MET cc_start: 0.3756 (tmm) cc_final: 0.3483 (tpp) REVERT: E 964 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5530 (tt) REVERT: E 993 CYS cc_start: 0.6416 (OUTLIER) cc_final: 0.6142 (t) outliers start: 61 outliers final: 55 residues processed: 544 average time/residue: 0.9546 time to fit residues: 814.1874 Evaluate side-chains 564 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 506 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 916 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 623 CYS Chi-restraints excluded: chain D residue 841 THR Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 868 SER Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 896 ASP Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 993 CYS Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1149 CYS 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: 0.4980 chunk 263 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 299 optimal weight: 7.9990 chunk 452 optimal weight: 4.9990 chunk 416 optimal weight: 10.0000 chunk 360 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 278 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 421 HIS ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 36107 Z= 0.195 Angle : 0.636 9.723 48971 Z= 0.333 Chirality : 0.043 0.398 5367 Planarity : 0.005 0.071 6480 Dihedral : 7.489 121.687 5513 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.79 % Favored : 84.90 % Rotamer: Outliers : 1.17 % Allowed : 12.04 % Favored : 86.79 % 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: -2.79 (0.12), residues: 4548 helix: -0.44 (0.22), residues: 546 sheet: -0.25 (0.22), residues: 690 loop : -2.69 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 285 HIS 0.006 0.001 HIS A 421 PHE 0.027 0.001 PHE D 165 TYR 0.020 0.001 TYR D 527 ARG 0.011 0.000 ARG A 108 ********************** 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 565 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 519 time to evaluate : 4.162 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: A 80 LYS cc_start: 0.6825 (mmmm) cc_final: 0.6587 (mmmm) REVERT: A 185 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.5694 (t80) REVERT: A 280 MET cc_start: 0.7299 (tmm) cc_final: 0.6969 (ppp) REVERT: A 333 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 420 ASP cc_start: 0.5739 (t0) cc_final: 0.5285 (t0) REVERT: A 447 ARG cc_start: 0.7062 (ttt-90) cc_final: 0.6236 (ttm-80) REVERT: A 466 MET cc_start: 0.6431 (tpt) cc_final: 0.6088 (tpt) REVERT: A 519 LYS cc_start: 0.7226 (pttm) cc_final: 0.6545 (ptpt) REVERT: A 560 GLN cc_start: 0.8552 (pm20) cc_final: 0.8165 (mt0) REVERT: A 564 LYS cc_start: 0.7543 (ttmm) cc_final: 0.7308 (tptp) REVERT: A 802 MET cc_start: 0.1729 (ptp) cc_final: 0.1406 (mmm) REVERT: A 814 MET cc_start: 0.7301 (tpp) cc_final: 0.6862 (tpp) REVERT: A 855 LYS cc_start: 0.5043 (mtpp) cc_final: 0.4819 (mttp) REVERT: A 920 LYS cc_start: 0.4085 (mtmm) cc_final: 0.3742 (mmmm) REVERT: A 947 MET cc_start: 0.6295 (tpp) cc_final: 0.5291 (ttm) REVERT: A 1145 ARG cc_start: 0.6806 (mtt90) cc_final: 0.6471 (mtt-85) REVERT: B 226 GLN cc_start: 0.7090 (mp10) cc_final: 0.6509 (mp10) REVERT: B 338 ASP cc_start: 0.7551 (t0) cc_final: 0.7158 (t70) REVERT: B 564 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7547 (tptt) REVERT: B 609 ARG cc_start: 0.6684 (ttm-80) cc_final: 0.6040 (mtp-110) REVERT: B 736 MET cc_start: 0.3767 (mmt) cc_final: 0.3378 (mmt) REVERT: B 816 ARG cc_start: 0.6634 (ttt180) cc_final: 0.6103 (ttt180) REVERT: B 990 GLU cc_start: 0.7507 (tp30) cc_final: 0.7187 (tt0) REVERT: B 1051 MET cc_start: 0.6657 (tmm) cc_final: 0.6361 (tmm) REVERT: B 1160 PRO cc_start: 0.9240 (Cg_endo) cc_final: 0.9023 (Cg_exo) REVERT: D 113 TYR cc_start: 0.7281 (t80) cc_final: 0.6530 (t80) REVERT: D 139 ARG cc_start: 0.5069 (mtp85) cc_final: 0.4079 (mtm-85) REVERT: D 174 MET cc_start: 0.5016 (ttp) cc_final: 0.4476 (ptm) REVERT: D 419 GLN cc_start: 0.6614 (tm-30) cc_final: 0.6045 (tm-30) REVERT: D 639 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7791 (mmm-85) REVERT: D 732 GLU cc_start: 0.7414 (tt0) cc_final: 0.7195 (tt0) REVERT: D 830 PHE cc_start: 0.7624 (m-80) cc_final: 0.7014 (m-80) REVERT: D 1174 HIS cc_start: 0.7312 (t-90) cc_final: 0.6732 (t-90) REVERT: E 111 MET cc_start: 0.4488 (tmm) cc_final: 0.4191 (tpt) REVERT: E 139 ARG cc_start: 0.5064 (mtm180) cc_final: 0.4526 (ttm110) REVERT: E 198 GLN cc_start: 0.5748 (tp40) cc_final: 0.4775 (tt0) REVERT: E 324 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6619 (mtp-110) REVERT: E 436 ARG cc_start: 0.6600 (tpt90) cc_final: 0.6280 (ttm-80) REVERT: E 505 ARG cc_start: 0.4339 (mmm160) cc_final: 0.4025 (tpt170) REVERT: E 573 ASN cc_start: 0.6609 (t0) cc_final: 0.6366 (t0) REVERT: E 800 MET cc_start: 0.3814 (tmm) cc_final: 0.3534 (tpp) REVERT: E 964 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5579 (tt) REVERT: E 993 CYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5860 (t) outliers start: 46 outliers final: 42 residues processed: 546 average time/residue: 0.9557 time to fit residues: 819.4161 Evaluate side-chains 553 residues out of total 3932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 508 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 916 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 623 CYS Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain E residue 799 CYS Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 896 ASP Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 993 CYS Chi-restraints excluded: chain E residue 1082 ASP Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1149 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 286 optimal weight: 3.9990 chunk 383 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 332 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 370 optimal weight: 20.0000 chunk 45 optimal weight: 0.0270 chunk 66 optimal weight: 8.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.214581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.176793 restraints weight = 160834.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.168908 restraints weight = 170535.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.162509 restraints weight = 97994.903| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 36107 Z= 0.219 Angle : 0.733 57.296 48971 Z= 0.437 Chirality : 0.044 0.440 5367 Planarity : 0.005 0.176 6480 Dihedral : 7.485 121.672 5513 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.12 % Favored : 84.57 % Rotamer: Outliers : 1.15 % Allowed : 12.26 % Favored : 86.59 % 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: -0.25 (0.22), residues: 690 loop : -2.69 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 285 HIS 0.246 0.002 HIS A 421 PHE 0.026 0.001 PHE D 165 TYR 0.019 0.001 TYR D 527 ARG 0.008 0.000 ARG A 108 =============================================================================== Job complete usr+sys time: 13776.65 seconds wall clock time: 239 minutes 10.69 seconds (14350.69 seconds total)