Starting phenix.real_space_refine on Mon Mar 25 00:04:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut7_20868/03_2024/6ut7_20868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut7_20868/03_2024/6ut7_20868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut7_20868/03_2024/6ut7_20868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut7_20868/03_2024/6ut7_20868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut7_20868/03_2024/6ut7_20868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut7_20868/03_2024/6ut7_20868.pdb" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 12 5.21 5 S 54 5.16 5 C 29266 2.51 5 N 7730 2.21 5 O 7968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 200": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 542": "OE1" <-> "OE2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 448": "NH1" <-> "NH2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D GLU 572": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E ARG 435": "NH1" <-> "NH2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "E GLU 442": "OE1" <-> "OE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "F ARG 200": "NH1" <-> "NH2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F GLU 323": "OE1" <-> "OE2" Residue "F ARG 360": "NH1" <-> "NH2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F ARG 435": "NH1" <-> "NH2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 511": "OE1" <-> "OE2" Residue "F GLU 542": "OE1" <-> "OE2" Residue "G ARG 47": "NH1" <-> "NH2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G ARG 233": "NH1" <-> "NH2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G ARG 270": "NH1" <-> "NH2" Residue "H ARG 200": "NH1" <-> "NH2" Residue "H GLU 235": "OE1" <-> "OE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 255": "OE1" <-> "OE2" Residue "H GLU 258": "OE1" <-> "OE2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H GLU 268": "OE1" <-> "OE2" Residue "H ARG 271": "NH1" <-> "NH2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H GLU 323": "OE1" <-> "OE2" Residue "H ARG 360": "NH1" <-> "NH2" Residue "H GLU 369": "OE1" <-> "OE2" Residue "H ARG 414": "NH1" <-> "NH2" Residue "H ARG 425": "NH1" <-> "NH2" Residue "H GLU 455": "OE1" <-> "OE2" Residue "H ARG 459": "NH1" <-> "NH2" Residue "H GLU 462": "OE1" <-> "OE2" Residue "H GLU 466": "OE1" <-> "OE2" Residue "H GLU 483": "OE1" <-> "OE2" Residue "H GLU 508": "OE1" <-> "OE2" Residue "H GLU 511": "OE1" <-> "OE2" Residue "H GLU 527": "OE1" <-> "OE2" Residue "H GLU 546": "OE1" <-> "OE2" Residue "I ARG 200": "NH1" <-> "NH2" Residue "I ARG 261": "NH1" <-> "NH2" Residue "I ARG 271": "NH1" <-> "NH2" Residue "I ARG 330": "NH1" <-> "NH2" Residue "I GLU 383": "OE1" <-> "OE2" Residue "I GLU 395": "OE1" <-> "OE2" Residue "I ARG 414": "NH1" <-> "NH2" Residue "I GLU 442": "OE1" <-> "OE2" Residue "I ARG 448": "NH1" <-> "NH2" Residue "I GLU 455": "OE1" <-> "OE2" Residue "I GLU 466": "OE1" <-> "OE2" Residue "I GLU 511": "OE1" <-> "OE2" Residue "I GLU 534": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 553": "OE1" <-> "OE2" Residue "I GLU 572": "OE1" <-> "OE2" Residue "J ARG 226": "NH1" <-> "NH2" Residue "J GLU 267": "OE1" <-> "OE2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J GLU 323": "OE1" <-> "OE2" Residue "J ARG 360": "NH1" <-> "NH2" Residue "J GLU 369": "OE1" <-> "OE2" Residue "J GLU 375": "OE1" <-> "OE2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J ARG 389": "NH1" <-> "NH2" Residue "J ARG 425": "NH1" <-> "NH2" Residue "J GLU 431": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "J GLU 437": "OE1" <-> "OE2" Residue "J GLU 442": "OE1" <-> "OE2" Residue "J ARG 448": "NH1" <-> "NH2" Residue "J GLU 449": "OE1" <-> "OE2" Residue "J GLU 455": "OE1" <-> "OE2" Residue "J ARG 459": "NH1" <-> "NH2" Residue "J GLU 483": "OE1" <-> "OE2" Residue "J GLU 542": "OE1" <-> "OE2" Residue "J GLU 563": "OE1" <-> "OE2" Residue "K ARG 226": "NH1" <-> "NH2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "K ARG 263": "NH1" <-> "NH2" Residue "K GLU 268": "OE1" <-> "OE2" Residue "K ARG 271": "NH1" <-> "NH2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K GLU 315": "OE1" <-> "OE2" Residue "K GLU 383": "OE1" <-> "OE2" Residue "K ARG 389": "NH1" <-> "NH2" Residue "K GLU 395": "OE1" <-> "OE2" Residue "K ARG 414": "NH1" <-> "NH2" Residue "K ARG 448": "NH1" <-> "NH2" Residue "K GLU 462": "OE1" <-> "OE2" Residue "K GLU 508": "OE1" <-> "OE2" Residue "K GLU 534": "OE1" <-> "OE2" Residue "K ARG 556": "NH1" <-> "NH2" Residue "K GLU 572": "OE1" <-> "OE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 243": "OE1" <-> "OE2" Residue "L GLU 258": "OE1" <-> "OE2" Residue "L ARG 261": "NH1" <-> "NH2" Residue "L GLU 267": "OE1" <-> "OE2" Residue "L ARG 306": "NH1" <-> "NH2" Residue "L GLU 324": "OE1" <-> "OE2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "L ARG 426": "NH1" <-> "NH2" Residue "L GLU 433": "OE1" <-> "OE2" Residue "L ARG 435": "NH1" <-> "NH2" Residue "L GLU 437": "OE1" <-> "OE2" Residue "L GLU 442": "OE1" <-> "OE2" Residue "L GLU 455": "OE1" <-> "OE2" Residue "L GLU 466": "OE1" <-> "OE2" Residue "L TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 527": "OE1" <-> "OE2" Residue "L GLU 564": "OE1" <-> "OE2" Residue "M ARG 200": "NH1" <-> "NH2" Residue "M GLU 243": "OE1" <-> "OE2" Residue "M GLU 267": "OE1" <-> "OE2" Residue "M ARG 271": "NH1" <-> "NH2" Residue "M GLU 315": "OE1" <-> "OE2" Residue "M GLU 323": "OE1" <-> "OE2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M ARG 424": "NH1" <-> "NH2" Residue "M ARG 425": "NH1" <-> "NH2" Residue "M ARG 435": "NH1" <-> "NH2" Residue "M ARG 448": "NH1" <-> "NH2" Residue "M GLU 466": "OE1" <-> "OE2" Residue "M GLU 511": "OE1" <-> "OE2" Residue "M GLU 542": "OE1" <-> "OE2" Residue "N ARG 47": "NH1" <-> "NH2" Residue "N ARG 75": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 139": "NH1" <-> "NH2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N ARG 174": "NH1" <-> "NH2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N GLU 208": "OE1" <-> "OE2" Residue "N ARG 226": "NH1" <-> "NH2" Residue "N ARG 233": "NH1" <-> "NH2" Residue "N GLU 257": "OE1" <-> "OE2" Residue "N GLU 266": "OE1" <-> "OE2" Residue "N ARG 267": "NH1" <-> "NH2" Residue "N ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45062 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3193 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3218 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3178 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3227 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 374} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3186 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3183 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3156 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 4 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 253 Chain: "H" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3193 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3218 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3178 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "K" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3227 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 374} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3186 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "M" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3183 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "N" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3156 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 4 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 253 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.86, per 1000 atoms: 0.49 Number of scatterers: 45062 At special positions: 0 Unit cell: (183.75, 213.75, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 32 15.00 Mg 12 11.99 O 7968 8.00 N 7730 7.00 C 29266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.00 Conformation dependent library (CDL) restraints added in 7.9 seconds 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10388 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 60 sheets defined 47.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 197 through 208 removed outlier: 3.689A pdb=" N ASP A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.505A pdb=" N PHE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.775A pdb=" N ARG A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.798A pdb=" N THR A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 299 " --> pdb=" O ASP A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.626A pdb=" N GLU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.859A pdb=" N PHE A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.898A pdb=" N ILE A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.828A pdb=" N LEU A 419 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 removed outlier: 3.984A pdb=" N PHE A 438 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.625A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.541A pdb=" N LYS A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.720A pdb=" N LEU A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.596A pdb=" N HIS A 497 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 498 " --> pdb=" O ARG A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 503 through 507 removed outlier: 4.144A pdb=" N ASN A 506 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.615A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.554A pdb=" N ASN B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.934A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.972A pdb=" N ARG B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.568A pdb=" N GLU B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.559A pdb=" N ILE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.512A pdb=" N LEU B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.854A pdb=" N PHE B 438 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 4.314A pdb=" N LYS B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 471 removed outlier: 4.129A pdb=" N ARG B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.373A pdb=" N ARG B 488 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.120A pdb=" N ASN B 506 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 507 " --> pdb=" O PHE B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 507' Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.714A pdb=" N LYS B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.666A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 removed outlier: 3.517A pdb=" N VAL C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.790A pdb=" N VAL C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.202A pdb=" N ARG C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 318 through 337 removed outlier: 3.758A pdb=" N GLU C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 362 through 367 removed outlier: 3.682A pdb=" N PHE C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.578A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 removed outlier: 3.939A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 427' Processing helix chain 'C' and resid 435 through 439 removed outlier: 3.711A pdb=" N PHE C 438 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.578A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 471 removed outlier: 4.137A pdb=" N LYS C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 removed outlier: 4.542A pdb=" N ARG C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 521 through 529 Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.663A pdb=" N ILE C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.961A pdb=" N ASN D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 234 Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.759A pdb=" N ARG D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.535A pdb=" N ARG D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 336 removed outlier: 4.555A pdb=" N GLU D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 removed outlier: 4.321A pdb=" N ASN D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.678A pdb=" N THR D 372 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 439 removed outlier: 3.905A pdb=" N PHE D 438 " --> pdb=" O ARG D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 476 through 491 removed outlier: 3.755A pdb=" N THR D 480 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 488 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.983A pdb=" N ASN D 506 " --> pdb=" O TYR D 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 507 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 507' Processing helix chain 'D' and resid 509 through 518 Processing helix chain 'D' and resid 521 through 529 removed outlier: 3.760A pdb=" N PHE D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.522A pdb=" N ILE D 536 " --> pdb=" O ASP D 532 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 540 " --> pdb=" O ILE D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 4.049A pdb=" N ILE D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.521A pdb=" N MET E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 234 removed outlier: 3.502A pdb=" N VAL E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 291 removed outlier: 3.959A pdb=" N ARG E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 318 through 336 removed outlier: 4.160A pdb=" N GLU E 323 " --> pdb=" O PRO E 319 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 334 " --> pdb=" O ARG E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.560A pdb=" N GLY E 361 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 368 through 372 removed outlier: 3.982A pdb=" N ILE E 371 " --> pdb=" O GLY E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.623A pdb=" N ARG E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 3.690A pdb=" N PHE E 438 " --> pdb=" O ARG E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 452 removed outlier: 3.729A pdb=" N LYS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 471 Processing helix chain 'E' and resid 476 through 491 removed outlier: 4.164A pdb=" N ARG E 488 " --> pdb=" O LYS E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.894A pdb=" N ASN E 506 " --> pdb=" O TYR E 503 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL E 507 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 507' Processing helix chain 'E' and resid 509 through 519 removed outlier: 3.502A pdb=" N TYR E 519 " --> pdb=" O HIS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 529 Processing helix chain 'E' and resid 532 through 540 removed outlier: 3.553A pdb=" N TRP E 538 " --> pdb=" O GLU E 534 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 540 " --> pdb=" O ILE E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 581 removed outlier: 3.715A pdb=" N ILE E 577 " --> pdb=" O GLY E 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.630A pdb=" N VAL F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP F 202 " --> pdb=" O TYR F 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 204 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.685A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.645A pdb=" N PHE F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 294 removed outlier: 3.941A pdb=" N ARG F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE F 292 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 318 through 337 removed outlier: 4.026A pdb=" N GLU F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.537A pdb=" N LYS F 343 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 344 " --> pdb=" O LYS F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 344' Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.530A pdb=" N ARG F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 421 through 426' Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.872A pdb=" N PHE F 438 " --> pdb=" O ARG F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 451 removed outlier: 3.507A pdb=" N LYS F 450 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 451 " --> pdb=" O ILE F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 471 removed outlier: 3.569A pdb=" N ARG F 457 " --> pdb=" O LYS F 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 493 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.901A pdb=" N ASN F 506 " --> pdb=" O TYR F 503 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 509 through 518 Processing helix chain 'F' and resid 521 through 529 Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.712A pdb=" N VAL F 539 " --> pdb=" O THR F 535 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 540 " --> pdb=" O ILE F 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 535 through 540' Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'G' and resid 23 through 41 removed outlier: 3.639A pdb=" N ILE G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 removed outlier: 3.624A pdb=" N SER G 61 " --> pdb=" O ILE G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 123 removed outlier: 3.709A pdb=" N LEU G 114 " --> pdb=" O TRP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 134 removed outlier: 3.667A pdb=" N LEU G 133 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 162 Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.036A pdb=" N ARG G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 196 removed outlier: 4.002A pdb=" N LEU G 196 " --> pdb=" O PRO G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 225 removed outlier: 3.626A pdb=" N ARG G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'G' and resid 254 through 259 removed outlier: 3.909A pdb=" N VAL G 259 " --> pdb=" O HIS G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 268 through 279 removed outlier: 3.546A pdb=" N PHE G 272 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 274 " --> pdb=" O ARG G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 314 removed outlier: 3.629A pdb=" N GLU G 307 " --> pdb=" O GLU G 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL G 309 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 311 " --> pdb=" O GLU G 307 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 364 removed outlier: 3.903A pdb=" N ARG G 363 " --> pdb=" O LEU G 360 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 364 " --> pdb=" O LYS G 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 360 through 364' Processing helix chain 'G' and resid 366 through 379 removed outlier: 3.694A pdb=" N GLN G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 375 " --> pdb=" O ARG G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 453 removed outlier: 3.701A pdb=" N ASN G 444 " --> pdb=" O LYS G 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 208 removed outlier: 3.690A pdb=" N ASP H 202 " --> pdb=" O TYR H 198 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 207 " --> pdb=" O MET H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 234 Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.505A pdb=" N PHE H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 291 removed outlier: 3.775A pdb=" N ARG H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 299 removed outlier: 3.798A pdb=" N THR H 298 " --> pdb=" O GLU H 295 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE H 299 " --> pdb=" O ASP H 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 295 through 299' Processing helix chain 'H' and resid 300 through 313 Processing helix chain 'H' and resid 318 through 337 removed outlier: 3.626A pdb=" N GLU H 324 " --> pdb=" O THR H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 removed outlier: 3.860A pdb=" N PHE H 367 " --> pdb=" O ILE H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 374 removed outlier: 3.898A pdb=" N ILE H 371 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR H 372 " --> pdb=" O GLU H 369 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU H 374 " --> pdb=" O ILE H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 419 removed outlier: 3.828A pdb=" N LEU H 419 " --> pdb=" O ILE H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 removed outlier: 3.983A pdb=" N PHE H 438 " --> pdb=" O ARG H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 449 removed outlier: 3.625A pdb=" N LYS H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 471 removed outlier: 3.541A pdb=" N LYS H 458 " --> pdb=" O THR H 454 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS H 470 " --> pdb=" O GLU H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 490 removed outlier: 3.720A pdb=" N LEU H 482 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG H 488 " --> pdb=" O LYS H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 498 removed outlier: 3.596A pdb=" N HIS H 497 " --> pdb=" O ASP H 494 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG H 498 " --> pdb=" O ARG H 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 494 through 498' Processing helix chain 'H' and resid 503 through 507 removed outlier: 4.144A pdb=" N ASN H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL H 507 " --> pdb=" O PHE H 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 503 through 507' Processing helix chain 'H' and resid 509 through 520 Processing helix chain 'H' and resid 521 through 529 Processing helix chain 'H' and resid 533 through 540 Processing helix chain 'H' and resid 573 through 581 removed outlier: 3.616A pdb=" N ILE H 577 " --> pdb=" O GLY H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 584 No H-bonds generated for 'chain 'H' and resid 582 through 584' Processing helix chain 'I' and resid 194 through 207 removed outlier: 3.554A pdb=" N ASN I 206 " --> pdb=" O ASP I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 234 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 278 through 293 removed outlier: 3.934A pdb=" N GLU I 293 " --> pdb=" O LYS I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.972A pdb=" N ARG I 306 " --> pdb=" O ASP I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 337 removed outlier: 3.568A pdb=" N GLU I 334 " --> pdb=" O ARG I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 367 removed outlier: 3.559A pdb=" N ILE I 366 " --> pdb=" O ASN I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 379 removed outlier: 3.512A pdb=" N LEU I 374 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU I 375 " --> pdb=" O THR I 372 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS I 376 " --> pdb=" O LEU I 373 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP I 377 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG I 379 " --> pdb=" O LYS I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 439 removed outlier: 3.853A pdb=" N PHE I 438 " --> pdb=" O ARG I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 452 removed outlier: 4.314A pdb=" N LYS I 451 " --> pdb=" O ILE I 447 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU I 452 " --> pdb=" O ARG I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 removed outlier: 4.129A pdb=" N ARG I 459 " --> pdb=" O GLU I 455 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 491 removed outlier: 4.373A pdb=" N ARG I 488 " --> pdb=" O LYS I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 507 removed outlier: 4.119A pdb=" N ASN I 506 " --> pdb=" O TYR I 503 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 507 " --> pdb=" O PHE I 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 503 through 507' Processing helix chain 'I' and resid 509 through 520 Processing helix chain 'I' and resid 521 through 526 Processing helix chain 'I' and resid 532 through 540 removed outlier: 3.715A pdb=" N LYS I 537 " --> pdb=" O TRP I 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP I 538 " --> pdb=" O GLU I 534 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU I 540 " --> pdb=" O ILE I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 582 removed outlier: 3.667A pdb=" N ILE I 577 " --> pdb=" O GLY I 573 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG I 582 " --> pdb=" O GLY I 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 206 removed outlier: 3.515A pdb=" N VAL J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 234 removed outlier: 3.789A pdb=" N VAL J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 292 removed outlier: 4.202A pdb=" N ARG J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 310 Processing helix chain 'J' and resid 318 through 337 removed outlier: 3.758A pdb=" N GLU J 323 " --> pdb=" O PRO J 319 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU J 324 " --> pdb=" O THR J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 345 Processing helix chain 'J' and resid 362 through 367 removed outlier: 3.681A pdb=" N PHE J 367 " --> pdb=" O ILE J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 379 removed outlier: 3.579A pdb=" N ARG J 379 " --> pdb=" O LYS J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 427 removed outlier: 3.939A pdb=" N ARG J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE J 427 " --> pdb=" O LEU J 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 422 through 427' Processing helix chain 'J' and resid 435 through 439 removed outlier: 3.711A pdb=" N PHE J 438 " --> pdb=" O ARG J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 451 removed outlier: 3.578A pdb=" N LEU J 444 " --> pdb=" O GLU J 440 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS J 451 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 471 removed outlier: 4.137A pdb=" N LYS J 458 " --> pdb=" O THR J 454 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG J 459 " --> pdb=" O GLU J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 493 removed outlier: 4.543A pdb=" N ARG J 488 " --> pdb=" O LYS J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 520 Processing helix chain 'J' and resid 521 through 529 Processing helix chain 'J' and resid 532 through 540 removed outlier: 3.663A pdb=" N ILE J 536 " --> pdb=" O ASP J 532 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP J 538 " --> pdb=" O GLU J 534 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU J 540 " --> pdb=" O ILE J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 579 Processing helix chain 'K' and resid 195 through 208 removed outlier: 3.961A pdb=" N ASN K 206 " --> pdb=" O ASP K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 234 Processing helix chain 'K' and resid 279 through 291 removed outlier: 3.759A pdb=" N ARG K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 310 removed outlier: 3.535A pdb=" N ARG K 306 " --> pdb=" O ASP K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 336 removed outlier: 4.556A pdb=" N GLU K 324 " --> pdb=" O THR K 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 346 removed outlier: 4.320A pdb=" N ASN K 346 " --> pdb=" O ASP K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 367 Processing helix chain 'K' and resid 368 through 372 removed outlier: 3.678A pdb=" N THR K 372 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 439 removed outlier: 3.905A pdb=" N PHE K 438 " --> pdb=" O ARG K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 441 through 449 Processing helix chain 'K' and resid 456 through 469 Processing helix chain 'K' and resid 476 through 491 removed outlier: 3.754A pdb=" N THR K 480 " --> pdb=" O TYR K 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 488 " --> pdb=" O LYS K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 507 removed outlier: 3.982A pdb=" N ASN K 506 " --> pdb=" O TYR K 503 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL K 507 " --> pdb=" O PHE K 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 503 through 507' Processing helix chain 'K' and resid 509 through 518 Processing helix chain 'K' and resid 521 through 529 removed outlier: 3.760A pdb=" N PHE K 529 " --> pdb=" O LEU K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 540 removed outlier: 3.522A pdb=" N ILE K 536 " --> pdb=" O ASP K 532 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP K 538 " --> pdb=" O GLU K 534 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU K 540 " --> pdb=" O ILE K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 573 through 581 removed outlier: 4.050A pdb=" N ILE K 577 " --> pdb=" O GLY K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 209 removed outlier: 3.521A pdb=" N MET L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU L 204 " --> pdb=" O ARG L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 234 removed outlier: 3.501A pdb=" N VAL L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 291 removed outlier: 3.959A pdb=" N ARG L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 313 Processing helix chain 'L' and resid 318 through 336 removed outlier: 4.159A pdb=" N GLU L 323 " --> pdb=" O PRO L 319 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU L 324 " --> pdb=" O THR L 320 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 334 " --> pdb=" O ARG L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 361 removed outlier: 3.560A pdb=" N GLY L 361 " --> pdb=" O ILE L 358 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 367 Processing helix chain 'L' and resid 368 through 372 removed outlier: 3.983A pdb=" N ILE L 371 " --> pdb=" O GLY L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 425 removed outlier: 3.623A pdb=" N ARG L 425 " --> pdb=" O VAL L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 439 removed outlier: 3.690A pdb=" N PHE L 438 " --> pdb=" O ARG L 435 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 452 removed outlier: 3.728A pdb=" N LYS L 450 " --> pdb=" O LYS L 446 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS L 451 " --> pdb=" O ILE L 447 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 452 " --> pdb=" O ARG L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 471 Processing helix chain 'L' and resid 476 through 491 removed outlier: 4.164A pdb=" N ARG L 488 " --> pdb=" O LYS L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 507 removed outlier: 3.895A pdb=" N ASN L 506 " --> pdb=" O TYR L 503 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL L 507 " --> pdb=" O PHE L 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 503 through 507' Processing helix chain 'L' and resid 509 through 519 removed outlier: 3.502A pdb=" N TYR L 519 " --> pdb=" O HIS L 515 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 540 removed outlier: 3.553A pdb=" N TRP L 538 " --> pdb=" O GLU L 534 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU L 540 " --> pdb=" O ILE L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 573 through 581 removed outlier: 3.715A pdb=" N ILE L 577 " --> pdb=" O GLY L 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 206 removed outlier: 3.631A pdb=" N VAL M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 204 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN M 206 " --> pdb=" O ASP M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 233 removed outlier: 3.685A pdb=" N GLU M 231 " --> pdb=" O LYS M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 257 removed outlier: 3.643A pdb=" N PHE M 256 " --> pdb=" O SER M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 294 removed outlier: 3.941A pdb=" N ARG M 285 " --> pdb=" O LYS M 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE M 292 " --> pdb=" O VAL M 288 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU M 293 " --> pdb=" O LYS M 289 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU M 294 " --> pdb=" O GLY M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 312 Processing helix chain 'M' and resid 318 through 337 removed outlier: 4.026A pdb=" N GLU M 323 " --> pdb=" O PRO M 319 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU M 324 " --> pdb=" O THR M 320 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY M 337 " --> pdb=" O TRP M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 344 removed outlier: 3.536A pdb=" N LYS M 343 " --> pdb=" O PRO M 340 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU M 344 " --> pdb=" O LYS M 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 340 through 344' Processing helix chain 'M' and resid 362 through 367 Processing helix chain 'M' and resid 421 through 426 removed outlier: 3.530A pdb=" N ARG M 425 " --> pdb=" O VAL M 421 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG M 426 " --> pdb=" O ALA M 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 421 through 426' Processing helix chain 'M' and resid 435 through 439 removed outlier: 3.872A pdb=" N PHE M 438 " --> pdb=" O ARG M 435 " (cutoff:3.500A) Processing helix chain 'M' and resid 440 through 451 removed outlier: 3.508A pdb=" N LYS M 450 " --> pdb=" O LYS M 446 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS M 451 " --> pdb=" O ILE M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 471 removed outlier: 3.569A pdb=" N ARG M 457 " --> pdb=" O LYS M 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS M 458 " --> pdb=" O THR M 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG M 459 " --> pdb=" O GLU M 455 " (cutoff:3.500A) Processing helix chain 'M' and resid 476 through 493 Processing helix chain 'M' and resid 503 through 507 removed outlier: 3.901A pdb=" N ASN M 506 " --> pdb=" O TYR M 503 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL M 507 " --> pdb=" O PHE M 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 503 through 507' Processing helix chain 'M' and resid 509 through 518 Processing helix chain 'M' and resid 521 through 529 Processing helix chain 'M' and resid 535 through 540 removed outlier: 3.712A pdb=" N VAL M 539 " --> pdb=" O THR M 535 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 540 " --> pdb=" O ILE M 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 535 through 540' Processing helix chain 'M' and resid 573 through 581 Processing helix chain 'N' and resid 23 through 41 removed outlier: 3.638A pdb=" N ILE N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN N 28 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE N 32 " --> pdb=" O GLN N 28 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS N 33 " --> pdb=" O ASP N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 61 removed outlier: 3.624A pdb=" N SER N 61 " --> pdb=" O ILE N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 3.709A pdb=" N LEU N 114 " --> pdb=" O TRP N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 134 removed outlier: 3.668A pdb=" N LEU N 133 " --> pdb=" O LYS N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 162 Processing helix chain 'N' and resid 185 through 190 removed outlier: 4.036A pdb=" N ARG N 190 " --> pdb=" O SER N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 196 removed outlier: 4.002A pdb=" N LEU N 196 " --> pdb=" O PRO N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 225 removed outlier: 3.627A pdb=" N ARG N 225 " --> pdb=" O ARG N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 231 through 243 Processing helix chain 'N' and resid 254 through 259 removed outlier: 3.909A pdb=" N VAL N 259 " --> pdb=" O HIS N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 267 No H-bonds generated for 'chain 'N' and resid 265 through 267' Processing helix chain 'N' and resid 268 through 279 removed outlier: 3.546A pdb=" N PHE N 272 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU N 274 " --> pdb=" O ARG N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 314 removed outlier: 3.629A pdb=" N GLU N 307 " --> pdb=" O GLU N 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL N 309 " --> pdb=" O PHE N 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 311 " --> pdb=" O GLU N 307 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG N 312 " --> pdb=" O ARG N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 364 removed outlier: 3.904A pdb=" N ARG N 363 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE N 364 " --> pdb=" O LYS N 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 360 through 364' Processing helix chain 'N' and resid 366 through 379 removed outlier: 3.694A pdb=" N GLN N 372 " --> pdb=" O ASP N 368 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL N 375 " --> pdb=" O ARG N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 440 through 453 removed outlier: 3.702A pdb=" N ASN N 444 " --> pdb=" O LYS N 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 246 removed outlier: 6.419A pdb=" N GLU A 243 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP A 356 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 245 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 211 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET A 409 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 213 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 430 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 212 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 263 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AA5, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.497A pdb=" N GLU B 243 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 356 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 245 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 353 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 408 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 355 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASN B 410 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL B 211 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N MET B 409 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 213 " --> pdb=" O MET B 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 552 through 554 Processing sheet with id=AA9, first strand: chain 'C' and resid 242 through 246 removed outlier: 6.350A pdb=" N GLU C 243 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP C 356 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE C 245 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN C 210 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE C 430 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 212 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 258 through 263 removed outlier: 3.562A pdb=" N ARG C 263 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 271 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AB4, first strand: chain 'D' and resid 242 through 244 removed outlier: 7.804A pdb=" N THR D 408 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE D 355 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN D 410 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 211 " --> pdb=" O GLY D 407 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET D 409 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU D 213 " --> pdb=" O MET D 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 262 removed outlier: 3.757A pdb=" N VAL D 273 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AB7, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB8, first strand: chain 'E' and resid 210 through 212 Processing sheet with id=AB9, first strand: chain 'E' and resid 258 through 263 removed outlier: 3.552A pdb=" N VAL E 273 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 271 " --> pdb=" O ARG E 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AC2, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AC3, first strand: chain 'F' and resid 211 through 214 removed outlier: 5.944A pdb=" N ILE F 212 " --> pdb=" O ILE F 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 245 through 246 removed outlier: 6.710A pdb=" N ILE F 245 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 258 through 260 Processing sheet with id=AC6, first strand: chain 'F' and resid 263 through 264 Processing sheet with id=AC7, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AC8, first strand: chain 'F' and resid 552 through 554 Processing sheet with id=AC9, first strand: chain 'G' and resid 6 through 10 removed outlier: 3.587A pdb=" N VAL G 83 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE G 294 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 14 through 16 Processing sheet with id=AD2, first strand: chain 'G' and resid 168 through 176 removed outlier: 3.841A pdb=" N LYS G 182 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 318 through 321 removed outlier: 3.622A pdb=" N TYR G 318 " --> pdb=" O ARG G 344 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL G 352 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE G 415 " --> pdb=" O ALA G 427 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 242 through 246 removed outlier: 6.419A pdb=" N GLU H 243 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP H 356 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE H 245 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL H 211 " --> pdb=" O GLY H 407 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET H 409 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU H 213 " --> pdb=" O MET H 409 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE H 430 " --> pdb=" O GLN H 210 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE H 212 " --> pdb=" O ILE H 430 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 258 through 263 Processing sheet with id=AD6, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AD7, first strand: chain 'H' and resid 552 through 553 Processing sheet with id=AD8, first strand: chain 'I' and resid 242 through 246 removed outlier: 6.497A pdb=" N GLU I 243 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP I 356 " --> pdb=" O GLU I 243 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE I 245 " --> pdb=" O ASP I 356 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU I 353 " --> pdb=" O ILE I 406 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR I 408 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE I 355 " --> pdb=" O THR I 408 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASN I 410 " --> pdb=" O ILE I 355 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL I 211 " --> pdb=" O GLY I 407 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET I 409 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU I 213 " --> pdb=" O MET I 409 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 258 through 262 Processing sheet with id=AE1, first strand: chain 'I' and resid 388 through 389 Processing sheet with id=AE2, first strand: chain 'I' and resid 552 through 554 Processing sheet with id=AE3, first strand: chain 'J' and resid 242 through 246 removed outlier: 6.350A pdb=" N GLU J 243 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP J 356 " --> pdb=" O GLU J 243 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE J 245 " --> pdb=" O ASP J 356 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN J 210 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE J 430 " --> pdb=" O GLN J 210 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE J 212 " --> pdb=" O ILE J 430 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 258 through 263 removed outlier: 3.562A pdb=" N ARG J 263 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 271 " --> pdb=" O ARG J 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AE6, first strand: chain 'J' and resid 552 through 554 Processing sheet with id=AE7, first strand: chain 'K' and resid 242 through 244 removed outlier: 7.805A pdb=" N THR K 408 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE K 355 " --> pdb=" O THR K 408 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN K 410 " --> pdb=" O ILE K 355 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL K 211 " --> pdb=" O GLY K 407 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET K 409 " --> pdb=" O VAL K 211 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU K 213 " --> pdb=" O MET K 409 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 258 through 262 removed outlier: 3.757A pdb=" N VAL K 273 " --> pdb=" O ARG K 261 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 388 through 389 Processing sheet with id=AF1, first strand: chain 'K' and resid 552 through 554 Processing sheet with id=AF2, first strand: chain 'L' and resid 210 through 212 Processing sheet with id=AF3, first strand: chain 'L' and resid 258 through 263 removed outlier: 3.552A pdb=" N VAL L 273 " --> pdb=" O ARG L 261 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG L 271 " --> pdb=" O ARG L 263 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 388 through 389 Processing sheet with id=AF5, first strand: chain 'L' and resid 552 through 554 Processing sheet with id=AF6, first strand: chain 'M' and resid 211 through 214 removed outlier: 5.944A pdb=" N ILE M 212 " --> pdb=" O ILE M 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'M' and resid 245 through 246 removed outlier: 6.708A pdb=" N ILE M 245 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 258 through 260 Processing sheet with id=AF9, first strand: chain 'M' and resid 263 through 264 Processing sheet with id=AG1, first strand: chain 'M' and resid 388 through 389 Processing sheet with id=AG2, first strand: chain 'M' and resid 552 through 554 Processing sheet with id=AG3, first strand: chain 'N' and resid 6 through 10 removed outlier: 3.588A pdb=" N VAL N 83 " --> pdb=" O VAL N 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE N 294 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 14 through 16 Processing sheet with id=AG5, first strand: chain 'N' and resid 168 through 176 removed outlier: 3.841A pdb=" N LYS N 182 " --> pdb=" O GLU N 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 318 through 321 removed outlier: 3.622A pdb=" N TYR N 318 " --> pdb=" O ARG N 344 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL N 352 " --> pdb=" O VAL N 397 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE N 415 " --> pdb=" O ALA N 427 " (cutoff:3.500A) 1596 hydrogen bonds defined for protein. 4602 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: 17.88 Time building geometry restraints manager: 17.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7415 1.32 - 1.44: 12146 1.44 - 1.57: 26381 1.57 - 1.69: 52 1.69 - 1.81: 100 Bond restraints: 46094 Sorted by residual: bond pdb=" CA ALA D 417 " pdb=" CB ALA D 417 " ideal model delta sigma weight residual 1.535 1.469 0.066 1.93e-02 2.68e+03 1.16e+01 bond pdb=" CA ALA K 417 " pdb=" CB ALA K 417 " ideal model delta sigma weight residual 1.535 1.470 0.065 1.93e-02 2.68e+03 1.13e+01 bond pdb=" CA ALA K 422 " pdb=" CB ALA K 422 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.74e-02 3.30e+03 1.02e+01 bond pdb=" CA ALA D 422 " pdb=" CB ALA D 422 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.74e-02 3.30e+03 9.94e+00 bond pdb=" C LEU K 423 " pdb=" O LEU K 423 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.39e-02 5.18e+03 7.59e+00 ... (remaining 46089 not shown) Histogram of bond angle deviations from ideal: 100.02 - 107.22: 1492 107.22 - 114.42: 26324 114.42 - 121.62: 24319 121.62 - 128.82: 9891 128.82 - 136.02: 344 Bond angle restraints: 62370 Sorted by residual: angle pdb=" N ILE C 485 " pdb=" CA ILE C 485 " pdb=" C ILE C 485 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.50e+01 angle pdb=" N ILE J 485 " pdb=" CA ILE J 485 " pdb=" C ILE J 485 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.50e+01 angle pdb=" N LEU D 423 " pdb=" CA LEU D 423 " pdb=" C LEU D 423 " ideal model delta sigma weight residual 112.94 105.11 7.83 1.41e+00 5.03e-01 3.08e+01 angle pdb=" N LEU K 423 " pdb=" CA LEU K 423 " pdb=" C LEU K 423 " ideal model delta sigma weight residual 112.94 105.14 7.80 1.41e+00 5.03e-01 3.06e+01 angle pdb=" CA ALA K 417 " pdb=" C ALA K 417 " pdb=" O ALA K 417 " ideal model delta sigma weight residual 121.46 115.61 5.85 1.17e+00 7.31e-01 2.50e+01 ... (remaining 62365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 27110 35.75 - 71.51: 482 71.51 - 107.26: 48 107.26 - 143.02: 0 143.02 - 178.77: 2 Dihedral angle restraints: 27642 sinusoidal: 11486 harmonic: 16156 Sorted by residual: dihedral pdb=" O2B GDP F 701 " pdb=" O3A GDP F 701 " pdb=" PB GDP F 701 " pdb=" PA GDP F 701 " ideal model delta sinusoidal sigma weight residual 180.00 1.23 178.77 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2B GDP M 701 " pdb=" O3A GDP M 701 " pdb=" PB GDP M 701 " pdb=" PA GDP M 701 " ideal model delta sinusoidal sigma weight residual 180.00 1.28 178.72 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GSP E 701 " pdb=" O3A GSP E 701 " pdb=" PB GSP E 701 " pdb=" PA GSP E 701 " ideal model delta sinusoidal sigma weight residual 93.55 170.01 -76.46 1 2.00e+01 2.50e-03 1.84e+01 ... (remaining 27639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 6072 0.080 - 0.160: 680 0.160 - 0.240: 67 0.240 - 0.320: 23 0.320 - 0.400: 4 Chirality restraints: 6846 Sorted by residual: chirality pdb=" CA ILE K 416 " pdb=" N ILE K 416 " pdb=" C ILE K 416 " pdb=" CB ILE K 416 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA ILE D 416 " pdb=" N ILE D 416 " pdb=" C ILE D 416 " pdb=" CB ILE D 416 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA ASP D 420 " pdb=" N ASP D 420 " pdb=" C ASP D 420 " pdb=" CB ASP D 420 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 6843 not shown) Planarity restraints: 7814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 522 " -0.050 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO H 523 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 523 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 523 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 522 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO A 523 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 237 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO C 238 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " 0.034 5.00e-02 4.00e+02 ... (remaining 7811 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 811 2.67 - 3.23: 39510 3.23 - 3.79: 69275 3.79 - 4.34: 96067 4.34 - 4.90: 157280 Nonbonded interactions: 362943 Sorted by model distance: nonbonded pdb=" OG1 THR L 222 " pdb="MG MG L 702 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR E 222 " pdb="MG MG E 702 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR C 222 " pdb="MG MG C 702 " model vdw 2.131 2.170 nonbonded pdb=" OG1 THR J 222 " pdb="MG MG J 702 " model vdw 2.131 2.170 nonbonded pdb=" OG1 THR D 222 " pdb="MG MG D 702 " model vdw 2.143 2.170 ... (remaining 362938 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 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 through 300 or (resid 301 through 3 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 or (resid 320 through 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 342 or (resid 343 and (name N or name CA or nam \ e C or name O or name CB )) or resid 344 or (resid 345 and (name N or name CA or \ name C or name O or name CB )) or resid 346 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 and ( \ name N or name CA or name C or name O or name CB )) or resid 372 through 382 or \ (resid 383 and (name N or name CA or name C or name O or name CB )) or resid 384 \ through 394 or (resid 395 and (name N or name CA or name C or name O or name CB \ )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C or n \ ame O or name CB )) or resid 406 through 414 or (resid 415 through 423 and (name \ N or name CA or name C or name O or name CB )) or resid 424 through 439 or (res \ id 440 and (name N or name CA or name C or name O or name CB )) or resid 441 thr \ ough 442 or (resid 443 and (name N or name CA or name C or name O or name CB )) \ or resid 444 or (resid 445 through 446 and (name N or name CA or name C or name \ O or name CB )) or resid 447 through 450 or (resid 451 through 457 and (name N o \ r name CA or name C or name O or name CB )) or resid 458 through 459 or (resid 4 \ 60 through 462 and (name N or name CA or name C or name O or name CB )) or resid \ 463 through 493 or (resid 494 and (name N or name CA or name C or name O or nam \ e CB )) or resid 495 through 519 or (resid 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 through 544 or (resid 545 through 547 and ( \ name N or name CA or name C or name O or name CB )) or resid 548 or (resid 549 a \ nd (name N or name CA or name C or name O or name CB )) or resid 550 through 552 \ or (resid 553 and (name N or name CA or name C or name O or name CB )) or resid \ 554 through 555 or (resid 556 and (name N or name CA or name C or name O or nam \ e CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or name C \ or name O or name CB )) or resid 562 through 584 or resid 702)) selection = (chain 'B' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 or (resid 295 through 298 and (name \ N or name CA or name C or name O or name CB )) or resid 299 through 300 or (res \ id 301 through 302 and (name N or name CA or name C or name O or name CB )) or r \ esid 303 through 314 or (resid 315 and (name N or name CA or name C or name O or \ name CB )) or resid 316 or (resid 317 through 318 and (name N or name CA or nam \ e C or name O or name CB )) or resid 319 or (resid 320 through 321 and (name N o \ r name CA or name C or name O or name CB )) or resid 322 through 342 or (resid 3 \ 43 and (name N or name CA or name C or name O or name CB )) or resid 344 or (res \ id 345 and (name N or name CA or name C or name O or name CB )) or resid 346 thr \ ough 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) \ or resid 372 through 382 or (resid 383 and (name N or name CA or name C or name \ O or name CB )) or resid 384 through 394 or (resid 395 and (name N or name CA or \ name C or name O or name CB )) or resid 396 through 404 or (resid 405 and (name \ N or name CA or name C or name O or name CB )) or resid 406 through 414 or (res \ id 415 through 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 442 or (resid 443 and (name N or name CA or nam \ e C or name O or name CB )) or resid 444 or (resid 445 through 446 and (name N o \ r name CA or name C or name O or name CB )) or resid 447 through 450 or (resid 4 \ 51 through 457 and (name N or name CA or name C or name O or name CB )) or resid \ 458 through 459 or (resid 460 through 462 and (name N or name CA or name C or n \ ame O or name CB )) or resid 463 through 493 or (resid 494 and (name N or name C \ A or name C or name O or name CB )) or resid 495 through 519 or (resid 520 and ( \ name N or name CA or name C or name O or name CB )) or resid 521 through 544 or \ (resid 545 through 547 and (name N or name CA or name C or name O or name CB )) \ or resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 550 through 552 or (resid 553 and (name N or name CA or name C or n \ ame O or name CB )) or resid 554 through 555 or (resid 556 and (name N or name C \ A or name C or name O or name CB )) or resid 557 through 560 or (resid 561 and ( \ name N or name CA or name C or name O or name CB )) or resid 562 through 563 or \ (resid 564 through 565 and (name N or name CA or name C or name O or name CB )) \ or resid 566 through 571 or (resid 572 and (name N or name CA or name C or name \ O or name CB )) or resid 573 through 584 or resid 702)) selection = (chain 'C' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 242 or (resid 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 253 or (res \ id 254 through 255 and (name N or name CA or name C or name O or name CB )) or r \ esid 256 through 264 or (resid 265 through 271 and (name N or name CA or name C \ or name O or name CB )) or resid 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 300 or (res \ id 301 through 302 and (name N or name CA or name C or name O or name CB )) or r \ esid 303 through 316 or (resid 317 through 318 and (name N or name CA or name C \ or name O or name CB )) or resid 319 through 368 or (resid 369 and (name N or na \ me CA or name C or name O or name CB )) or resid 370 or (resid 371 and (name N o \ r name CA or name C or name O or name CB )) or resid 372 through 382 or (resid 3 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 384 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or r \ esid 396 through 404 or (resid 405 and (name N or name CA or name C or name O or \ name CB )) or resid 406 through 414 or (resid 415 through 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 439 or (resid 440 a \ nd (name N or name CA or name C or name O or name CB )) or resid 441 through 444 \ or (resid 445 through 446 and (name N or name CA or name C or name O or name CB \ )) or resid 447 through 448 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 or (resid 451 through 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 459 or (resid 460 throu \ gh 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) \ or resid 495 through 545 or (resid 546 through 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 or (resid 549 and (name N or name CA or \ name C or name O or name CB )) or resid 550 through 552 or (resid 553 and (name \ N or name CA or name C or name O or name CB )) or resid 554 through 555 or (res \ id 556 and (name N or name CA or name C or name O or name CB )) or resid 557 thr \ ough 560 or (resid 561 and (name N or name CA or name C or name O or name CB )) \ or resid 562 through 563 or (resid 564 through 565 and (name N or name CA or nam \ e C or name O or name CB )) or resid 566 through 571 or (resid 572 and (name N o \ r name CA or name C or name O or name CB )) or resid 573 through 584 or resid 70 \ 2)) selection = (chain 'D' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 through 301 or (resid 302 and (name \ N or name CA or name C or name O or name CB )) or resid 303 through 314 or (res \ id 315 and (name N or name CA or name C or name O or name CB )) or resid 316 or \ (resid 317 through 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 342 or (resid 343 and (name N or name CA or \ name C or name O or name CB )) or resid 344 or (resid 345 and (name N or name C \ A or name C or name O or name CB )) or resid 346 through 368 or (resid 369 and ( \ name N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 a \ nd (name N or name CA or name C or name O or name CB )) or resid 372 through 382 \ or (resid 383 and (name N or name CA or name C or name O or name CB )) or resid \ 384 through 394 or (resid 395 and (name N or name CA or name C or name O or nam \ e CB )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 414 or (resid 415 through 423 and ( \ name N or name CA or name C or name O or name CB )) or resid 424 through 439 or \ (resid 440 and (name N or name CA or name C or name O or name CB )) or resid 441 \ through 442 or (resid 443 and (name N or name CA or name C or name O or name CB \ )) or resid 444 or (resid 445 through 446 and (name N or name CA or name C or n \ ame O or name CB )) or resid 447 through 450 or (resid 451 through 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 through 459 or (res \ id 460 through 462 and (name N or name CA or name C or name O or name CB )) or r \ esid 463 through 493 or (resid 494 and (name N or name CA or name C or name O or \ name CB )) or resid 495 through 519 or (resid 520 and (name N or name CA or nam \ e C or name O or name CB )) or resid 521 through 544 or (resid 545 through 547 a \ nd (name N or name CA or name C or name O or name CB )) or resid 548 or (resid 5 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) or r \ esid 557 through 563 or (resid 564 through 565 and (name N or name CA or name C \ or name O or name CB )) or resid 566 through 571 or (resid 572 and (name N or na \ me CA or name C or name O or name CB )) or resid 573 through 584 or resid 702)) selection = (chain 'E' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 262 or (resid 263 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 or (res \ id 273 and (name N or name CA or name C or name O or name CB )) or resid 274 or \ (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 276 \ through 292 or (resid 293 and (name N or name CA or name C or name O or name CB \ )) or resid 294 or (resid 295 through 298 and (name N or name CA or name C or n \ ame O or name CB )) or resid 299 through 300 or (resid 301 through 302 and (name \ N or name CA or name C or name O or name CB )) or resid 303 through 314 or (res \ id 315 and (name N or name CA or name C or name O or name CB )) or resid 316 or \ (resid 317 through 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 342 or (resid 343 and (name N or name CA or \ name C or name O or name CB )) or resid 344 or (resid 345 and (name N or name C \ A or name C or name O or name CB )) or resid 346 through 368 or (resid 369 and ( \ name N or name CA or name C or name O or name CB )) or resid 370 through 404 or \ (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 through 423 and (name N or name CA or name C or name \ O or name CB )) or resid 424 through 442 or (resid 443 and (name N or name CA or \ name C or name O or name CB )) or resid 444 or (resid 445 through 446 and (name \ N or name CA or name C or name O or name CB )) or resid 447 through 452 or (res \ id 453 through 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 459 or (resid 460 through 462 and (name N or name CA or name C \ or name O or name CB )) or resid 463 through 519 or (resid 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 555 or (resid 556 a \ nd (name N or name CA or name C or name O or name CB )) or resid 557 through 563 \ or (resid 564 through 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 584 or resid 702)) selection = (chain 'F' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 297 or (resid 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 300 or (resid 301 through 302 and ( \ name N or name CA or name C or name O or name CB )) or resid 303 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ or (resid 317 through 318 and (name N or name CA or name C or name O or name CB \ )) or resid 319 or (resid 320 through 321 and (name N or name CA or name C or n \ ame O or name CB )) or resid 322 through 342 or (resid 343 and (name N or name C \ A or name C or name O or name CB )) or resid 344 or (resid 345 and (name N or na \ me CA or name C or name O or name CB )) or resid 346 through 368 or (resid 369 a \ nd (name N or name CA or name C or name O or name CB )) or resid 370 or (resid 3 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 372 through \ 382 or (resid 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 through 394 or (resid 395 and (name N or name CA or name C or name O or \ name CB )) or resid 396 through 417 or (resid 418 through 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 439 or (resid 440 a \ nd (name N or name CA or name C or name O or name CB )) or resid 441 through 442 \ or (resid 443 and (name N or name CA or name C or name O or name CB )) or resid \ 444 through 445 or (resid 446 and (name N or name CA or name C or name O or nam \ e CB )) or resid 447 through 450 or (resid 451 through 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 460 or (resid 461 throu \ gh 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) \ or resid 495 through 519 or (resid 520 and (name N or name CA or name C or name \ O or name CB )) or resid 521 through 546 or (resid 547 and (name N or name CA or \ name C or name O or name CB )) or resid 548 or (resid 549 and (name N or name C \ A or name C or name O or name CB )) or resid 550 through 552 or (resid 553 and ( \ name N or name CA or name C or name O or name CB )) or resid 554 through 560 or \ (resid 561 and (name N or name CA or name C or name O or name CB )) or resid 562 \ through 563 or (resid 564 through 565 and (name N or name CA or name C or name \ O or name CB )) or resid 566 through 584 or resid 702)) selection = (chain 'H' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 through 300 or (resid 301 through 3 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 or (resid 320 through 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 342 or (resid 343 and (name N or name CA or nam \ e C or name O or name CB )) or resid 344 or (resid 345 and (name N or name CA or \ name C or name O or name CB )) or resid 346 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 and ( \ name N or name CA or name C or name O or name CB )) or resid 372 through 382 or \ (resid 383 and (name N or name CA or name C or name O or name CB )) or resid 384 \ through 394 or (resid 395 and (name N or name CA or name C or name O or name CB \ )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C or n \ ame O or name CB )) or resid 406 through 414 or (resid 415 through 423 and (name \ N or name CA or name C or name O or name CB )) or resid 424 through 439 or (res \ id 440 and (name N or name CA or name C or name O or name CB )) or resid 441 thr \ ough 442 or (resid 443 and (name N or name CA or name C or name O or name CB )) \ or resid 444 or (resid 445 through 446 and (name N or name CA or name C or name \ O or name CB )) or resid 447 through 450 or (resid 451 through 457 and (name N o \ r name CA or name C or name O or name CB )) or resid 458 through 459 or (resid 4 \ 60 through 462 and (name N or name CA or name C or name O or name CB )) or resid \ 463 through 493 or (resid 494 and (name N or name CA or name C or name O or nam \ e CB )) or resid 495 through 519 or (resid 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 through 544 or (resid 545 through 547 and ( \ name N or name CA or name C or name O or name CB )) or resid 548 or (resid 549 a \ nd (name N or name CA or name C or name O or name CB )) or resid 550 through 552 \ or (resid 553 and (name N or name CA or name C or name O or name CB )) or resid \ 554 through 555 or (resid 556 and (name N or name CA or name C or name O or nam \ e CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or name C \ or name O or name CB )) or resid 562 through 584 or resid 702)) selection = (chain 'I' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 or (resid 295 through 298 and (name \ N or name CA or name C or name O or name CB )) or resid 299 through 300 or (res \ id 301 through 302 and (name N or name CA or name C or name O or name CB )) or r \ esid 303 through 314 or (resid 315 and (name N or name CA or name C or name O or \ name CB )) or resid 316 or (resid 317 through 318 and (name N or name CA or nam \ e C or name O or name CB )) or resid 319 or (resid 320 through 321 and (name N o \ r name CA or name C or name O or name CB )) or resid 322 through 342 or (resid 3 \ 43 and (name N or name CA or name C or name O or name CB )) or resid 344 or (res \ id 345 and (name N or name CA or name C or name O or name CB )) or resid 346 thr \ ough 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) \ or resid 372 through 382 or (resid 383 and (name N or name CA or name C or name \ O or name CB )) or resid 384 through 394 or (resid 395 and (name N or name CA or \ name C or name O or name CB )) or resid 396 through 404 or (resid 405 and (name \ N or name CA or name C or name O or name CB )) or resid 406 through 414 or (res \ id 415 through 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 442 or (resid 443 and (name N or name CA or nam \ e C or name O or name CB )) or resid 444 or (resid 445 through 446 and (name N o \ r name CA or name C or name O or name CB )) or resid 447 through 450 or (resid 4 \ 51 through 457 and (name N or name CA or name C or name O or name CB )) or resid \ 458 through 459 or (resid 460 through 462 and (name N or name CA or name C or n \ ame O or name CB )) or resid 463 through 493 or (resid 494 and (name N or name C \ A or name C or name O or name CB )) or resid 495 through 519 or (resid 520 and ( \ name N or name CA or name C or name O or name CB )) or resid 521 through 544 or \ (resid 545 through 547 and (name N or name CA or name C or name O or name CB )) \ or resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 550 through 552 or (resid 553 and (name N or name CA or name C or n \ ame O or name CB )) or resid 554 through 555 or (resid 556 and (name N or name C \ A or name C or name O or name CB )) or resid 557 through 560 or (resid 561 and ( \ name N or name CA or name C or name O or name CB )) or resid 562 through 563 or \ (resid 564 through 565 and (name N or name CA or name C or name O or name CB )) \ or resid 566 through 571 or (resid 572 and (name N or name CA or name C or name \ O or name CB )) or resid 573 through 584 or resid 702)) selection = (chain 'J' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 242 or (resid 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 253 or (res \ id 254 through 255 and (name N or name CA or name C or name O or name CB )) or r \ esid 256 through 264 or (resid 265 through 271 and (name N or name CA or name C \ or name O or name CB )) or resid 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 300 or (res \ id 301 through 302 and (name N or name CA or name C or name O or name CB )) or r \ esid 303 through 316 or (resid 317 through 318 and (name N or name CA or name C \ or name O or name CB )) or resid 319 through 368 or (resid 369 and (name N or na \ me CA or name C or name O or name CB )) or resid 370 or (resid 371 and (name N o \ r name CA or name C or name O or name CB )) or resid 372 through 382 or (resid 3 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 384 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or r \ esid 396 through 404 or (resid 405 and (name N or name CA or name C or name O or \ name CB )) or resid 406 through 414 or (resid 415 through 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 439 or (resid 440 a \ nd (name N or name CA or name C or name O or name CB )) or resid 441 through 444 \ or (resid 445 through 446 and (name N or name CA or name C or name O or name CB \ )) or resid 447 through 448 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 or (resid 451 through 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 459 or (resid 460 throu \ gh 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) \ or resid 495 through 545 or (resid 546 through 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 or (resid 549 and (name N or name CA or \ name C or name O or name CB )) or resid 550 through 552 or (resid 553 and (name \ N or name CA or name C or name O or name CB )) or resid 554 through 555 or (res \ id 556 and (name N or name CA or name C or name O or name CB )) or resid 557 thr \ ough 560 or (resid 561 and (name N or name CA or name C or name O or name CB )) \ or resid 562 through 563 or (resid 564 through 565 and (name N or name CA or nam \ e C or name O or name CB )) or resid 566 through 571 or (resid 572 and (name N o \ r name CA or name C or name O or name CB )) or resid 573 through 584 or resid 70 \ 2)) selection = (chain 'K' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name \ O or name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or \ name C or name O or name CB )) or resid 294 through 301 or (resid 302 and (name \ N or name CA or name C or name O or name CB )) or resid 303 through 314 or (res \ id 315 and (name N or name CA or name C or name O or name CB )) or resid 316 or \ (resid 317 through 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 342 or (resid 343 and (name N or name CA or \ name C or name O or name CB )) or resid 344 or (resid 345 and (name N or name C \ A or name C or name O or name CB )) or resid 346 through 368 or (resid 369 and ( \ name N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 a \ nd (name N or name CA or name C or name O or name CB )) or resid 372 through 382 \ or (resid 383 and (name N or name CA or name C or name O or name CB )) or resid \ 384 through 394 or (resid 395 and (name N or name CA or name C or name O or nam \ e CB )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 414 or (resid 415 through 423 and ( \ name N or name CA or name C or name O or name CB )) or resid 424 through 439 or \ (resid 440 and (name N or name CA or name C or name O or name CB )) or resid 441 \ through 442 or (resid 443 and (name N or name CA or name C or name O or name CB \ )) or resid 444 or (resid 445 through 446 and (name N or name CA or name C or n \ ame O or name CB )) or resid 447 through 450 or (resid 451 through 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 through 459 or (res \ id 460 through 462 and (name N or name CA or name C or name O or name CB )) or r \ esid 463 through 493 or (resid 494 and (name N or name CA or name C or name O or \ name CB )) or resid 495 through 519 or (resid 520 and (name N or name CA or nam \ e C or name O or name CB )) or resid 521 through 544 or (resid 545 through 547 a \ nd (name N or name CA or name C or name O or name CB )) or resid 548 or (resid 5 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) or r \ esid 557 through 563 or (resid 564 through 565 and (name N or name CA or name C \ or name O or name CB )) or resid 566 through 571 or (resid 572 and (name N or na \ me CA or name C or name O or name CB )) or resid 573 through 584 or resid 702)) selection = (chain 'L' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 262 or (resid 263 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 or (res \ id 273 and (name N or name CA or name C or name O or name CB )) or resid 274 or \ (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 276 \ through 292 or (resid 293 and (name N or name CA or name C or name O or name CB \ )) or resid 294 or (resid 295 through 298 and (name N or name CA or name C or n \ ame O or name CB )) or resid 299 through 300 or (resid 301 through 302 and (name \ N or name CA or name C or name O or name CB )) or resid 303 through 314 or (res \ id 315 and (name N or name CA or name C or name O or name CB )) or resid 316 or \ (resid 317 through 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 342 or (resid 343 and (name N or name CA or \ name C or name O or name CB )) or resid 344 or (resid 345 and (name N or name C \ A or name C or name O or name CB )) or resid 346 through 368 or (resid 369 and ( \ name N or name CA or name C or name O or name CB )) or resid 370 through 404 or \ (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 through 423 and (name N or name CA or name C or name \ O or name CB )) or resid 424 through 442 or (resid 443 and (name N or name CA or \ name C or name O or name CB )) or resid 444 or (resid 445 through 446 and (name \ N or name CA or name C or name O or name CB )) or resid 447 through 452 or (res \ id 453 through 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 459 or (resid 460 through 462 and (name N or name CA or name C \ or name O or name CB )) or resid 463 through 519 or (resid 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 555 or (resid 556 a \ nd (name N or name CA or name C or name O or name CB )) or resid 557 through 563 \ or (resid 564 through 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 584 or resid 702)) selection = (chain 'M' and ((resid 195 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 253 or (resid 254 through 2 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 256 through \ 262 or (resid 263 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 297 or (resid 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 300 or (resid 301 through 302 and ( \ name N or name CA or name C or name O or name CB )) or resid 303 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ or (resid 317 through 318 and (name N or name CA or name C or name O or name CB \ )) or resid 319 or (resid 320 through 321 and (name N or name CA or name C or n \ ame O or name CB )) or resid 322 through 342 or (resid 343 and (name N or name C \ A or name C or name O or name CB )) or resid 344 or (resid 345 and (name N or na \ me CA or name C or name O or name CB )) or resid 346 through 368 or (resid 369 a \ nd (name N or name CA or name C or name O or name CB )) or resid 370 or (resid 3 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 372 through \ 382 or (resid 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 through 394 or (resid 395 and (name N or name CA or name C or name O or \ name CB )) or resid 396 through 417 or (resid 418 through 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 439 or (resid 440 a \ nd (name N or name CA or name C or name O or name CB )) or resid 441 through 442 \ or (resid 443 and (name N or name CA or name C or name O or name CB )) or resid \ 444 through 445 or (resid 446 and (name N or name CA or name C or name O or nam \ e CB )) or resid 447 through 450 or (resid 451 through 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 460 or (resid 461 throu \ gh 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) \ or resid 495 through 519 or (resid 520 and (name N or name CA or name C or name \ O or name CB )) or resid 521 through 546 or (resid 547 and (name N or name CA or \ name C or name O or name CB )) or resid 548 or (resid 549 and (name N or name C \ A or name C or name O or name CB )) or resid 550 through 552 or (resid 553 and ( \ name N or name CA or name C or name O or name CB )) or resid 554 through 560 or \ (resid 561 and (name N or name CA or name C or name O or name CB )) or resid 562 \ through 563 or (resid 564 through 565 and (name N or name CA or name C or name \ O or name CB )) or resid 566 through 584 or resid 702)) } ncs_group { reference = chain 'G' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.080 Extract box with map and model: 6.330 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 111.080 Find NCS groups from input model: 3.930 Set up NCS constraints: 0.190 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 : 0.005 0.066 46094 Z= 0.291 Angle : 0.842 10.412 62370 Z= 0.465 Chirality : 0.055 0.400 6846 Planarity : 0.006 0.075 7814 Dihedral : 14.740 178.770 17254 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.44 % Allowed : 6.46 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.22 (0.08), residues: 5478 helix: -4.58 (0.04), residues: 2284 sheet: -2.80 (0.20), residues: 510 loop : -2.45 (0.10), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 538 HIS 0.007 0.001 HIS M 515 PHE 0.019 0.002 PHE G 294 TYR 0.018 0.002 TYR B 251 ARG 0.014 0.001 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1442 time to evaluate : 5.355 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 ASN cc_start: 0.8968 (t0) cc_final: 0.8615 (t0) REVERT: B 421 VAL cc_start: 0.8102 (t) cc_final: 0.7450 (t) REVERT: C 250 SER cc_start: 0.8221 (p) cc_final: 0.7909 (t) REVERT: C 439 LEU cc_start: 0.4985 (mt) cc_final: 0.4758 (mt) REVERT: C 513 LEU cc_start: 0.9148 (tp) cc_final: 0.8808 (tt) REVERT: C 574 ASP cc_start: 0.5577 (t70) cc_final: 0.5188 (t70) REVERT: D 359 ASN cc_start: 0.8964 (p0) cc_final: 0.8347 (p0) REVERT: D 364 SER cc_start: 0.8545 (m) cc_final: 0.7650 (t) REVERT: D 371 ILE cc_start: 0.7942 (tp) cc_final: 0.7531 (tp) REVERT: D 486 ASN cc_start: 0.7536 (m-40) cc_final: 0.7248 (m-40) REVERT: D 497 HIS cc_start: 0.6553 (m170) cc_final: 0.6151 (m170) REVERT: D 522 LEU cc_start: 0.8150 (tp) cc_final: 0.7938 (tp) REVERT: E 248 HIS cc_start: 0.9040 (p-80) cc_final: 0.8740 (p90) REVERT: E 363 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8218 (mm) REVERT: E 364 SER cc_start: 0.8493 (m) cc_final: 0.8172 (p) REVERT: E 370 LEU cc_start: 0.8907 (mp) cc_final: 0.8633 (mm) REVERT: G 65 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7679 (t) REVERT: G 196 LEU cc_start: 0.8384 (tp) cc_final: 0.7252 (tp) REVERT: G 197 ASN cc_start: 0.8317 (p0) cc_final: 0.7837 (p0) REVERT: G 205 GLU cc_start: 0.7550 (pt0) cc_final: 0.7331 (pt0) REVERT: G 207 ILE cc_start: 0.9168 (pt) cc_final: 0.8878 (pt) REVERT: G 208 GLU cc_start: 0.7283 (mp0) cc_final: 0.7001 (mp0) REVERT: I 410 ASN cc_start: 0.8979 (t0) cc_final: 0.8591 (t0) REVERT: I 421 VAL cc_start: 0.8117 (t) cc_final: 0.7465 (t) REVERT: J 250 SER cc_start: 0.8229 (p) cc_final: 0.7900 (t) REVERT: J 513 LEU cc_start: 0.9176 (tp) cc_final: 0.8841 (tt) REVERT: J 574 ASP cc_start: 0.5579 (t70) cc_final: 0.5168 (t70) REVERT: K 359 ASN cc_start: 0.8967 (p0) cc_final: 0.8349 (p0) REVERT: K 364 SER cc_start: 0.8589 (m) cc_final: 0.7597 (t) REVERT: K 371 ILE cc_start: 0.7907 (tp) cc_final: 0.7700 (tp) REVERT: K 486 ASN cc_start: 0.7548 (m-40) cc_final: 0.7285 (m-40) REVERT: K 497 HIS cc_start: 0.6552 (m170) cc_final: 0.6141 (m170) REVERT: K 522 LEU cc_start: 0.8169 (tp) cc_final: 0.7969 (tp) REVERT: K 530 TYR cc_start: 0.7332 (t80) cc_final: 0.7056 (t80) REVERT: L 248 HIS cc_start: 0.9049 (p-80) cc_final: 0.8723 (p90) REVERT: L 363 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8190 (mm) REVERT: L 364 SER cc_start: 0.8471 (m) cc_final: 0.8165 (p) REVERT: L 370 LEU cc_start: 0.8899 (mp) cc_final: 0.8607 (mm) REVERT: L 374 LEU cc_start: 0.8134 (mt) cc_final: 0.7921 (mt) REVERT: N 65 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7598 (t) REVERT: N 196 LEU cc_start: 0.8383 (tp) cc_final: 0.7245 (tp) REVERT: N 197 ASN cc_start: 0.8310 (p0) cc_final: 0.7838 (p0) REVERT: N 199 PHE cc_start: 0.8572 (m-80) cc_final: 0.8291 (m-10) REVERT: N 205 GLU cc_start: 0.7534 (pt0) cc_final: 0.7297 (pt0) REVERT: N 207 ILE cc_start: 0.9166 (pt) cc_final: 0.8880 (pt) REVERT: N 208 GLU cc_start: 0.7278 (mp0) cc_final: 0.6966 (mp0) outliers start: 20 outliers final: 0 residues processed: 1454 average time/residue: 0.6085 time to fit residues: 1426.6951 Evaluate side-chains 638 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 634 time to evaluate : 5.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 464 optimal weight: 1.9990 chunk 416 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 431 optimal weight: 0.0270 chunk 166 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 499 optimal weight: 6.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 541 ASN A 549 ASN B 248 HIS B 443 ASN B 515 HIS B 541 ASN C 385 GLN C 465 ASN C 475 ASN D 266 ASN D 384 ASN D 443 ASN E 249 GLN E 266 ASN E 346 ASN ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS F 266 ASN F 443 ASN F 461 ASN F 465 ASN F 541 ASN F 549 ASN G 162 GLN H 248 HIS H 541 ASN H 549 ASN I 248 HIS I 443 ASN I 515 HIS I 541 ASN J 385 GLN J 465 ASN J 475 ASN J 497 HIS K 248 HIS K 266 ASN K 384 ASN K 443 ASN L 234 ASN L 249 GLN L 266 ASN L 346 ASN L 385 GLN ** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS M 266 ASN M 443 ASN M 461 ASN M 465 ASN M 541 ASN M 549 ASN M 567 GLN N 137 GLN N 162 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 46094 Z= 0.309 Angle : 0.694 9.602 62370 Z= 0.356 Chirality : 0.045 0.216 6846 Planarity : 0.005 0.053 7814 Dihedral : 6.881 176.824 6270 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.10), residues: 5478 helix: -2.07 (0.09), residues: 2338 sheet: -2.26 (0.18), residues: 654 loop : -1.91 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 533 HIS 0.009 0.002 HIS I 515 PHE 0.028 0.002 PHE M 429 TYR 0.027 0.002 TYR E 530 ARG 0.009 0.001 ARG F 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 714 time to evaluate : 5.422 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: C 210 GLN cc_start: 0.7360 (pm20) cc_final: 0.7041 (pm20) REVERT: C 513 LEU cc_start: 0.9321 (tp) cc_final: 0.8964 (tt) REVERT: C 522 LEU cc_start: 0.8118 (mm) cc_final: 0.7902 (tp) REVERT: D 364 SER cc_start: 0.8782 (m) cc_final: 0.7965 (t) REVERT: D 497 HIS cc_start: 0.7073 (m170) cc_final: 0.6815 (m-70) REVERT: E 302 ASP cc_start: 0.6505 (p0) cc_final: 0.6263 (p0) REVERT: E 364 SER cc_start: 0.8964 (m) cc_final: 0.8492 (p) REVERT: E 370 LEU cc_start: 0.8966 (mp) cc_final: 0.8759 (mm) REVERT: G 152 LEU cc_start: 0.9345 (mt) cc_final: 0.8959 (mt) REVERT: G 196 LEU cc_start: 0.8050 (tp) cc_final: 0.7731 (tp) REVERT: G 206 LEU cc_start: 0.8557 (pt) cc_final: 0.7363 (pt) REVERT: J 210 GLN cc_start: 0.7524 (pm20) cc_final: 0.7170 (pm20) REVERT: J 513 LEU cc_start: 0.9305 (tp) cc_final: 0.8949 (tt) REVERT: K 252 SER cc_start: 0.8217 (t) cc_final: 0.7958 (t) REVERT: K 364 SER cc_start: 0.8747 (m) cc_final: 0.7939 (t) REVERT: K 497 HIS cc_start: 0.7063 (m170) cc_final: 0.6783 (m-70) REVERT: L 203 MET cc_start: 0.6372 (tmm) cc_final: 0.6161 (tmm) REVERT: L 302 ASP cc_start: 0.6500 (p0) cc_final: 0.6273 (p0) REVERT: L 364 SER cc_start: 0.9023 (m) cc_final: 0.8599 (p) REVERT: L 527 GLU cc_start: 0.7820 (tt0) cc_final: 0.7498 (tm-30) REVERT: N 152 LEU cc_start: 0.9335 (mt) cc_final: 0.8934 (mt) REVERT: N 157 LEU cc_start: 0.9191 (tp) cc_final: 0.8942 (tp) REVERT: N 196 LEU cc_start: 0.7986 (tp) cc_final: 0.7649 (tp) REVERT: N 207 ILE cc_start: 0.8946 (pt) cc_final: 0.8739 (pt) outliers start: 6 outliers final: 0 residues processed: 718 average time/residue: 0.5422 time to fit residues: 653.2674 Evaluate side-chains 422 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 5.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 277 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 415 optimal weight: 0.8980 chunk 340 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 500 optimal weight: 4.9990 chunk 540 optimal weight: 7.9990 chunk 445 optimal weight: 0.9980 chunk 496 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN C 248 HIS ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 248 HIS E 234 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS G 260 HIS G 372 GLN J 248 HIS ** J 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 486 ASN ** M 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS N 372 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 46094 Z= 0.205 Angle : 0.595 8.136 62370 Z= 0.301 Chirality : 0.043 0.206 6846 Planarity : 0.004 0.050 7814 Dihedral : 6.474 179.284 6270 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.11 % Allowed : 4.50 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 5478 helix: -0.94 (0.10), residues: 2352 sheet: -1.97 (0.20), residues: 588 loop : -1.57 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 538 HIS 0.011 0.001 HIS M 497 PHE 0.027 0.002 PHE J 429 TYR 0.025 0.001 TYR L 530 ARG 0.018 0.000 ARG L 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 615 time to evaluate : 5.284 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: A 203 MET cc_start: 0.6917 (ppp) cc_final: 0.6625 (ppp) REVERT: A 419 LEU cc_start: 0.7775 (mm) cc_final: 0.7301 (mm) REVERT: C 513 LEU cc_start: 0.9131 (tp) cc_final: 0.8840 (tt) REVERT: D 364 SER cc_start: 0.8544 (m) cc_final: 0.8083 (t) REVERT: D 410 ASN cc_start: 0.9131 (t0) cc_final: 0.8538 (t0) REVERT: E 370 LEU cc_start: 0.9064 (mp) cc_final: 0.8789 (mm) REVERT: F 250 SER cc_start: 0.8783 (p) cc_final: 0.8508 (p) REVERT: F 489 ILE cc_start: 0.7853 (mm) cc_final: 0.7644 (mm) REVERT: F 580 LEU cc_start: 0.7838 (mt) cc_final: 0.7637 (tp) REVERT: G 152 LEU cc_start: 0.9318 (mt) cc_final: 0.8860 (mt) REVERT: G 157 LEU cc_start: 0.9033 (tp) cc_final: 0.8727 (tp) REVERT: G 196 LEU cc_start: 0.8155 (tp) cc_final: 0.7666 (tp) REVERT: G 207 ILE cc_start: 0.9086 (pt) cc_final: 0.8792 (pt) REVERT: G 213 ASN cc_start: 0.8897 (m-40) cc_final: 0.8671 (t0) REVERT: G 240 MET cc_start: 0.8385 (tpp) cc_final: 0.7975 (mmm) REVERT: H 419 LEU cc_start: 0.7721 (mm) cc_final: 0.7383 (mm) REVERT: I 364 SER cc_start: 0.8078 (m) cc_final: 0.7804 (m) REVERT: J 366 ILE cc_start: 0.7958 (mm) cc_final: 0.7752 (mm) REVERT: K 364 SER cc_start: 0.8527 (m) cc_final: 0.8098 (t) REVERT: K 410 ASN cc_start: 0.9123 (t0) cc_final: 0.8474 (t0) REVERT: L 526 MET cc_start: 0.7637 (mtm) cc_final: 0.7296 (mtm) REVERT: L 527 GLU cc_start: 0.7652 (tt0) cc_final: 0.7372 (tm-30) REVERT: M 489 ILE cc_start: 0.7993 (mm) cc_final: 0.7784 (mm) REVERT: M 580 LEU cc_start: 0.7910 (mt) cc_final: 0.7668 (tp) REVERT: N 152 LEU cc_start: 0.9322 (mt) cc_final: 0.8846 (mt) REVERT: N 196 LEU cc_start: 0.8117 (tp) cc_final: 0.7669 (tp) REVERT: N 199 PHE cc_start: 0.8479 (m-80) cc_final: 0.8260 (m-10) REVERT: N 207 ILE cc_start: 0.8893 (pt) cc_final: 0.8616 (pt) REVERT: N 213 ASN cc_start: 0.8906 (m-40) cc_final: 0.8641 (t0) outliers start: 5 outliers final: 0 residues processed: 617 average time/residue: 0.5007 time to fit residues: 531.0209 Evaluate side-chains 401 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 5.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 494 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 238 optimal weight: 1.9990 chunk 335 optimal weight: 10.0000 chunk 502 optimal weight: 10.0000 chunk 531 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 475 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN C 561 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN E 486 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 260 HIS I 461 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 443 ASN L 475 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 255 HIS N 260 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 46094 Z= 0.197 Angle : 0.577 11.029 62370 Z= 0.288 Chirality : 0.043 0.268 6846 Planarity : 0.004 0.050 7814 Dihedral : 6.264 178.527 6270 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5478 helix: -0.37 (0.11), residues: 2350 sheet: -1.90 (0.20), residues: 624 loop : -1.32 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 538 HIS 0.006 0.001 HIS B 515 PHE 0.030 0.001 PHE D 429 TYR 0.021 0.001 TYR L 530 ARG 0.007 0.000 ARG E 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 574 time to evaluate : 6.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 364 SER cc_start: 0.8217 (m) cc_final: 0.7962 (m) REVERT: C 513 LEU cc_start: 0.9170 (tp) cc_final: 0.8788 (tt) REVERT: C 533 TRP cc_start: 0.8241 (m100) cc_final: 0.8014 (m100) REVERT: D 252 SER cc_start: 0.8306 (t) cc_final: 0.8101 (t) REVERT: D 364 SER cc_start: 0.8536 (m) cc_final: 0.8098 (t) REVERT: D 410 ASN cc_start: 0.9143 (t0) cc_final: 0.8433 (t0) REVERT: E 363 ILE cc_start: 0.8926 (mp) cc_final: 0.8701 (tp) REVERT: E 374 LEU cc_start: 0.8181 (mt) cc_final: 0.7971 (mt) REVERT: E 403 LEU cc_start: 0.7839 (tp) cc_final: 0.7618 (tt) REVERT: E 512 ASP cc_start: 0.7547 (t0) cc_final: 0.7285 (t70) REVERT: E 526 MET cc_start: 0.7741 (mtm) cc_final: 0.7486 (mtm) REVERT: F 489 ILE cc_start: 0.7902 (mm) cc_final: 0.7643 (mm) REVERT: G 119 MET cc_start: 0.8105 (tmm) cc_final: 0.7732 (tmm) REVERT: G 152 LEU cc_start: 0.9270 (mt) cc_final: 0.8854 (mt) REVERT: G 157 LEU cc_start: 0.9047 (tp) cc_final: 0.8797 (tp) REVERT: G 196 LEU cc_start: 0.8303 (tp) cc_final: 0.7739 (tp) REVERT: G 197 ASN cc_start: 0.8243 (p0) cc_final: 0.7884 (p0) REVERT: G 207 ILE cc_start: 0.9085 (pt) cc_final: 0.8773 (pt) REVERT: H 203 MET cc_start: 0.7866 (ppp) cc_final: 0.7234 (ppp) REVERT: H 576 PHE cc_start: 0.4687 (t80) cc_final: 0.4456 (t80) REVERT: K 364 SER cc_start: 0.8516 (m) cc_final: 0.8099 (t) REVERT: K 410 ASN cc_start: 0.9177 (t0) cc_final: 0.8411 (t0) REVERT: L 512 ASP cc_start: 0.7562 (t0) cc_final: 0.7328 (t70) REVERT: M 489 ILE cc_start: 0.7944 (mm) cc_final: 0.7727 (mm) REVERT: M 580 LEU cc_start: 0.7911 (mt) cc_final: 0.7700 (tp) REVERT: N 119 MET cc_start: 0.8059 (tmm) cc_final: 0.7667 (tmm) REVERT: N 152 LEU cc_start: 0.9276 (mt) cc_final: 0.8875 (mt) REVERT: N 196 LEU cc_start: 0.8256 (tp) cc_final: 0.7756 (tp) REVERT: N 197 ASN cc_start: 0.8247 (p0) cc_final: 0.7907 (p0) REVERT: N 207 ILE cc_start: 0.8900 (pt) cc_final: 0.8634 (pt) outliers start: 3 outliers final: 1 residues processed: 575 average time/residue: 0.4779 time to fit residues: 479.7527 Evaluate side-chains 378 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 442 optimal weight: 8.9990 chunk 301 optimal weight: 0.1980 chunk 7 optimal weight: 10.0000 chunk 395 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 453 optimal weight: 6.9990 chunk 367 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 477 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 531 ASN D 266 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 531 ASN J 561 ASN K 266 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 46094 Z= 0.301 Angle : 0.650 12.879 62370 Z= 0.327 Chirality : 0.044 0.286 6846 Planarity : 0.004 0.052 7814 Dihedral : 6.324 170.341 6270 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.11), residues: 5478 helix: -0.14 (0.11), residues: 2384 sheet: -1.81 (0.18), residues: 758 loop : -1.18 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 538 HIS 0.012 0.001 HIS H 514 PHE 0.025 0.002 PHE D 429 TYR 0.023 0.002 TYR E 530 ARG 0.008 0.001 ARG N 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 5.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 419 LEU cc_start: 0.7839 (mm) cc_final: 0.7549 (mm) REVERT: A 522 LEU cc_start: 0.8245 (tp) cc_final: 0.7977 (tp) REVERT: B 364 SER cc_start: 0.8156 (m) cc_final: 0.7953 (m) REVERT: C 254 GLU cc_start: 0.7740 (mp0) cc_final: 0.7306 (mt-10) REVERT: C 513 LEU cc_start: 0.9181 (tp) cc_final: 0.8852 (tt) REVERT: D 410 ASN cc_start: 0.9270 (t0) cc_final: 0.8689 (t0) REVERT: E 403 LEU cc_start: 0.8057 (tp) cc_final: 0.7792 (tt) REVERT: F 250 SER cc_start: 0.8597 (p) cc_final: 0.8371 (p) REVERT: F 489 ILE cc_start: 0.8023 (mm) cc_final: 0.7732 (mm) REVERT: G 152 LEU cc_start: 0.9251 (mt) cc_final: 0.8853 (mt) REVERT: G 157 LEU cc_start: 0.9044 (tp) cc_final: 0.8655 (tp) REVERT: G 186 SER cc_start: 0.8532 (p) cc_final: 0.8309 (p) REVERT: G 196 LEU cc_start: 0.8432 (tp) cc_final: 0.7781 (tp) REVERT: G 207 ILE cc_start: 0.9067 (pt) cc_final: 0.8830 (pt) REVERT: H 419 LEU cc_start: 0.7804 (mm) cc_final: 0.7564 (mm) REVERT: H 522 LEU cc_start: 0.8298 (tp) cc_final: 0.8060 (tp) REVERT: J 254 GLU cc_start: 0.7710 (mp0) cc_final: 0.7326 (mt-10) REVERT: K 252 SER cc_start: 0.8410 (t) cc_final: 0.8183 (t) REVERT: K 410 ASN cc_start: 0.9302 (t0) cc_final: 0.8655 (t0) REVERT: M 250 SER cc_start: 0.8686 (p) cc_final: 0.8430 (p) REVERT: M 489 ILE cc_start: 0.8034 (mm) cc_final: 0.7794 (mm) REVERT: M 580 LEU cc_start: 0.7915 (mt) cc_final: 0.7682 (tp) REVERT: N 152 LEU cc_start: 0.9240 (mt) cc_final: 0.8837 (mt) REVERT: N 157 LEU cc_start: 0.9094 (tp) cc_final: 0.8886 (tp) REVERT: N 186 SER cc_start: 0.8523 (p) cc_final: 0.8302 (p) REVERT: N 196 LEU cc_start: 0.8370 (tp) cc_final: 0.7782 (tp) REVERT: N 207 ILE cc_start: 0.9041 (pt) cc_final: 0.8796 (pt) REVERT: N 240 MET cc_start: 0.8532 (tpp) cc_final: 0.8240 (tpp) REVERT: N 257 GLU cc_start: 0.7073 (tp30) cc_final: 0.6872 (tp30) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.5055 time to fit residues: 471.5749 Evaluate side-chains 346 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 5.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 178 optimal weight: 10.0000 chunk 478 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 532 optimal weight: 5.9990 chunk 441 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 279 optimal weight: 0.1980 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 514 HIS ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN G 204 HIS H 514 HIS ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 HIS N 255 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 46094 Z= 0.246 Angle : 0.602 12.031 62370 Z= 0.301 Chirality : 0.044 0.331 6846 Planarity : 0.004 0.050 7814 Dihedral : 6.124 158.025 6270 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 5478 helix: 0.09 (0.11), residues: 2404 sheet: -1.65 (0.19), residues: 726 loop : -1.11 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 538 HIS 0.005 0.001 HIS G 204 PHE 0.021 0.002 PHE A 551 TYR 0.019 0.002 TYR L 530 ARG 0.006 0.000 ARG F 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 498 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.7973 (ppp) cc_final: 0.7586 (ppp) REVERT: A 419 LEU cc_start: 0.7876 (mm) cc_final: 0.7596 (mm) REVERT: C 254 GLU cc_start: 0.7645 (mp0) cc_final: 0.7352 (mt-10) REVERT: C 494 ASP cc_start: 0.8019 (p0) cc_final: 0.7716 (p0) REVERT: D 410 ASN cc_start: 0.9238 (t0) cc_final: 0.8945 (t0) REVERT: E 403 LEU cc_start: 0.8040 (tp) cc_final: 0.7664 (tt) REVERT: G 152 LEU cc_start: 0.9202 (mt) cc_final: 0.8782 (mt) REVERT: G 157 LEU cc_start: 0.9074 (tp) cc_final: 0.8773 (tp) REVERT: G 196 LEU cc_start: 0.8412 (tp) cc_final: 0.7745 (tp) REVERT: G 197 ASN cc_start: 0.8149 (p0) cc_final: 0.7752 (p0) REVERT: G 207 ILE cc_start: 0.9042 (pt) cc_final: 0.8839 (pt) REVERT: H 203 MET cc_start: 0.7966 (ppp) cc_final: 0.7581 (ppp) REVERT: H 419 LEU cc_start: 0.7871 (mm) cc_final: 0.7634 (mm) REVERT: J 254 GLU cc_start: 0.7667 (mp0) cc_final: 0.7385 (mt-10) REVERT: K 252 SER cc_start: 0.8390 (t) cc_final: 0.8184 (t) REVERT: K 410 ASN cc_start: 0.9258 (t0) cc_final: 0.8940 (t0) REVERT: M 489 ILE cc_start: 0.8025 (mm) cc_final: 0.7794 (mm) REVERT: M 561 ASN cc_start: 0.7319 (p0) cc_final: 0.7108 (p0) REVERT: M 580 LEU cc_start: 0.8138 (mt) cc_final: 0.7852 (tp) REVERT: N 152 LEU cc_start: 0.9176 (mt) cc_final: 0.8807 (mt) REVERT: N 186 SER cc_start: 0.8522 (p) cc_final: 0.8273 (p) REVERT: N 196 LEU cc_start: 0.8348 (tp) cc_final: 0.7691 (tp) REVERT: N 207 ILE cc_start: 0.8987 (pt) cc_final: 0.8767 (pt) REVERT: N 240 MET cc_start: 0.8549 (tpp) cc_final: 0.8316 (tpp) outliers start: 2 outliers final: 0 residues processed: 500 average time/residue: 0.4851 time to fit residues: 426.4831 Evaluate side-chains 338 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 513 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 303 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 301 optimal weight: 0.9990 chunk 447 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 chunk 530 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 515 HIS ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 HIS ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 46094 Z= 0.153 Angle : 0.566 11.235 62370 Z= 0.280 Chirality : 0.043 0.323 6846 Planarity : 0.003 0.047 7814 Dihedral : 5.893 149.018 6270 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 5478 helix: 0.29 (0.11), residues: 2390 sheet: -1.36 (0.21), residues: 596 loop : -0.97 (0.13), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 242 HIS 0.011 0.001 HIS M 514 PHE 0.018 0.001 PHE H 576 TYR 0.028 0.001 TYR B 214 ARG 0.005 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 5.371 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: A 203 MET cc_start: 0.7759 (ppp) cc_final: 0.7460 (ppp) REVERT: A 419 LEU cc_start: 0.7497 (mm) cc_final: 0.7093 (mm) REVERT: C 360 ARG cc_start: 0.7984 (mmt180) cc_final: 0.7583 (mmm160) REVERT: C 494 ASP cc_start: 0.7690 (p0) cc_final: 0.7466 (p0) REVERT: C 528 TYR cc_start: 0.7494 (m-80) cc_final: 0.7111 (m-80) REVERT: F 252 SER cc_start: 0.8561 (t) cc_final: 0.7935 (t) REVERT: F 489 ILE cc_start: 0.7971 (mm) cc_final: 0.7733 (mm) REVERT: F 561 ASN cc_start: 0.7192 (p0) cc_final: 0.6965 (p0) REVERT: G 152 LEU cc_start: 0.9126 (mt) cc_final: 0.8768 (mt) REVERT: G 157 LEU cc_start: 0.9113 (tp) cc_final: 0.8867 (tp) REVERT: G 196 LEU cc_start: 0.8426 (tp) cc_final: 0.7741 (tp) REVERT: G 197 ASN cc_start: 0.8045 (p0) cc_final: 0.7713 (p0) REVERT: G 207 ILE cc_start: 0.8994 (pt) cc_final: 0.8763 (pt) REVERT: H 203 MET cc_start: 0.7849 (ppp) cc_final: 0.7514 (ppp) REVERT: H 419 LEU cc_start: 0.7718 (mm) cc_final: 0.7373 (mm) REVERT: J 254 GLU cc_start: 0.7652 (mp0) cc_final: 0.7296 (mt-10) REVERT: J 360 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7563 (mmm160) REVERT: J 528 TYR cc_start: 0.7516 (m-80) cc_final: 0.7119 (m-80) REVERT: K 252 SER cc_start: 0.8452 (t) cc_final: 0.8210 (t) REVERT: K 410 ASN cc_start: 0.9131 (t0) cc_final: 0.8646 (t0) REVERT: M 250 SER cc_start: 0.8614 (p) cc_final: 0.8393 (p) REVERT: M 252 SER cc_start: 0.8578 (t) cc_final: 0.7829 (t) REVERT: M 489 ILE cc_start: 0.8077 (mm) cc_final: 0.7872 (mm) REVERT: N 152 LEU cc_start: 0.9146 (mt) cc_final: 0.8799 (mt) REVERT: N 196 LEU cc_start: 0.8358 (tp) cc_final: 0.7580 (tp) REVERT: N 197 ASN cc_start: 0.8069 (p0) cc_final: 0.7592 (p0) REVERT: N 207 ILE cc_start: 0.9018 (pt) cc_final: 0.8739 (pt) REVERT: N 229 TRP cc_start: 0.8490 (m-10) cc_final: 0.8261 (m-10) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.4954 time to fit residues: 470.3930 Evaluate side-chains 357 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 327 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 316 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 416 optimal weight: 6.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 HIS ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46094 Z= 0.207 Angle : 0.590 11.551 62370 Z= 0.292 Chirality : 0.044 0.436 6846 Planarity : 0.004 0.057 7814 Dihedral : 5.812 139.007 6270 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 5478 helix: 0.39 (0.11), residues: 2394 sheet: -1.49 (0.20), residues: 672 loop : -0.85 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP J 538 HIS 0.010 0.001 HIS E 515 PHE 0.022 0.001 PHE M 576 TYR 0.031 0.001 TYR E 530 ARG 0.021 0.000 ARG K 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 4.877 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: A 419 LEU cc_start: 0.7446 (mm) cc_final: 0.6891 (mt) REVERT: E 526 MET cc_start: 0.7759 (mtm) cc_final: 0.7367 (mtm) REVERT: E 583 ILE cc_start: 0.8097 (mp) cc_final: 0.7843 (mp) REVERT: F 489 ILE cc_start: 0.7954 (mm) cc_final: 0.7716 (mm) REVERT: F 561 ASN cc_start: 0.7248 (p0) cc_final: 0.7047 (p0) REVERT: G 152 LEU cc_start: 0.9160 (mt) cc_final: 0.8785 (mt) REVERT: G 157 LEU cc_start: 0.9133 (tp) cc_final: 0.8891 (tp) REVERT: G 196 LEU cc_start: 0.8459 (tp) cc_final: 0.7719 (tp) REVERT: G 244 ASP cc_start: 0.8126 (p0) cc_final: 0.7896 (p0) REVERT: H 203 MET cc_start: 0.7883 (ppp) cc_final: 0.7571 (ppp) REVERT: H 258 GLU cc_start: 0.7837 (pt0) cc_final: 0.7610 (pt0) REVERT: H 419 LEU cc_start: 0.7367 (mm) cc_final: 0.7012 (mm) REVERT: K 410 ASN cc_start: 0.9099 (t0) cc_final: 0.8703 (t0) REVERT: L 248 HIS cc_start: 0.8926 (p90) cc_final: 0.8661 (p90) REVERT: L 526 MET cc_start: 0.7803 (mtm) cc_final: 0.7372 (mtm) REVERT: L 583 ILE cc_start: 0.8144 (mp) cc_final: 0.7867 (mp) REVERT: M 203 MET cc_start: 0.6520 (tmm) cc_final: 0.6029 (tmm) REVERT: M 250 SER cc_start: 0.8667 (p) cc_final: 0.8423 (p) REVERT: N 152 LEU cc_start: 0.9131 (mt) cc_final: 0.8790 (mt) REVERT: N 157 LEU cc_start: 0.9198 (tp) cc_final: 0.8985 (tp) REVERT: N 196 LEU cc_start: 0.8367 (tp) cc_final: 0.7646 (tp) REVERT: N 197 ASN cc_start: 0.8117 (p0) cc_final: 0.7602 (p0) REVERT: N 207 ILE cc_start: 0.8982 (pt) cc_final: 0.8699 (pt) REVERT: N 229 TRP cc_start: 0.8507 (m-10) cc_final: 0.8285 (m-10) REVERT: N 244 ASP cc_start: 0.8173 (p0) cc_final: 0.7892 (p0) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.5186 time to fit residues: 456.3891 Evaluate side-chains 340 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 5.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 482 optimal weight: 0.0060 chunk 507 optimal weight: 10.0000 chunk 463 optimal weight: 5.9990 chunk 493 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 215 optimal weight: 0.1980 chunk 387 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 446 optimal weight: 6.9990 chunk 467 optimal weight: 8.9990 chunk 492 optimal weight: 2.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46094 Z= 0.173 Angle : 0.581 10.852 62370 Z= 0.287 Chirality : 0.043 0.372 6846 Planarity : 0.003 0.059 7814 Dihedral : 5.645 125.527 6270 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 5478 helix: 0.47 (0.11), residues: 2400 sheet: -1.41 (0.21), residues: 616 loop : -0.80 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 242 HIS 0.017 0.001 HIS L 515 PHE 0.019 0.001 PHE M 576 TYR 0.028 0.001 TYR E 530 ARG 0.013 0.000 ARG K 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 5.582 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: D 252 SER cc_start: 0.8500 (t) cc_final: 0.8257 (t) REVERT: D 410 ASN cc_start: 0.9170 (t0) cc_final: 0.8919 (t0) REVERT: E 526 MET cc_start: 0.7652 (mtm) cc_final: 0.7277 (mtm) REVERT: E 583 ILE cc_start: 0.8105 (mp) cc_final: 0.7857 (mp) REVERT: F 489 ILE cc_start: 0.8067 (mm) cc_final: 0.7842 (mm) REVERT: G 152 LEU cc_start: 0.9116 (mt) cc_final: 0.8763 (mt) REVERT: G 157 LEU cc_start: 0.9128 (tp) cc_final: 0.8869 (tp) REVERT: G 189 ILE cc_start: 0.8881 (mm) cc_final: 0.8595 (mm) REVERT: G 196 LEU cc_start: 0.8477 (tp) cc_final: 0.7671 (tp) REVERT: G 197 ASN cc_start: 0.8178 (p0) cc_final: 0.7653 (p0) REVERT: G 229 TRP cc_start: 0.8501 (m-10) cc_final: 0.8217 (m-10) REVERT: H 203 MET cc_start: 0.7688 (ppp) cc_final: 0.7282 (ppp) REVERT: I 526 MET cc_start: 0.5525 (tpt) cc_final: 0.5305 (tpt) REVERT: I 533 TRP cc_start: 0.8006 (m100) cc_final: 0.7417 (m100) REVERT: K 252 SER cc_start: 0.8499 (t) cc_final: 0.8259 (t) REVERT: L 248 HIS cc_start: 0.8939 (p90) cc_final: 0.8662 (p90) REVERT: L 359 ASN cc_start: 0.8734 (p0) cc_final: 0.8390 (p0) REVERT: L 526 MET cc_start: 0.7685 (mtm) cc_final: 0.7251 (mtm) REVERT: L 583 ILE cc_start: 0.8145 (mp) cc_final: 0.7877 (mp) REVERT: M 489 ILE cc_start: 0.8013 (mm) cc_final: 0.7799 (mm) REVERT: N 152 LEU cc_start: 0.9061 (mt) cc_final: 0.8765 (mt) REVERT: N 157 LEU cc_start: 0.9184 (tp) cc_final: 0.8981 (tp) REVERT: N 186 SER cc_start: 0.8519 (m) cc_final: 0.8019 (t) REVERT: N 189 ILE cc_start: 0.8908 (mm) cc_final: 0.8614 (mm) REVERT: N 196 LEU cc_start: 0.8403 (tp) cc_final: 0.7704 (tp) REVERT: N 197 ASN cc_start: 0.7999 (p0) cc_final: 0.7435 (p0) REVERT: N 207 ILE cc_start: 0.9003 (pt) cc_final: 0.8754 (pt) REVERT: N 229 TRP cc_start: 0.8462 (m-10) cc_final: 0.8250 (m-10) REVERT: N 244 ASP cc_start: 0.8065 (p0) cc_final: 0.7807 (p0) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.4831 time to fit residues: 422.1830 Evaluate side-chains 347 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 324 optimal weight: 20.0000 chunk 522 optimal weight: 1.9990 chunk 318 optimal weight: 0.4980 chunk 247 optimal weight: 0.9990 chunk 363 optimal weight: 0.0050 chunk 547 optimal weight: 9.9990 chunk 504 optimal weight: 9.9990 chunk 436 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 46094 Z= 0.154 Angle : 0.577 11.468 62370 Z= 0.282 Chirality : 0.043 0.415 6846 Planarity : 0.003 0.046 7814 Dihedral : 5.485 116.055 6270 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 5478 helix: 0.54 (0.11), residues: 2394 sheet: -1.44 (0.21), residues: 618 loop : -0.68 (0.13), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 538 HIS 0.010 0.001 HIS L 515 PHE 0.018 0.001 PHE M 576 TYR 0.031 0.001 TYR J 528 ARG 0.004 0.000 ARG D 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 5.053 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: A 258 GLU cc_start: 0.7663 (pt0) cc_final: 0.7405 (pt0) REVERT: D 252 SER cc_start: 0.8504 (t) cc_final: 0.8261 (t) REVERT: E 526 MET cc_start: 0.7584 (mtm) cc_final: 0.7148 (mtm) REVERT: E 583 ILE cc_start: 0.8108 (mp) cc_final: 0.7838 (mp) REVERT: F 489 ILE cc_start: 0.8102 (mm) cc_final: 0.7727 (mm) REVERT: G 152 LEU cc_start: 0.9096 (mt) cc_final: 0.8733 (mt) REVERT: G 157 LEU cc_start: 0.9096 (tp) cc_final: 0.8809 (tp) REVERT: G 196 LEU cc_start: 0.8426 (tp) cc_final: 0.7696 (tp) REVERT: G 197 ASN cc_start: 0.8169 (p0) cc_final: 0.7613 (p0) REVERT: G 229 TRP cc_start: 0.8435 (m-10) cc_final: 0.8199 (m-10) REVERT: H 203 MET cc_start: 0.7684 (ppp) cc_final: 0.7257 (ppp) REVERT: H 392 TYR cc_start: 0.7436 (m-80) cc_final: 0.6792 (m-80) REVERT: I 526 MET cc_start: 0.5466 (tpt) cc_final: 0.5237 (tpt) REVERT: I 533 TRP cc_start: 0.7961 (m100) cc_final: 0.7261 (m100) REVERT: K 252 SER cc_start: 0.8431 (t) cc_final: 0.8204 (t) REVERT: K 410 ASN cc_start: 0.9170 (t0) cc_final: 0.8815 (t0) REVERT: L 248 HIS cc_start: 0.8927 (p90) cc_final: 0.8674 (p90) REVERT: L 359 ASN cc_start: 0.8656 (p0) cc_final: 0.8351 (p0) REVERT: L 526 MET cc_start: 0.7569 (mtm) cc_final: 0.7174 (mtm) REVERT: L 583 ILE cc_start: 0.8126 (mp) cc_final: 0.7876 (mp) REVERT: M 489 ILE cc_start: 0.8029 (mm) cc_final: 0.7796 (mm) REVERT: N 152 LEU cc_start: 0.9020 (mt) cc_final: 0.8671 (mt) REVERT: N 196 LEU cc_start: 0.8344 (tp) cc_final: 0.7663 (tp) REVERT: N 197 ASN cc_start: 0.7916 (p0) cc_final: 0.7545 (p0) REVERT: N 207 ILE cc_start: 0.9033 (pt) cc_final: 0.8743 (pt) REVERT: N 244 ASP cc_start: 0.8098 (p0) cc_final: 0.7836 (p0) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.4974 time to fit residues: 438.6031 Evaluate side-chains 361 residues out of total 5010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 346 optimal weight: 10.0000 chunk 464 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 402 optimal weight: 0.0470 chunk 64 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 437 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 448 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN E 515 HIS ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 384 ASN N 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076370 restraints weight = 149001.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078444 restraints weight = 88980.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079797 restraints weight = 62470.278| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 46094 Z= 0.148 Angle : 0.572 10.928 62370 Z= 0.280 Chirality : 0.043 0.415 6846 Planarity : 0.003 0.041 7814 Dihedral : 5.383 112.524 6270 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5478 helix: 0.60 (0.11), residues: 2390 sheet: -1.33 (0.22), residues: 590 loop : -0.67 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 538 HIS 0.012 0.001 HIS F 514 PHE 0.018 0.001 PHE M 576 TYR 0.028 0.001 TYR C 528 ARG 0.012 0.000 ARG M 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9840.87 seconds wall clock time: 178 minutes 52.35 seconds (10732.35 seconds total)