Starting phenix.real_space_refine on Sun Feb 18 00:36:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5k_35987/02_2024/8j5k_35987_updated.pdb" } resolution = 2.93 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= 0.018 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: 10 Type Number sf(0) Gaussians Ca 2 9.91 5 Mn 8 7.51 5 Fe 6 7.16 5 P 14 5.49 5 Mg 206 5.21 5 S 162 5.16 5 Cl 2 4.86 5 C 49140 2.51 5 N 10324 2.21 5 O 11582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "O GLU 172": "OE1" <-> "OE2" Residue "O GLU 268": "OE1" <-> "OE2" Residue "Q GLU 123": "OE1" <-> "OE2" Residue "Q GLU 172": "OE1" <-> "OE2" Residue "V GLU 24": "OE1" <-> "OE2" Residue "V TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 2": "OE1" <-> "OE2" Residue "o GLU 172": "OE1" <-> "OE2" Residue "o GLU 268": "OE1" <-> "OE2" Residue "q GLU 123": "OE1" <-> "OE2" Residue "q GLU 172": "OE1" <-> "OE2" Residue "v GLU 24": "OE1" <-> "OE2" Residue "v TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 137": "OE1" <-> "OE2" Residue "0 GLU 137": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 71446 Number of models: 1 Model: "" Number of chains: 94 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2530 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 318} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 28, 'TRANS': 452} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3437 Classifications: {'peptide': 450} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 425} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2667 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 325} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 69} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 242 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 499 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 61} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 247 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "K" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 32} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 34} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 295 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "O" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1824 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 236} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1050 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 6, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "T" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 678 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 85} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 979 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "W" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 338 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4, 'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 233 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 216 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Z" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 413 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2530 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 318} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "b" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 28, 'TRANS': 452} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3437 Classifications: {'peptide': 450} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 425} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "d" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2667 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 325} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "e" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 69} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 242 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 499 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 61} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 247 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "k" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 32} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 34} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 295 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "o" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1824 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 236} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "q" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1050 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 6, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "t" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 678 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 85} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "v" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 979 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "w" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 338 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4, 'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 43 Chain: "x" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 233 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "y" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 216 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "z" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 413 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "5" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1280 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 156} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "7" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1222 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 154} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "6" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1209 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 51 Chain: "p" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1265 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 16, 'TRANS': 197} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 12, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 275 Chain: "4" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 765 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'TRANS': 152} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 153 Planarities with less than four sites: {'UNK:plan-1': 153} Unresolved non-hydrogen planarities: 153 Chain: "3" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 992 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 152} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "P" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1265 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 16, 'TRANS': 197} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 534 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 12, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 275 Chain: "9" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 765 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'TRANS': 152} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 153 Planarities with less than four sites: {'UNK:plan-1': 153} Unresolved non-hydrogen planarities: 153 Chain: "8" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 992 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 152} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "0" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1280 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 156} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "2" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1222 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 154} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "1" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1209 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 562 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'LHG': 2, 'OEX': 1, 'PHO': 2, 'PL9': 1, 'SQD': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1250 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 1, 'SQD': 2} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-4': 3, 'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1143 Unusual residues: {' CL': 1, 'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 518 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 3, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCR': 1, 'DGD': 1, 'LHG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'LMG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "V" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'CLA': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "Z" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 508 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'LHG': 2, 'OEX': 1, 'PHO': 2, 'PL9': 1, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1196 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-4': 3, 'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 27 Chain: "c" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1143 Unusual residues: {' CL': 1, 'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 518 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 3, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCR': 1, 'DGD': 1, 'LHG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "k" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'LMG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "v" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'CLA': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "z" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 810 Unusual residues: {'A86': 3, 'CLA': 11, 'ET4': 1, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'CLA:plan-3': 2, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 58 Chain: "7" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 707 Unusual residues: {'A86': 2, 'CLA': 12, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-3': 4, 'CLA:plan-4': 7, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 84 Chain: "6" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 714 Unusual residues: {'A86': 1, 'CLA': 13, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 11} Unresolved non-hydrogen planarities: 86 Chain: "p" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 432 Unusual residues: {'A86': 1, 'CLA': 9, 'DD6': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-3': 6, 'CLA:plan-4': 9, 'CLA:plan-5': 9} Unresolved non-hydrogen planarities: 95 Chain: "4" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 516 Unusual residues: {'A86': 3, 'CLA': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-2': 4, 'CLA:plan-3': 8, 'CLA:plan-4': 10, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 113 Chain: "3" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 555 Unusual residues: {'A86': 2, 'CLA': 11, 'DD6': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 7, 'CLA:plan-4': 10, 'CLA:plan-5': 11, 'CLA:plan-6': 1} Unresolved non-hydrogen planarities: 119 Chain: "P" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 432 Unusual residues: {'A86': 1, 'CLA': 9, 'DD6': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-3': 6, 'CLA:plan-4': 9, 'CLA:plan-5': 9} Unresolved non-hydrogen planarities: 95 Chain: "9" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 516 Unusual residues: {'A86': 3, 'CLA': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-2': 4, 'CLA:plan-3': 8, 'CLA:plan-4': 10, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 113 Chain: "8" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 555 Unusual residues: {'A86': 2, 'CLA': 11, 'DD6': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 7, 'CLA:plan-4': 10, 'CLA:plan-5': 11, 'CLA:plan-6': 1} Unresolved non-hydrogen planarities: 119 Chain: "0" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 810 Unusual residues: {'A86': 3, 'CLA': 11, 'ET4': 1, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'CLA:plan-3': 2, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 58 Chain: "2" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 707 Unusual residues: {'A86': 2, 'CLA': 12, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-3': 4, 'CLA:plan-4': 7, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 84 Chain: "1" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 714 Unusual residues: {'A86': 1, 'CLA': 13, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 11} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 29.05, per 1000 atoms: 0.41 Number of scatterers: 71446 At special positions: 0 Unit cell: (219.42, 301.04, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Fe 6 26.01 Mn 8 24.99 Ca 2 19.99 Cl 2 17.00 S 162 16.00 P 14 15.00 Mg 206 11.99 O 11582 8.00 N 10324 7.00 C 49140 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=120, symmetry=0 Number of additional bonds: simple=120, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.03 Conformation dependent library (CDL) restraints added in 7.9 seconds 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 290 helices and 22 sheets defined 54.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.34 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.665A pdb=" N CYS A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix removed outlier: 3.555A pdb=" N ILE A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.191A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 268 through 295 Proline residue: A 279 - end of helix removed outlier: 3.832A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'B' and resid 5 through 13 removed outlier: 5.396A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.868A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 135 through 156 removed outlier: 3.642A pdb=" N GLY B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 195 through 218 removed outlier: 3.612A pdb=" N ALA B 205 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 210 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 234 through 258 Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.677A pdb=" N ASP B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 331 through 334 No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.673A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 154 through 181 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.012A pdb=" N TYR C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 253 Processing helix chain 'C' and resid 258 through 261 No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 268 through 292 removed outlier: 3.522A pdb=" N TRP C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 302 No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 306 through 323 removed outlier: 3.653A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.643A pdb=" N ARG C 357 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Proline residue: C 368 - end of helix No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 386 through 397 Processing helix chain 'C' and resid 422 through 453 Processing helix chain 'C' and resid 465 through 468 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 33 through 51 removed outlier: 5.066A pdb=" N PHE D 38 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Proline residue: D 39 - end of helix removed outlier: 3.555A pdb=" N THR D 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 109 through 136 Processing helix chain 'D' and resid 140 through 157 Proline residue: D 149 - end of helix removed outlier: 3.509A pdb=" N VAL D 156 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D 157 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 175 through 189 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 195 through 219 Processing helix chain 'D' and resid 231 through 234 removed outlier: 3.593A pdb=" N ALA D 234 " --> pdb=" O THR D 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 234' Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 264 through 291 Proline residue: D 275 - end of helix removed outlier: 4.015A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 314 through 333 removed outlier: 4.692A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 17 through 20 No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 27 through 39 removed outlier: 4.010A pdb=" N ILE E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 72 through 79 Processing helix chain 'F' and resid 18 through 42 Proline residue: F 29 - end of helix removed outlier: 3.835A pdb=" N PHE F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 28 Proline residue: H 25 - end of helix Processing helix chain 'H' and resid 40 through 61 Processing helix chain 'I' and resid 2 through 23 Processing helix chain 'J' and resid 10 through 33 Processing helix chain 'K' and resid 30 through 55 Proline residue: K 33 - end of helix Proline residue: K 39 - end of helix Proline residue: K 42 - end of helix Processing helix chain 'L' and resid 15 through 37 removed outlier: 4.703A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 36 Proline residue: M 18 - end of helix Processing helix chain 'N' and resid 9 through 22 removed outlier: 3.926A pdb=" N UNK N 22 " --> pdb=" O UNK N 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 95 No H-bonds generated for 'chain 'O' and resid 92 through 95' Processing helix chain 'O' and resid 100 through 103 No H-bonds generated for 'chain 'O' and resid 100 through 103' Processing helix chain 'O' and resid 262 through 264 No H-bonds generated for 'chain 'O' and resid 262 through 264' Processing helix chain 'O' and resid 275 through 278 No H-bonds generated for 'chain 'O' and resid 275 through 278' Processing helix chain 'Q' and resid 113 through 136 removed outlier: 4.266A pdb=" N LYS Q 130 " --> pdb=" O ASN Q 126 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE Q 131 " --> pdb=" O ARG Q 127 " (cutoff:3.500A) Proline residue: Q 132 - end of helix Processing helix chain 'Q' and resid 141 through 149 Processing helix chain 'Q' and resid 151 through 161 removed outlier: 3.901A pdb=" N ARG Q 155 " --> pdb=" O TYR Q 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY Q 156 " --> pdb=" O GLU Q 153 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Q 161 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 187 Processing helix chain 'Q' and resid 190 through 205 Processing helix chain 'T' and resid 2 through 22 removed outlier: 3.513A pdb=" N VAL T 21 " --> pdb=" O ILE T 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 20 No H-bonds generated for 'chain 'U' and resid 18 through 20' Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 47 through 51 Processing helix chain 'U' and resid 59 through 64 removed outlier: 3.532A pdb=" N LYS U 64 " --> pdb=" O ASP U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 78 Processing helix chain 'U' and resid 90 through 95 removed outlier: 4.468A pdb=" N ASP U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 23 through 36 Processing helix chain 'V' and resid 38 through 44 removed outlier: 8.256A pdb=" N GLY V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY V 44 " --> pdb=" O CYS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 61 Processing helix chain 'V' and resid 69 through 77 Processing helix chain 'V' and resid 89 through 91 No H-bonds generated for 'chain 'V' and resid 89 through 91' Processing helix chain 'V' and resid 102 through 106 removed outlier: 4.117A pdb=" N SER V 106 " --> pdb=" O ARG V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 125 Proline residue: V 123 - end of helix Processing helix chain 'W' and resid 103 through 123 Proline residue: W 111 - end of helix removed outlier: 3.946A pdb=" N ARG W 123 " --> pdb=" O ARG W 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 112 Processing helix chain 'Y' and resid 16 through 41 Proline residue: Y 23 - end of helix removed outlier: 4.329A pdb=" N LEU Y 32 " --> pdb=" O ALA Y 28 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE Y 33 " --> pdb=" O SER Y 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 28 removed outlier: 3.573A pdb=" N THR Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.513A pdb=" N ALA Z 28 " --> pdb=" O PRO Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 60 removed outlier: 5.073A pdb=" N ASP Z 38 " --> pdb=" O GLU Z 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN Z 39 " --> pdb=" O THR Z 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE Z 40 " --> pdb=" O SER Z 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 21 Processing helix chain 'a' and resid 31 through 54 removed outlier: 3.666A pdb=" N CYS a 35 " --> pdb=" O GLY a 31 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU a 36 " --> pdb=" O TRP a 32 " (cutoff:3.500A) Proline residue: a 39 - end of helix removed outlier: 3.554A pdb=" N ILE a 53 " --> pdb=" O ILE a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 73 No H-bonds generated for 'chain 'a' and resid 71 through 73' Processing helix chain 'a' and resid 96 through 98 No H-bonds generated for 'chain 'a' and resid 96 through 98' Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 110 through 136 Processing helix chain 'a' and resid 143 through 158 removed outlier: 4.190A pdb=" N ALA a 149 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Proline residue: a 150 - end of helix Processing helix chain 'a' and resid 160 through 165 Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 176 through 190 Processing helix chain 'a' and resid 196 through 221 Processing helix chain 'a' and resid 233 through 236 Processing helix chain 'a' and resid 248 through 258 Processing helix chain 'a' and resid 268 through 295 Proline residue: a 279 - end of helix removed outlier: 3.831A pdb=" N PHE a 295 " --> pdb=" O SER a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 329 Processing helix chain 'b' and resid 5 through 13 removed outlier: 5.395A pdb=" N HIS b 9 " --> pdb=" O TYR b 6 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL b 11 " --> pdb=" O VAL b 8 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL b 12 " --> pdb=" O HIS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 44 Processing helix chain 'b' and resid 56 through 58 No H-bonds generated for 'chain 'b' and resid 56 through 58' Processing helix chain 'b' and resid 63 through 69 removed outlier: 3.868A pdb=" N LEU b 69 " --> pdb=" O PHE b 65 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 116 Processing helix chain 'b' and resid 121 through 123 No H-bonds generated for 'chain 'b' and resid 121 through 123' Processing helix chain 'b' and resid 135 through 156 removed outlier: 3.642A pdb=" N GLY b 140 " --> pdb=" O PRO b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 190 Processing helix chain 'b' and resid 195 through 218 removed outlier: 3.612A pdb=" N ALA b 205 " --> pdb=" O HIS b 202 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE b 210 " --> pdb=" O ILE b 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 223 through 228 Processing helix chain 'b' and resid 234 through 258 Processing helix chain 'b' and resid 265 through 268 No H-bonds generated for 'chain 'b' and resid 265 through 268' Processing helix chain 'b' and resid 272 through 276 removed outlier: 3.677A pdb=" N ASP b 276 " --> pdb=" O ARG b 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 272 through 276' Processing helix chain 'b' and resid 279 through 293 Processing helix chain 'b' and resid 298 through 304 Processing helix chain 'b' and resid 307 through 312 Processing helix chain 'b' and resid 315 through 317 No H-bonds generated for 'chain 'b' and resid 315 through 317' Processing helix chain 'b' and resid 319 through 321 No H-bonds generated for 'chain 'b' and resid 319 through 321' Processing helix chain 'b' and resid 331 through 334 No H-bonds generated for 'chain 'b' and resid 331 through 334' Processing helix chain 'b' and resid 414 through 424 Processing helix chain 'b' and resid 447 through 474 removed outlier: 3.674A pdb=" N PHE b 464 " --> pdb=" O LEU b 460 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 42 Processing helix chain 'c' and resid 46 through 73 Processing helix chain 'c' and resid 81 through 83 No H-bonds generated for 'chain 'c' and resid 81 through 83' Processing helix chain 'c' and resid 89 through 94 Processing helix chain 'c' and resid 101 through 103 No H-bonds generated for 'chain 'c' and resid 101 through 103' Processing helix chain 'c' and resid 109 through 134 Processing helix chain 'c' and resid 140 through 143 No H-bonds generated for 'chain 'c' and resid 140 through 143' Processing helix chain 'c' and resid 154 through 181 Processing helix chain 'c' and resid 206 through 213 removed outlier: 4.012A pdb=" N TYR c 212 " --> pdb=" O VAL c 208 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL c 213 " --> pdb=" O ILE c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 230 through 253 Processing helix chain 'c' and resid 258 through 261 No H-bonds generated for 'chain 'c' and resid 258 through 261' Processing helix chain 'c' and resid 268 through 292 removed outlier: 3.522A pdb=" N TRP c 291 " --> pdb=" O ALA c 287 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR c 292 " --> pdb=" O LEU c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 302 No H-bonds generated for 'chain 'c' and resid 299 through 302' Processing helix chain 'c' and resid 306 through 323 removed outlier: 3.653A pdb=" N SER c 310 " --> pdb=" O GLY c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 353 through 358 removed outlier: 3.642A pdb=" N ARG c 357 " --> pdb=" O GLU c 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 364 through 369 Proline residue: c 368 - end of helix No H-bonds generated for 'chain 'c' and resid 364 through 369' Processing helix chain 'c' and resid 377 through 381 Processing helix chain 'c' and resid 386 through 397 Processing helix chain 'c' and resid 422 through 453 Processing helix chain 'c' and resid 465 through 468 Processing helix chain 'd' and resid 14 through 22 Processing helix chain 'd' and resid 33 through 51 removed outlier: 5.066A pdb=" N PHE d 38 " --> pdb=" O LEU d 35 " (cutoff:3.500A) Proline residue: d 39 - end of helix removed outlier: 3.555A pdb=" N THR d 50 " --> pdb=" O GLY d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 107 Processing helix chain 'd' and resid 109 through 136 Processing helix chain 'd' and resid 140 through 157 Proline residue: d 149 - end of helix removed outlier: 3.509A pdb=" N VAL d 156 " --> pdb=" O PHE d 153 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE d 157 " --> pdb=" O VAL d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 163 Processing helix chain 'd' and resid 167 through 169 No H-bonds generated for 'chain 'd' and resid 167 through 169' Processing helix chain 'd' and resid 175 through 189 Processing helix chain 'd' and resid 191 through 193 No H-bonds generated for 'chain 'd' and resid 191 through 193' Processing helix chain 'd' and resid 195 through 219 Processing helix chain 'd' and resid 231 through 234 removed outlier: 3.593A pdb=" N ALA d 234 " --> pdb=" O THR d 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 231 through 234' Processing helix chain 'd' and resid 246 through 256 Processing helix chain 'd' and resid 264 through 291 Proline residue: d 275 - end of helix removed outlier: 4.015A pdb=" N LEU d 291 " --> pdb=" O VAL d 287 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 306 Processing helix chain 'd' and resid 314 through 333 removed outlier: 4.692A pdb=" N ALA d 331 " --> pdb=" O ALA d 327 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLN d 332 " --> pdb=" O TRP d 328 " (cutoff:3.500A) Processing helix chain 'd' and resid 335 through 337 No H-bonds generated for 'chain 'd' and resid 335 through 337' Processing helix chain 'e' and resid 10 through 14 Processing helix chain 'e' and resid 17 through 20 No H-bonds generated for 'chain 'e' and resid 17 through 20' Processing helix chain 'e' and resid 27 through 39 removed outlier: 4.010A pdb=" N ILE e 38 " --> pdb=" O GLY e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 72 through 79 Processing helix chain 'f' and resid 18 through 42 Proline residue: f 29 - end of helix removed outlier: 3.835A pdb=" N PHE f 42 " --> pdb=" O THR f 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 18 through 28 Proline residue: h 25 - end of helix Processing helix chain 'h' and resid 40 through 61 Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'j' and resid 10 through 33 Processing helix chain 'k' and resid 30 through 55 Proline residue: k 33 - end of helix Proline residue: k 39 - end of helix Proline residue: k 42 - end of helix Processing helix chain 'l' and resid 15 through 37 removed outlier: 4.702A pdb=" N SER l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR l 35 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 36 Proline residue: m 18 - end of helix Processing helix chain 'n' and resid 9 through 22 removed outlier: 3.926A pdb=" N UNK n 22 " --> pdb=" O UNK n 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 95 No H-bonds generated for 'chain 'o' and resid 92 through 95' Processing helix chain 'o' and resid 100 through 103 No H-bonds generated for 'chain 'o' and resid 100 through 103' Processing helix chain 'o' and resid 262 through 264 No H-bonds generated for 'chain 'o' and resid 262 through 264' Processing helix chain 'o' and resid 275 through 278 No H-bonds generated for 'chain 'o' and resid 275 through 278' Processing helix chain 'q' and resid 113 through 136 removed outlier: 4.267A pdb=" N LYS q 130 " --> pdb=" O ASN q 126 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE q 131 " --> pdb=" O ARG q 127 " (cutoff:3.500A) Proline residue: q 132 - end of helix Processing helix chain 'q' and resid 141 through 149 Processing helix chain 'q' and resid 151 through 161 removed outlier: 3.901A pdb=" N ARG q 155 " --> pdb=" O TYR q 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY q 156 " --> pdb=" O GLU q 153 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU q 161 " --> pdb=" O VAL q 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 165 through 187 Processing helix chain 'q' and resid 190 through 205 Processing helix chain 't' and resid 2 through 22 removed outlier: 3.513A pdb=" N VAL t 21 " --> pdb=" O ILE t 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 18 through 20 No H-bonds generated for 'chain 'u' and resid 18 through 20' Processing helix chain 'u' and resid 33 through 35 No H-bonds generated for 'chain 'u' and resid 33 through 35' Processing helix chain 'u' and resid 47 through 51 Processing helix chain 'u' and resid 59 through 64 removed outlier: 3.531A pdb=" N LYS u 64 " --> pdb=" O ASP u 61 " (cutoff:3.500A) Processing helix chain 'u' and resid 70 through 78 Processing helix chain 'u' and resid 90 through 95 removed outlier: 4.468A pdb=" N ASP u 95 " --> pdb=" O ASP u 91 " (cutoff:3.500A) Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 23 through 36 Processing helix chain 'v' and resid 38 through 44 removed outlier: 8.255A pdb=" N GLY v 43 " --> pdb=" O ALA v 39 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY v 44 " --> pdb=" O CYS v 40 " (cutoff:3.500A) Processing helix chain 'v' and resid 56 through 61 Processing helix chain 'v' and resid 69 through 77 Processing helix chain 'v' and resid 89 through 91 No H-bonds generated for 'chain 'v' and resid 89 through 91' Processing helix chain 'v' and resid 102 through 106 removed outlier: 4.117A pdb=" N SER v 106 " --> pdb=" O ARG v 103 " (cutoff:3.500A) Processing helix chain 'v' and resid 109 through 125 Proline residue: v 123 - end of helix Processing helix chain 'w' and resid 103 through 123 Proline residue: w 111 - end of helix removed outlier: 3.946A pdb=" N ARG w 123 " --> pdb=" O ARG w 119 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 112 Processing helix chain 'y' and resid 16 through 41 Proline residue: y 23 - end of helix removed outlier: 4.328A pdb=" N LEU y 32 " --> pdb=" O ALA y 28 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE y 33 " --> pdb=" O SER y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 5 through 28 removed outlier: 3.574A pdb=" N THR z 22 " --> pdb=" O ALA z 18 " (cutoff:3.500A) Proline residue: z 24 - end of helix removed outlier: 3.514A pdb=" N ALA z 28 " --> pdb=" O PRO z 24 " (cutoff:3.500A) Processing helix chain 'z' and resid 32 through 60 removed outlier: 5.073A pdb=" N ASP z 38 " --> pdb=" O GLU z 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN z 39 " --> pdb=" O THR z 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE z 40 " --> pdb=" O SER z 36 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 94 removed outlier: 3.589A pdb=" N SER 5 66 " --> pdb=" O PRO 5 62 " (cutoff:3.500A) Proline residue: 5 89 - end of helix Processing helix chain '5' and resid 109 through 111 No H-bonds generated for 'chain '5' and resid 109 through 111' Processing helix chain '5' and resid 117 through 137 Processing helix chain '5' and resid 159 through 188 Processing helix chain '5' and resid 193 through 201 removed outlier: 4.451A pdb=" N SER 5 200 " --> pdb=" O ASN 5 196 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY 5 201 " --> pdb=" O LEU 5 197 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 75 removed outlier: 4.459A pdb=" N ILE 7 72 " --> pdb=" O VAL 7 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 7 73 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) Proline residue: 7 74 - end of helix Processing helix chain '7' and resid 104 through 118 removed outlier: 3.637A pdb=" N LEU 7 113 " --> pdb=" O GLN 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 129 No H-bonds generated for 'chain '7' and resid 127 through 129' Processing helix chain '7' and resid 140 through 167 removed outlier: 3.649A pdb=" N LEU 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 184 No H-bonds generated for 'chain '7' and resid 182 through 184' Processing helix chain '6' and resid 60 through 88 Proline residue: 6 87 - end of helix Processing helix chain '6' and resid 117 through 131 Processing helix chain '6' and resid 140 through 142 No H-bonds generated for 'chain '6' and resid 140 through 142' Processing helix chain '6' and resid 150 through 180 Processing helix chain '6' and resid 195 through 197 No H-bonds generated for 'chain '6' and resid 195 through 197' Processing helix chain 'p' and resid 84 through 107 removed outlier: 3.622A pdb=" N LEU p 104 " --> pdb=" O GLN p 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 132 through 138 Processing helix chain 'p' and resid 141 through 164 removed outlier: 3.845A pdb=" N GLU p 164 " --> pdb=" O ILE p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 170 through 172 No H-bonds generated for 'chain 'p' and resid 170 through 172' Processing helix chain 'p' and resid 191 through 220 removed outlier: 3.795A pdb=" N PHE p 213 " --> pdb=" O MET p 209 " (cutoff:3.500A) Processing helix chain 'p' and resid 226 through 233 Proline residue: p 232 - end of helix Processing helix chain '4' and resid 20 through 23 Processing helix chain '4' and resid 26 through 52 removed outlier: 3.753A pdb=" N UNK 4 42 " --> pdb=" O UNK 4 38 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N UNK 4 45 " --> pdb=" O UNK 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 104 removed outlier: 4.145A pdb=" N UNK 4 89 " --> pdb=" O UNK 4 85 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N UNK 4 103 " --> pdb=" O UNK 4 99 " (cutoff:3.500A) Processing helix chain '4' and resid 130 through 159 removed outlier: 4.273A pdb=" N UNK 4 137 " --> pdb=" O UNK 4 133 " (cutoff:3.500A) Processing helix chain '3' and resid 59 through 85 Proline residue: 3 83 - end of helix Processing helix chain '3' and resid 99 through 101 No H-bonds generated for 'chain '3' and resid 99 through 101' Processing helix chain '3' and resid 106 through 111 Processing helix chain '3' and resid 114 through 130 Processing helix chain '3' and resid 144 through 177 removed outlier: 3.603A pdb=" N LEU 3 163 " --> pdb=" O ARG 3 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 107 removed outlier: 3.622A pdb=" N LEU P 104 " --> pdb=" O GLN P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 141 through 164 removed outlier: 3.845A pdb=" N GLU P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 172 No H-bonds generated for 'chain 'P' and resid 170 through 172' Processing helix chain 'P' and resid 191 through 220 removed outlier: 3.794A pdb=" N PHE P 213 " --> pdb=" O MET P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 233 Proline residue: P 232 - end of helix Processing helix chain '9' and resid 20 through 23 Processing helix chain '9' and resid 26 through 52 removed outlier: 3.754A pdb=" N UNK 9 42 " --> pdb=" O UNK 9 38 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N UNK 9 45 " --> pdb=" O UNK 9 41 " (cutoff:3.500A) Processing helix chain '9' and resid 85 through 104 removed outlier: 4.144A pdb=" N UNK 9 89 " --> pdb=" O UNK 9 85 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N UNK 9 103 " --> pdb=" O UNK 9 99 " (cutoff:3.500A) Processing helix chain '9' and resid 130 through 159 removed outlier: 4.273A pdb=" N UNK 9 137 " --> pdb=" O UNK 9 133 " (cutoff:3.500A) Processing helix chain '8' and resid 59 through 85 Proline residue: 8 83 - end of helix Processing helix chain '8' and resid 99 through 101 No H-bonds generated for 'chain '8' and resid 99 through 101' Processing helix chain '8' and resid 106 through 111 Processing helix chain '8' and resid 114 through 130 Processing helix chain '8' and resid 144 through 177 removed outlier: 3.603A pdb=" N LEU 8 163 " --> pdb=" O ARG 8 159 " (cutoff:3.500A) Processing helix chain '0' and resid 62 through 94 removed outlier: 3.589A pdb=" N SER 0 66 " --> pdb=" O PRO 0 62 " (cutoff:3.500A) Proline residue: 0 89 - end of helix Processing helix chain '0' and resid 109 through 111 No H-bonds generated for 'chain '0' and resid 109 through 111' Processing helix chain '0' and resid 117 through 137 Processing helix chain '0' and resid 159 through 188 Processing helix chain '0' and resid 193 through 201 removed outlier: 4.451A pdb=" N SER 0 200 " --> pdb=" O ASN 0 196 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY 0 201 " --> pdb=" O LEU 0 197 " (cutoff:3.500A) Processing helix chain '2' and resid 47 through 75 removed outlier: 4.460A pdb=" N ILE 2 72 " --> pdb=" O VAL 2 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 2 73 " --> pdb=" O LEU 2 69 " (cutoff:3.500A) Proline residue: 2 74 - end of helix Processing helix chain '2' and resid 104 through 118 removed outlier: 3.637A pdb=" N LEU 2 113 " --> pdb=" O GLN 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 129 No H-bonds generated for 'chain '2' and resid 127 through 129' Processing helix chain '2' and resid 140 through 167 removed outlier: 3.648A pdb=" N LEU 2 153 " --> pdb=" O ARG 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 184 No H-bonds generated for 'chain '2' and resid 182 through 184' Processing helix chain '1' and resid 60 through 88 Proline residue: 1 87 - end of helix Processing helix chain '1' and resid 117 through 131 Processing helix chain '1' and resid 140 through 142 No H-bonds generated for 'chain '1' and resid 140 through 142' Processing helix chain '1' and resid 150 through 180 Processing helix chain '1' and resid 195 through 197 No H-bonds generated for 'chain '1' and resid 195 through 197' Processing sheet with id= A, first strand: chain 'B' and resid 166 through 168 Processing sheet with id= B, first strand: chain 'B' and resid 346 through 348 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.456A pdb=" N GLU B 431 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= E, first strand: chain 'C' and resid 185 through 187 Processing sheet with id= F, first strand: chain 'C' and resid 341 through 343 Processing sheet with id= G, first strand: chain 'O' and resid 151 through 157 removed outlier: 3.576A pdb=" N GLU O 152 " --> pdb=" O VAL O 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL O 145 " --> pdb=" O GLU O 152 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS O 324 " --> pdb=" O GLU O 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU O 312 " --> pdb=" O GLN O 286 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN O 286 " --> pdb=" O LEU O 312 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 194 through 198 Processing sheet with id= I, first strand: chain 'O' and resid 128 through 136 removed outlier: 6.717A pdb=" N LYS O 334 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET O 132 " --> pdb=" O TYR O 332 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR O 332 " --> pdb=" O MET O 132 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE O 134 " --> pdb=" O ILE O 330 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE O 330 " --> pdb=" O ILE O 134 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'O' and resid 169 through 172 removed outlier: 3.654A pdb=" N ASP O 169 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE O 190 " --> pdb=" O ASP O 169 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE O 171 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU O 188 " --> pdb=" O ILE O 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'V' and resid 9 through 11 Processing sheet with id= L, first strand: chain 'b' and resid 166 through 168 Processing sheet with id= M, first strand: chain 'b' and resid 346 through 348 Processing sheet with id= N, first strand: chain 'b' and resid 336 through 340 removed outlier: 6.455A pdb=" N GLU b 431 " --> pdb=" O GLU b 338 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'b' and resid 369 through 371 Processing sheet with id= P, first strand: chain 'c' and resid 185 through 187 Processing sheet with id= Q, first strand: chain 'c' and resid 341 through 343 Processing sheet with id= R, first strand: chain 'o' and resid 151 through 157 removed outlier: 3.576A pdb=" N GLU o 152 " --> pdb=" O VAL o 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL o 145 " --> pdb=" O GLU o 152 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS o 324 " --> pdb=" O GLU o 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU o 312 " --> pdb=" O GLN o 286 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN o 286 " --> pdb=" O LEU o 312 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'o' and resid 194 through 198 Processing sheet with id= T, first strand: chain 'o' and resid 128 through 136 removed outlier: 6.718A pdb=" N LYS o 334 " --> pdb=" O VAL o 130 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET o 132 " --> pdb=" O TYR o 332 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR o 332 " --> pdb=" O MET o 132 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE o 134 " --> pdb=" O ILE o 330 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE o 330 " --> pdb=" O ILE o 134 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'o' and resid 169 through 172 removed outlier: 3.654A pdb=" N ASP o 169 " --> pdb=" O ILE o 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE o 190 " --> pdb=" O ASP o 169 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE o 171 " --> pdb=" O GLU o 188 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU o 188 " --> pdb=" O ILE o 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'v' and resid 9 through 11 2746 hydrogen bonds defined for protein. 7734 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: 19.63 Time building geometry restraints manager: 26.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.69: 73522 1.69 - 2.21: 1132 2.21 - 2.74: 10 2.74 - 3.26: 2 3.26 - 3.78: 8 Bond restraints: 74674 Sorted by residual: bond pdb=" C27 DD6 1 204 " pdb=" C29 DD6 1 204 " ideal model delta sigma weight residual 1.575 1.241 0.334 2.00e-02 2.50e+03 2.78e+02 bond pdb=" C27 DD6 6 204 " pdb=" C29 DD6 6 204 " ideal model delta sigma weight residual 1.575 1.242 0.333 2.00e-02 2.50e+03 2.77e+02 bond pdb=" C30 DD6 6 204 " pdb=" C31 DD6 6 204 " ideal model delta sigma weight residual 1.569 1.242 0.327 2.00e-02 2.50e+03 2.68e+02 bond pdb=" C30 DD6 1 204 " pdb=" C31 DD6 1 204 " ideal model delta sigma weight residual 1.569 1.243 0.326 2.00e-02 2.50e+03 2.66e+02 bond pdb=" C27 DD6 7 304 " pdb=" C29 DD6 7 304 " ideal model delta sigma weight residual 1.575 1.253 0.322 2.00e-02 2.50e+03 2.59e+02 ... (remaining 74669 not shown) Histogram of bond angle deviations from ideal: 55.62 - 80.49: 110 80.49 - 105.36: 3058 105.36 - 130.23: 99920 130.23 - 155.10: 1480 155.10 - 179.97: 476 Bond angle restraints: 105044 Sorted by residual: angle pdb=" C6 DD6 8 303 " pdb=" C8 DD6 8 303 " pdb=" C9 DD6 8 303 " ideal model delta sigma weight residual 85.88 147.99 -62.11 3.00e+00 1.11e-01 4.29e+02 angle pdb=" C6 DD6 3 303 " pdb=" C8 DD6 3 303 " pdb=" C9 DD6 3 303 " ideal model delta sigma weight residual 85.88 147.93 -62.05 3.00e+00 1.11e-01 4.28e+02 angle pdb=" C28 DD6 6 204 " pdb=" C27 DD6 6 204 " pdb=" C29 DD6 6 204 " ideal model delta sigma weight residual 68.15 122.89 -54.74 3.00e+00 1.11e-01 3.33e+02 angle pdb=" C28 DD6 1 204 " pdb=" C27 DD6 1 204 " pdb=" C29 DD6 1 204 " ideal model delta sigma weight residual 68.15 122.89 -54.74 3.00e+00 1.11e-01 3.33e+02 angle pdb=" C28 DD6 2 304 " pdb=" C27 DD6 2 304 " pdb=" C29 DD6 2 304 " ideal model delta sigma weight residual 68.15 121.03 -52.88 3.00e+00 1.11e-01 3.11e+02 ... (remaining 105039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 36784 35.44 - 70.88: 1928 70.88 - 106.32: 400 106.32 - 141.76: 182 141.76 - 177.20: 36 Dihedral angle restraints: 39330 sinusoidal: 17596 harmonic: 21734 Sorted by residual: dihedral pdb=" C34 A86 5 303 " pdb=" C38 A86 5 303 " pdb=" O4 A86 5 303 " pdb=" C39 A86 5 303 " ideal model delta sinusoidal sigma weight residual -177.27 -0.07 -177.20 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C34 A86 0 303 " pdb=" C38 A86 0 303 " pdb=" O4 A86 0 303 " pdb=" C39 A86 0 303 " ideal model delta sinusoidal sigma weight residual -177.27 -0.13 -177.14 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C34 A86 4 202 " pdb=" C38 A86 4 202 " pdb=" O4 A86 4 202 " pdb=" C39 A86 4 202 " ideal model delta sinusoidal sigma weight residual -177.27 -0.73 -176.54 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 39327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 9976 0.315 - 0.631: 28 0.631 - 0.946: 4 0.946 - 1.261: 10 1.261 - 1.577: 4 Chirality restraints: 10022 Sorted by residual: chirality pdb=" C15 DD6 8 303 " pdb=" C14 DD6 8 303 " pdb=" C16 DD6 8 303 " pdb=" O1 DD6 8 303 " both_signs ideal model delta sigma weight residual True 0.73 -2.31 -1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" C15 DD6 3 303 " pdb=" C14 DD6 3 303 " pdb=" C16 DD6 3 303 " pdb=" O1 DD6 3 303 " both_signs ideal model delta sigma weight residual True 0.73 -2.31 -1.57 2.00e-01 2.50e+01 6.18e+01 chirality pdb=" C15 A86 5 301 " pdb=" C14 A86 5 301 " pdb=" C16 A86 5 301 " pdb=" C20 A86 5 301 " both_signs ideal model delta sigma weight residual True 1.20 2.58 -1.38 2.00e-01 2.50e+01 4.75e+01 ... (remaining 10019 not shown) Planarity restraints: 13622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR K 101 " -0.056 2.00e-02 2.50e+03 2.57e-01 6.59e+02 pdb=" C11 BCR K 101 " 0.285 2.00e-02 2.50e+03 pdb=" C12 BCR K 101 " -0.391 2.00e-02 2.50e+03 pdb=" C13 BCR K 101 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR k 101 " -0.056 2.00e-02 2.50e+03 2.57e-01 6.59e+02 pdb=" C11 BCR k 101 " 0.285 2.00e-02 2.50e+03 pdb=" C12 BCR k 101 " -0.391 2.00e-02 2.50e+03 pdb=" C13 BCR k 101 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR B 519 " 0.187 2.00e-02 2.50e+03 2.23e-01 4.98e+02 pdb=" C23 BCR B 519 " -0.120 2.00e-02 2.50e+03 pdb=" C24 BCR B 519 " -0.305 2.00e-02 2.50e+03 pdb=" C25 BCR B 519 " 0.238 2.00e-02 2.50e+03 ... (remaining 13619 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7457 2.74 - 3.28: 69769 3.28 - 3.82: 122368 3.82 - 4.36: 144047 4.36 - 4.90: 243011 Nonbonded interactions: 586652 Sorted by model distance: nonbonded pdb=" O LEU D 36 " pdb=" OG1 THR D 40 " model vdw 2.201 2.440 nonbonded pdb=" O LEU d 36 " pdb=" OG1 THR d 40 " model vdw 2.202 2.440 nonbonded pdb=" O LEU d 193 " pdb=" OH TYR l 35 " model vdw 2.205 2.440 nonbonded pdb=" O LEU D 193 " pdb=" OH TYR L 35 " model vdw 2.205 2.440 nonbonded pdb=" NH2 ARG a 140 " pdb=" O5 LHG a 412 " model vdw 2.221 2.520 ... (remaining 586647 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 '0' selection = chain '5' } ncs_group { reference = chain '1' selection = chain '6' } ncs_group { reference = chain '2' selection = chain '7' } ncs_group { reference = chain '3' selection = chain '8' } ncs_group { reference = chain '4' selection = chain '9' } ncs_group { reference = (chain 'A' and (resid 11 through 343 or resid 401 through 410 or (resid 412 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name C23 \ or name C24 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O1 or name O10 or name O2 or name O3 or name O4 or name O5 or n \ ame O6 or name O7 or name O8 or name O9 or name P )))) selection = (chain 'a' and (resid 11 through 343 or resid 401 through 410 or resid 412)) } ncs_group { reference = (chain 'B' and (resid 2 through 482 or (resid 502 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CGA or name CGD or name CHA or \ name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name CM \ D or name NA or name NC or name O1D or name OBD or name MG )) or (resid 503 and \ (name NB or name ND or name C1 or name C10 or name C11 or name C12 or name C13 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C1A or name C \ 1B or name C1C or name C1D or name C2 or name C20 or name C2A or name C2B or nam \ e C2C or name C2D or name C3 or name C3A or name C3B or name C3C or name C3D or \ name C4A or name C4B or name C4C or name C4D or name C5 or name C6 or name C7 or \ name C8 or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB \ or name CBC or name CBD or name CGA or name CGD or name CHA or name CHB or name \ CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or n \ ame NC or name O1A or name O1D or name O2A or name OBD or name MG )) or (resid 5 \ 04 and (name NB or name ND or name C1 or name C10 or name C11 or name C12 or nam \ e C13 or name C15 or name C16 or name C17 or name C18 or name C19 or name C1A or \ name C1B or name C1C or name C1D or name C2 or name C20 or name C2A or name C2B \ or name C2C or name C2D or name C3 or name C3A or name C3B or name C3C or name \ C3D or name C4 or name C4A or name C4B or name C4C or name C4D or name C5 or nam \ e C6 or name C7 or name C8 or name C9 or name CAA or name CAB or name CAC or nam \ e CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or \ name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CM \ B or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name \ O2A or name O2D or name OBD or name MG )) or resid 505 through 507 or (resid 508 \ and (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name \ C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or \ name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB \ or name CAC or name CAD or name CBB or name CBC or name CBD or name CED or name \ CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1D or name O2D or name OBD o \ r name MG )) or resid 509 through 512 or (resid 513 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBB or name CBC or name CBD or name CED or name CGD or name CHA or name CHB \ or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name \ NA or name NC or name O1D or name O2D or name OBD or name MG )) or (resid 514 th \ rough 515 and (name NB or name ND or name C1 or name C10 or name C11 or name C12 \ or name C13 or name C15 or name C16 or name C1A or name C1B or name C1C or name \ C1D or name C2 or name C2A or name C2B or name C2C or name C2D or name C3 or na \ me C3A or name C3B or name C3C or name C3D or name C4 or name C4A or name C4B or \ name C4C or name C4D or name C5 or name C6 or name C7 or name C8 or name C9 or \ name CAA or name CAB or name CAC or name CAD or name CBA or name CBB or name CBC \ or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or name \ CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or n \ ame NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) \ or resid 516 or resid 518 through 519)) selection = (chain 'b' and (resid 2 through 482 or (resid 502 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CGA or name CGD or name CHA or \ name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name CM \ D or name NA or name NC or name O1D or name OBD or name MG )) or (resid 503 and \ (name NB or name ND or name C1 or name C10 or name C11 or name C12 or name C13 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C1A or name C \ 1B or name C1C or name C1D or name C2 or name C20 or name C2A or name C2B or nam \ e C2C or name C2D or name C3 or name C3A or name C3B or name C3C or name C3D or \ name C4A or name C4B or name C4C or name C4D or name C5 or name C6 or name C7 or \ name C8 or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB \ or name CBC or name CBD or name CGA or name CGD or name CHA or name CHB or name \ CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or n \ ame NC or name O1A or name O1D or name O2A or name OBD or name MG )) or resid 50 \ 4 through 506 or (resid 507 through 508 and (name NB or name ND or name C1A or n \ ame C1B or name C1C or name C1D or name C2A or name C2B or name C2C or name C2D \ or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or name \ C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CBB or n \ ame CBC or name CBD or name CED or name CGD or name CHA or name CHB or name CHC \ or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name N \ C or name O1D or name O2D or name OBD or name MG )) or resid 509 through 510 or \ (resid 511 and (name NB or name ND or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C1A or name C1B or name C1C or name C1D or name C2 or name C20 or name C2A or \ name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name C3C \ or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name CAA or name CAB or name CA \ C or name CAD or name CBA or name CBB or name CBC or name CBD or name CED or nam \ e CGA or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or \ name CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D \ or name O2A or name O2D or name OBD or name MG )) or (resid 512 through 513 and \ (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name CBB or name CBC or name CBD or name CED or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1D or name O2D or name OBD or nam \ e MG )) or (resid 514 through 515 and (name NB or name ND or name C1 or name C10 \ or name C11 or name C12 or name C13 or name C15 or name C16 or name C1A or name \ C1B or name C1C or name C1D or name C2 or name C2A or name C2B or name C2C or n \ ame C2D or name C3 or name C3A or name C3B or name C3C or name C3D or name C4 or \ name C4A or name C4B or name C4C or name C4D or name C5 or name C6 or name C7 o \ r name C8 or name C9 or name CAA or name CAB or name CAC or name CAD or name CBA \ or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or name \ CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or \ name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2D o \ r name OBD or name MG )) or resid 516 or resid 518 through 519)) } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = chain 'U' selection = chain 'u' } ncs_group { reference = chain 'V' selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'w' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 12.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 24.940 Check model and map are aligned: 0.800 Set scattering table: 0.500 Process input model: 142.470 Find NCS groups from input model: 3.880 Set up NCS constraints: 1.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.012 0.334 74674 Z= 0.667 Angle : 1.912 62.109 105044 Z= 0.708 Chirality : 0.078 1.577 10022 Planarity : 0.010 0.257 13622 Dihedral : 23.563 177.202 25438 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.65 % Favored : 91.51 % Rotamer: Outliers : 2.91 % Allowed : 1.43 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: -0.72 (0.10), residues: 7198 helix: 0.82 (0.08), residues: 3814 sheet: -0.29 (0.38), residues: 216 loop : -2.20 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 131 HIS 0.009 0.002 HIS c 237 PHE 0.036 0.002 PHE B 246 TYR 0.013 0.001 TYR J 30 ARG 0.010 0.000 ARG 3 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1081 time to evaluate : 5.152 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7938 (pm20) cc_final: 0.7665 (pm20) REVERT: E 62 GLN cc_start: 0.8359 (pm20) cc_final: 0.8088 (pm20) REVERT: F 15 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6930 (pt) REVERT: H 71 ASP cc_start: 0.8262 (p0) cc_final: 0.8059 (p0) REVERT: Q 130 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8471 (pptt) REVERT: Q 197 ASN cc_start: 0.7798 (m110) cc_final: 0.7515 (m110) REVERT: U 19 TYR cc_start: 0.8890 (m-80) cc_final: 0.8649 (m-80) REVERT: U 77 LYS cc_start: 0.9321 (tppp) cc_final: 0.9023 (tppp) REVERT: U 95 ASP cc_start: 0.8207 (m-30) cc_final: 0.7862 (m-30) REVERT: V 57 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8119 (tm-30) REVERT: W 114 TRP cc_start: 0.8303 (m100) cc_final: 0.7993 (m-90) REVERT: W 128 ASN cc_start: 0.4909 (t0) cc_final: 0.4439 (p0) REVERT: a 243 GLU cc_start: 0.7915 (pm20) cc_final: 0.7611 (pm20) REVERT: b 60 MET cc_start: 0.9150 (mmp) cc_final: 0.8867 (mmp) REVERT: e 62 GLN cc_start: 0.8339 (pm20) cc_final: 0.8116 (pm20) REVERT: f 15 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6997 (pt) REVERT: o 94 GLN cc_start: 0.8823 (mt0) cc_final: 0.8550 (mt0) REVERT: o 134 ILE cc_start: 0.8896 (mm) cc_final: 0.8692 (mp) REVERT: q 130 LYS cc_start: 0.8990 (ptmt) cc_final: 0.8572 (pptt) REVERT: q 166 THR cc_start: 0.8921 (p) cc_final: 0.8577 (p) REVERT: q 169 GLU cc_start: 0.8275 (tt0) cc_final: 0.8059 (tm-30) REVERT: q 197 ASN cc_start: 0.7707 (m110) cc_final: 0.7471 (m110) REVERT: u 19 TYR cc_start: 0.8872 (m-80) cc_final: 0.8583 (m-80) REVERT: u 77 LYS cc_start: 0.9311 (tppp) cc_final: 0.9086 (tppp) REVERT: u 95 ASP cc_start: 0.8211 (m-30) cc_final: 0.7866 (m-30) REVERT: v 57 GLU cc_start: 0.8221 (tm-30) cc_final: 0.8002 (tm-30) REVERT: w 114 TRP cc_start: 0.8293 (m100) cc_final: 0.8052 (m-90) REVERT: w 128 ASN cc_start: 0.4890 (t0) cc_final: 0.4305 (p0) REVERT: x 112 ASP cc_start: 0.8465 (t0) cc_final: 0.8198 (t0) REVERT: 5 145 ASP cc_start: 0.8926 (t0) cc_final: 0.8716 (t0) REVERT: 7 65 MET cc_start: 0.8763 (mtt) cc_final: 0.8419 (mtm) REVERT: 3 59 PHE cc_start: 0.5934 (t80) cc_final: 0.5645 (t80) REVERT: 3 84 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7471 (tm-30) REVERT: 8 59 PHE cc_start: 0.5841 (t80) cc_final: 0.5598 (t80) REVERT: 0 145 ASP cc_start: 0.8929 (t0) cc_final: 0.8719 (t0) REVERT: 2 65 MET cc_start: 0.8770 (mtt) cc_final: 0.8431 (mtm) outliers start: 149 outliers final: 23 residues processed: 1175 average time/residue: 1.2490 time to fit residues: 2021.6091 Evaluate side-chains 830 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 805 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain W residue 102 ILE Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain o residue 176 THR Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 95 SER Chi-restraints excluded: chain v residue 74 ASP Chi-restraints excluded: chain w residue 102 ILE Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 6 residue 192 THR Chi-restraints excluded: chain 0 residue 127 ILE Chi-restraints excluded: chain 1 residue 192 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 629 optimal weight: 9.9990 chunk 565 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 381 optimal weight: 0.0770 chunk 302 optimal weight: 0.8980 chunk 584 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 355 optimal weight: 0.5980 chunk 435 optimal weight: 0.7980 chunk 677 optimal weight: 50.0000 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** M 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 337 GLN U 30 ASN U 99 ASN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 385 GLN ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 33 ASN o 219 ASN o 228 GLN o 337 GLN q 126 ASN u 30 ASN u 99 ASN 5 80 GLN p 146 GLN ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 80 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 74674 Z= 0.193 Angle : 0.915 29.725 105044 Z= 0.365 Chirality : 0.055 0.973 10022 Planarity : 0.005 0.106 13622 Dihedral : 22.037 178.308 14680 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.35 % Rotamer: Outliers : 2.91 % Allowed : 13.03 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.31 (0.10), residues: 7198 helix: 1.13 (0.08), residues: 3794 sheet: -1.00 (0.33), residues: 250 loop : -1.88 (0.11), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.012 0.002 HIS b 142 PHE 0.033 0.001 PHE P 234 TYR 0.018 0.001 TYR q 94 ARG 0.008 0.000 ARG x 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 859 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7732 (pt0) cc_final: 0.7484 (pt0) REVERT: A 243 GLU cc_start: 0.7989 (pm20) cc_final: 0.7700 (pm20) REVERT: B 60 MET cc_start: 0.9234 (mmp) cc_final: 0.8994 (mmt) REVERT: C 255 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8023 (ttmm) REVERT: D 308 ASP cc_start: 0.8739 (t0) cc_final: 0.8496 (t0) REVERT: E 62 GLN cc_start: 0.8354 (pm20) cc_final: 0.8107 (pm20) REVERT: E 77 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7560 (mt-10) REVERT: Q 197 ASN cc_start: 0.7855 (m110) cc_final: 0.7577 (m110) REVERT: Q 199 LYS cc_start: 0.8888 (tppt) cc_final: 0.8167 (tptt) REVERT: U 19 TYR cc_start: 0.8904 (m-80) cc_final: 0.8701 (m-80) REVERT: U 77 LYS cc_start: 0.9330 (tppp) cc_final: 0.9029 (tppp) REVERT: U 95 ASP cc_start: 0.8161 (m-30) cc_final: 0.7870 (m-30) REVERT: V 57 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7877 (tm-30) REVERT: W 114 TRP cc_start: 0.8244 (m100) cc_final: 0.8009 (m100) REVERT: W 128 ASN cc_start: 0.4830 (t0) cc_final: 0.4536 (p0) REVERT: X 112 ASP cc_start: 0.7658 (t0) cc_final: 0.7165 (t0) REVERT: Y 14 ASP cc_start: 0.7857 (p0) cc_final: 0.7566 (t0) REVERT: a 243 GLU cc_start: 0.7951 (pm20) cc_final: 0.7613 (pm20) REVERT: b 60 MET cc_start: 0.9169 (mmp) cc_final: 0.8949 (mmp) REVERT: d 308 ASP cc_start: 0.8748 (t0) cc_final: 0.8514 (t0) REVERT: e 62 GLN cc_start: 0.8305 (pm20) cc_final: 0.8098 (pm20) REVERT: o 94 GLN cc_start: 0.8866 (mt0) cc_final: 0.8498 (mt0) REVERT: u 19 TYR cc_start: 0.8871 (m-80) cc_final: 0.8523 (m-80) REVERT: u 77 LYS cc_start: 0.9329 (tppp) cc_final: 0.9086 (tppp) REVERT: u 95 ASP cc_start: 0.8184 (m-30) cc_final: 0.7905 (m-30) REVERT: v 57 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7732 (tm-30) REVERT: w 114 TRP cc_start: 0.8244 (m100) cc_final: 0.7831 (m-90) REVERT: w 128 ASN cc_start: 0.4790 (t0) cc_final: 0.4341 (p0) REVERT: x 112 ASP cc_start: 0.7812 (t0) cc_final: 0.7324 (t0) REVERT: y 14 ASP cc_start: 0.7829 (p0) cc_final: 0.7503 (t0) REVERT: z 32 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6636 (tm-30) REVERT: 5 94 TYR cc_start: 0.8924 (t80) cc_final: 0.8676 (t80) REVERT: 5 128 SER cc_start: 0.9092 (p) cc_final: 0.8877 (m) REVERT: 5 145 ASP cc_start: 0.9118 (t0) cc_final: 0.8826 (t0) REVERT: 3 59 PHE cc_start: 0.5875 (t80) cc_final: 0.5613 (t80) REVERT: 3 80 TYR cc_start: 0.7338 (m-10) cc_final: 0.6817 (m-80) REVERT: 0 94 TYR cc_start: 0.8929 (t80) cc_final: 0.8684 (t80) REVERT: 0 128 SER cc_start: 0.9105 (p) cc_final: 0.8887 (m) REVERT: 0 145 ASP cc_start: 0.9113 (t0) cc_final: 0.8815 (t0) outliers start: 149 outliers final: 64 residues processed: 934 average time/residue: 1.1450 time to fit residues: 1524.7071 Evaluate side-chains 851 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 787 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 334 ASP Chi-restraints excluded: chain b residue 440 ASP Chi-restraints excluded: chain b residue 478 VAL Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 173 PHE Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain f residue 17 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 176 THR Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain t residue 29 ILE Chi-restraints excluded: chain u residue 60 SER Chi-restraints excluded: chain u residue 74 ASP Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain z residue 8 LEU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 6 residue 176 SER Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain 3 residue 173 SER Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain 8 residue 173 SER Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 1 residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 3.9990 chunk 210 optimal weight: 0.0670 chunk 563 optimal weight: 9.9990 chunk 461 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 678 optimal weight: 30.0000 chunk 733 optimal weight: 8.9990 chunk 604 optimal weight: 0.9980 chunk 673 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 chunk 544 optimal weight: 0.9980 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 228 GLN O 337 GLN Q 126 ASN Y 34 ASN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN o 337 GLN ** q 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 34 ASN 5 196 ASN ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 196 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 74674 Z= 0.248 Angle : 0.832 24.944 105044 Z= 0.337 Chirality : 0.056 0.988 10022 Planarity : 0.005 0.092 13622 Dihedral : 19.291 174.029 14659 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 3.30 % Allowed : 14.22 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: -0.01 (0.10), residues: 7198 helix: 1.33 (0.08), residues: 3812 sheet: -1.00 (0.31), residues: 276 loop : -1.68 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.012 0.002 HIS b 466 PHE 0.019 0.001 PHE C 432 TYR 0.022 0.001 TYR Q 150 ARG 0.004 0.000 ARG q 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 824 time to evaluate : 5.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7841 (pt0) cc_final: 0.7622 (pt0) REVERT: A 243 GLU cc_start: 0.8063 (pm20) cc_final: 0.7759 (pm20) REVERT: B 18 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8787 (mtt180) REVERT: B 60 MET cc_start: 0.9254 (mmp) cc_final: 0.8886 (mmt) REVERT: B 438 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 62 GLN cc_start: 0.8409 (pm20) cc_final: 0.8140 (pm20) REVERT: F 15 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6693 (tp) REVERT: L 14 ASN cc_start: 0.8208 (m110) cc_final: 0.7888 (m-40) REVERT: O 288 ARG cc_start: 0.8623 (tpt170) cc_final: 0.8308 (tpt170) REVERT: Q 150 TYR cc_start: 0.7893 (t80) cc_final: 0.7671 (t80) REVERT: Q 153 GLU cc_start: 0.7952 (mp0) cc_final: 0.7712 (mp0) REVERT: Q 197 ASN cc_start: 0.7989 (m110) cc_final: 0.7742 (m110) REVERT: U 77 LYS cc_start: 0.9352 (tppp) cc_final: 0.9071 (tppp) REVERT: U 95 ASP cc_start: 0.8169 (m-30) cc_final: 0.7941 (m-30) REVERT: V 57 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7888 (tm-30) REVERT: V 110 GLU cc_start: 0.8451 (tp30) cc_final: 0.8195 (tp30) REVERT: W 114 TRP cc_start: 0.8204 (m100) cc_final: 0.7780 (m-90) REVERT: W 128 ASN cc_start: 0.5385 (t0) cc_final: 0.5041 (p0) REVERT: X 112 ASP cc_start: 0.7717 (t0) cc_final: 0.7072 (t0) REVERT: Y 14 ASP cc_start: 0.8073 (p0) cc_final: 0.7714 (t0) REVERT: b 60 MET cc_start: 0.9222 (mmp) cc_final: 0.8913 (mmt) REVERT: b 81 THR cc_start: 0.9624 (OUTLIER) cc_final: 0.9269 (p) REVERT: b 438 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7456 (tm-30) REVERT: e 77 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7664 (mt-10) REVERT: f 15 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6655 (tp) REVERT: o 94 GLN cc_start: 0.8847 (mt0) cc_final: 0.8490 (mt0) REVERT: q 123 GLU cc_start: 0.8138 (tp30) cc_final: 0.7734 (tp30) REVERT: q 150 TYR cc_start: 0.7787 (t80) cc_final: 0.7246 (t80) REVERT: q 153 GLU cc_start: 0.7878 (mp0) cc_final: 0.7666 (mp0) REVERT: u 19 TYR cc_start: 0.8955 (m-80) cc_final: 0.8545 (m-80) REVERT: u 95 ASP cc_start: 0.8220 (m-30) cc_final: 0.7936 (m-30) REVERT: v 55 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8630 (p0) REVERT: v 57 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7788 (tm-30) REVERT: v 110 GLU cc_start: 0.8429 (tp30) cc_final: 0.8107 (tp30) REVERT: w 114 TRP cc_start: 0.8200 (m100) cc_final: 0.7797 (m-90) REVERT: w 128 ASN cc_start: 0.5045 (t0) cc_final: 0.4568 (p0) REVERT: x 112 ASP cc_start: 0.7900 (t0) cc_final: 0.7350 (t0) REVERT: y 14 ASP cc_start: 0.8101 (p0) cc_final: 0.7681 (t0) REVERT: 5 145 ASP cc_start: 0.9081 (t0) cc_final: 0.8795 (t0) REVERT: 7 162 ASP cc_start: 0.8865 (t0) cc_final: 0.8640 (t0) REVERT: 3 59 PHE cc_start: 0.5825 (t80) cc_final: 0.5583 (t80) REVERT: 3 172 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8134 (p0) REVERT: 0 145 ASP cc_start: 0.9083 (t0) cc_final: 0.8781 (t0) outliers start: 169 outliers final: 87 residues processed: 904 average time/residue: 1.1214 time to fit residues: 1444.1631 Evaluate side-chains 860 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 767 time to evaluate : 5.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 12 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 334 ASP Chi-restraints excluded: chain b residue 440 ASP Chi-restraints excluded: chain b residue 478 VAL Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain l residue 12 GLU Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 93 SER Chi-restraints excluded: chain o residue 176 THR Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 126 ASN Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain t residue 29 ILE Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain u residue 60 SER Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain v residue 114 SER Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 6 residue 176 SER Chi-restraints excluded: chain 6 residue 192 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain p residue 226 ILE Chi-restraints excluded: chain 3 residue 172 ASP Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 115 THR Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 0 residue 128 SER Chi-restraints excluded: chain 1 residue 176 SER Chi-restraints excluded: chain 1 residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 20.0000 chunk 510 optimal weight: 5.9990 chunk 352 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 455 optimal weight: 3.9990 chunk 681 optimal weight: 30.0000 chunk 721 optimal weight: 0.0570 chunk 355 optimal weight: 0.9990 chunk 645 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 228 GLN O 337 GLN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN 5 196 ASN ** p 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 229 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 229 GLN 0 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 74674 Z= 0.320 Angle : 0.826 24.974 105044 Z= 0.338 Chirality : 0.057 0.982 10022 Planarity : 0.005 0.076 13622 Dihedral : 18.497 177.464 14657 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Rotamer: Outliers : 3.67 % Allowed : 15.84 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: 0.06 (0.10), residues: 7198 helix: 1.35 (0.08), residues: 3810 sheet: -0.84 (0.32), residues: 268 loop : -1.59 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 223 HIS 0.011 0.002 HIS b 157 PHE 0.031 0.001 PHE p 234 TYR 0.015 0.001 TYR h 61 ARG 0.010 0.001 ARG j 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 791 time to evaluate : 5.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8011 (pt0) cc_final: 0.7792 (pt0) REVERT: A 243 GLU cc_start: 0.8129 (pm20) cc_final: 0.7790 (pm20) REVERT: B 18 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8760 (mtt180) REVERT: B 60 MET cc_start: 0.9246 (mmp) cc_final: 0.8947 (mmp) REVERT: B 438 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 467 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9180 (mp) REVERT: C 289 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8484 (t80) REVERT: D 199 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8729 (mtt) REVERT: E 62 GLN cc_start: 0.8473 (pm20) cc_final: 0.8171 (pm20) REVERT: E 77 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7623 (mt-10) REVERT: F 15 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6527 (tp) REVERT: L 14 ASN cc_start: 0.8319 (m110) cc_final: 0.8047 (m-40) REVERT: Q 69 LEU cc_start: 0.8158 (tp) cc_final: 0.7907 (tm) REVERT: Q 123 GLU cc_start: 0.8273 (tp30) cc_final: 0.7644 (tp30) REVERT: Q 150 TYR cc_start: 0.8320 (t80) cc_final: 0.7921 (t80) REVERT: Q 153 GLU cc_start: 0.7886 (mp0) cc_final: 0.7664 (mp0) REVERT: U 77 LYS cc_start: 0.9324 (tppp) cc_final: 0.9090 (tppp) REVERT: U 95 ASP cc_start: 0.8209 (m-30) cc_final: 0.7982 (m-30) REVERT: V 55 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8638 (p0) REVERT: V 57 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7910 (tm-30) REVERT: V 110 GLU cc_start: 0.8541 (tp30) cc_final: 0.8277 (tp30) REVERT: W 102 ILE cc_start: 0.8945 (tp) cc_final: 0.8621 (tt) REVERT: W 114 TRP cc_start: 0.8190 (m100) cc_final: 0.7727 (m100) REVERT: X 112 ASP cc_start: 0.7797 (t0) cc_final: 0.7183 (t0) REVERT: Y 14 ASP cc_start: 0.8075 (p0) cc_final: 0.7652 (t0) REVERT: b 60 MET cc_start: 0.9235 (mmp) cc_final: 0.8906 (mmt) REVERT: b 438 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7630 (tm-30) REVERT: b 467 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9174 (mp) REVERT: c 289 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8398 (t80) REVERT: f 15 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6614 (tp) REVERT: l 14 ASN cc_start: 0.8307 (m110) cc_final: 0.8036 (m-40) REVERT: o 94 GLN cc_start: 0.8819 (mt0) cc_final: 0.8456 (mt0) REVERT: q 69 LEU cc_start: 0.8235 (tp) cc_final: 0.8033 (tm) REVERT: q 123 GLU cc_start: 0.8219 (tp30) cc_final: 0.7796 (tp30) REVERT: u 19 TYR cc_start: 0.9014 (m-80) cc_final: 0.8554 (m-80) REVERT: u 95 ASP cc_start: 0.8234 (m-30) cc_final: 0.8006 (m-30) REVERT: v 55 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8543 (p0) REVERT: v 57 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7839 (tm-30) REVERT: v 110 GLU cc_start: 0.8524 (tp30) cc_final: 0.8264 (tp30) REVERT: w 102 ILE cc_start: 0.8951 (tp) cc_final: 0.8633 (tt) REVERT: w 114 TRP cc_start: 0.8188 (m100) cc_final: 0.7618 (m100) REVERT: x 112 ASP cc_start: 0.8034 (t0) cc_final: 0.7536 (t0) REVERT: y 14 ASP cc_start: 0.8069 (p0) cc_final: 0.7601 (t0) REVERT: z 32 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: 5 145 ASP cc_start: 0.9113 (t0) cc_final: 0.8855 (t0) REVERT: 7 71 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: 6 84 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8455 (t80) REVERT: 3 59 PHE cc_start: 0.5813 (t80) cc_final: 0.5591 (t80) REVERT: 3 80 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: 0 145 ASP cc_start: 0.9114 (t0) cc_final: 0.8840 (t0) REVERT: 1 84 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8435 (t80) outliers start: 188 outliers final: 98 residues processed: 888 average time/residue: 1.1364 time to fit residues: 1434.6305 Evaluate side-chains 865 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 752 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 444 ARG Chi-restraints excluded: chain b residue 467 LEU Chi-restraints excluded: chain b residue 478 VAL Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 325 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 93 SER Chi-restraints excluded: chain o residue 176 THR Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain q residue 126 ASN Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain t residue 29 ILE Chi-restraints excluded: chain u residue 33 ILE Chi-restraints excluded: chain u residue 60 SER Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain u residue 101 LEU Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain v residue 74 ASP Chi-restraints excluded: chain v residue 114 SER Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 32 GLU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 176 SER Chi-restraints excluded: chain 6 residue 192 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 0 residue 101 ASP Chi-restraints excluded: chain 0 residue 115 THR Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 0 residue 128 SER Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 176 SER Chi-restraints excluded: chain 1 residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 30.0000 chunk 409 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 536 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 615 optimal weight: 50.0000 chunk 498 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 368 optimal weight: 0.7980 chunk 647 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 228 GLN ** Q 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 99 ASN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN u 99 ASN 5 196 ASN p 118 ASN p 200 GLN P 118 ASN P 200 GLN P 229 GLN 0 196 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 74674 Z= 0.357 Angle : 0.831 25.211 105044 Z= 0.342 Chirality : 0.057 0.967 10022 Planarity : 0.005 0.077 13622 Dihedral : 18.074 178.341 14655 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 3.98 % Allowed : 16.54 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: 0.07 (0.10), residues: 7198 helix: 1.32 (0.08), residues: 3814 sheet: -0.92 (0.31), residues: 268 loop : -1.53 (0.11), residues: 3116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.016 0.002 HIS 8 69 PHE 0.021 0.001 PHE b 246 TYR 0.012 0.001 TYR h 61 ARG 0.008 0.001 ARG v 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 786 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8156 (pt0) cc_final: 0.7954 (pt0) REVERT: A 243 GLU cc_start: 0.8163 (pm20) cc_final: 0.7806 (pm20) REVERT: B 18 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8750 (mtt180) REVERT: B 60 MET cc_start: 0.9247 (mmp) cc_final: 0.8946 (mmp) REVERT: B 467 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9178 (mp) REVERT: C 289 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8434 (t80) REVERT: E 62 GLN cc_start: 0.8531 (pm20) cc_final: 0.8198 (pm20) REVERT: F 15 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6645 (tp) REVERT: L 14 ASN cc_start: 0.8343 (m110) cc_final: 0.8121 (m-40) REVERT: O 94 GLN cc_start: 0.8855 (mt0) cc_final: 0.8486 (mt0) REVERT: Q 123 GLU cc_start: 0.8275 (tp30) cc_final: 0.7757 (tp30) REVERT: U 77 LYS cc_start: 0.9317 (tppp) cc_final: 0.9111 (tppp) REVERT: U 95 ASP cc_start: 0.8263 (m-30) cc_final: 0.8022 (m-30) REVERT: V 55 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8554 (p0) REVERT: V 57 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7976 (tm-30) REVERT: V 110 GLU cc_start: 0.8584 (tp30) cc_final: 0.8323 (tp30) REVERT: W 102 ILE cc_start: 0.8923 (tp) cc_final: 0.8594 (tt) REVERT: W 114 TRP cc_start: 0.8185 (m100) cc_final: 0.7590 (m100) REVERT: W 128 ASN cc_start: 0.4815 (t0) cc_final: 0.4608 (p0) REVERT: X 112 ASP cc_start: 0.7958 (t0) cc_final: 0.7353 (t0) REVERT: Y 14 ASP cc_start: 0.8119 (p0) cc_final: 0.7652 (t0) REVERT: b 60 MET cc_start: 0.9244 (mmp) cc_final: 0.8957 (mmp) REVERT: b 438 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7693 (tm-30) REVERT: b 467 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9176 (mp) REVERT: c 289 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8337 (t80) REVERT: e 18 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8256 (ptm-80) REVERT: e 77 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7682 (mt-10) REVERT: f 15 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6755 (tp) REVERT: l 14 ASN cc_start: 0.8326 (m110) cc_final: 0.8110 (m-40) REVERT: q 123 GLU cc_start: 0.8278 (tp30) cc_final: 0.7751 (tp30) REVERT: q 128 LEU cc_start: 0.8818 (tp) cc_final: 0.8529 (tt) REVERT: u 19 TYR cc_start: 0.9051 (m-80) cc_final: 0.8635 (m-80) REVERT: u 95 ASP cc_start: 0.8295 (m-30) cc_final: 0.8062 (m-30) REVERT: v 55 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8502 (p0) REVERT: v 57 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7886 (tm-30) REVERT: v 110 GLU cc_start: 0.8560 (tp30) cc_final: 0.8296 (tp30) REVERT: w 102 ILE cc_start: 0.8918 (tp) cc_final: 0.8604 (tt) REVERT: w 114 TRP cc_start: 0.8182 (m100) cc_final: 0.7552 (m100) REVERT: w 128 ASN cc_start: 0.5122 (t0) cc_final: 0.4776 (p0) REVERT: x 112 ASP cc_start: 0.8123 (t0) cc_final: 0.7662 (t0) REVERT: y 14 ASP cc_start: 0.8175 (p0) cc_final: 0.7693 (t0) REVERT: z 32 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: 5 145 ASP cc_start: 0.9109 (t0) cc_final: 0.8882 (t0) REVERT: 7 71 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: 6 84 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8434 (t80) REVERT: 6 153 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8579 (mmt90) REVERT: 3 80 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: 8 80 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: 0 145 ASP cc_start: 0.9112 (t0) cc_final: 0.8906 (t0) REVERT: 2 71 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: 2 177 MET cc_start: 0.9043 (tpp) cc_final: 0.8796 (tpp) REVERT: 1 84 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8426 (t80) REVERT: 1 153 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8577 (mmt90) outliers start: 204 outliers final: 112 residues processed: 896 average time/residue: 1.1210 time to fit residues: 1434.4046 Evaluate side-chains 883 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 752 time to evaluate : 5.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 332 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 444 ARG Chi-restraints excluded: chain b residue 467 LEU Chi-restraints excluded: chain b residue 478 VAL Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 325 ILE Chi-restraints excluded: chain d residue 332 GLN Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain l residue 12 GLU Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 93 SER Chi-restraints excluded: chain o residue 176 THR Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 126 ASN Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain t residue 29 ILE Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain u residue 60 SER Chi-restraints excluded: chain u residue 69 SER Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain v residue 114 SER Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 32 GLU Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 153 ARG Chi-restraints excluded: chain 6 residue 176 SER Chi-restraints excluded: chain 6 residue 192 THR Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain 8 residue 80 TYR Chi-restraints excluded: chain 8 residue 146 ILE Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 0 residue 101 ASP Chi-restraints excluded: chain 0 residue 115 THR Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 0 residue 128 SER Chi-restraints excluded: chain 2 residue 71 TYR Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 104 ASP Chi-restraints excluded: chain 1 residue 153 ARG Chi-restraints excluded: chain 1 residue 176 SER Chi-restraints excluded: chain 1 residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 7.9990 chunk 649 optimal weight: 40.0000 chunk 142 optimal weight: 0.7980 chunk 423 optimal weight: 0.4980 chunk 178 optimal weight: 0.9980 chunk 721 optimal weight: 0.9980 chunk 599 optimal weight: 20.0000 chunk 334 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 chunk 378 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 228 GLN U 99 ASN ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN 5 196 ASN 6 199 ASN p 229 GLN P 229 GLN 0 196 ASN 1 199 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 74674 Z= 0.180 Angle : 0.770 25.456 105044 Z= 0.312 Chirality : 0.055 0.961 10022 Planarity : 0.004 0.069 13622 Dihedral : 17.526 179.611 14655 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 3.01 % Allowed : 18.16 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: 0.27 (0.10), residues: 7198 helix: 1.48 (0.08), residues: 3820 sheet: -0.84 (0.32), residues: 244 loop : -1.43 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.011 0.001 HIS 8 69 PHE 0.030 0.001 PHE p 234 TYR 0.013 0.001 TYR q 150 ARG 0.008 0.000 ARG V 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 793 time to evaluate : 5.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8141 (pt0) cc_final: 0.7921 (pt0) REVERT: A 243 GLU cc_start: 0.8147 (pm20) cc_final: 0.7802 (pm20) REVERT: B 18 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8683 (mtt180) REVERT: B 60 MET cc_start: 0.9218 (mmp) cc_final: 0.8921 (mmt) REVERT: B 426 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9043 (pp) REVERT: C 289 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8390 (t80) REVERT: C 379 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (mttm) REVERT: E 62 GLN cc_start: 0.8505 (pm20) cc_final: 0.8192 (pm20) REVERT: E 77 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7677 (mt-10) REVERT: F 15 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6695 (tt) REVERT: L 14 ASN cc_start: 0.8205 (m110) cc_final: 0.7926 (m-40) REVERT: Q 128 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8639 (tt) REVERT: Q 150 TYR cc_start: 0.8300 (t80) cc_final: 0.8012 (t80) REVERT: U 77 LYS cc_start: 0.9332 (tppp) cc_final: 0.9109 (tppp) REVERT: U 95 ASP cc_start: 0.8218 (m-30) cc_final: 0.7976 (m-30) REVERT: V 57 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7818 (tm-30) REVERT: V 110 GLU cc_start: 0.8591 (tp30) cc_final: 0.8305 (tp30) REVERT: W 102 ILE cc_start: 0.8910 (tp) cc_final: 0.8578 (tt) REVERT: X 112 ASP cc_start: 0.7769 (t0) cc_final: 0.7171 (t0) REVERT: Y 14 ASP cc_start: 0.8182 (p0) cc_final: 0.7687 (t0) REVERT: b 60 MET cc_start: 0.9180 (mmp) cc_final: 0.8914 (mmt) REVERT: b 81 THR cc_start: 0.9645 (OUTLIER) cc_final: 0.9266 (p) REVERT: b 426 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9020 (pp) REVERT: b 438 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7726 (tm-30) REVERT: c 173 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: c 289 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8312 (t80) REVERT: e 77 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7628 (mt-10) REVERT: f 15 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6656 (tt) REVERT: l 14 ASN cc_start: 0.8270 (m110) cc_final: 0.8005 (m-40) REVERT: q 123 GLU cc_start: 0.8321 (tp30) cc_final: 0.7892 (tp30) REVERT: q 128 LEU cc_start: 0.8778 (tp) cc_final: 0.8516 (tt) REVERT: u 19 TYR cc_start: 0.9004 (m-80) cc_final: 0.8571 (m-80) REVERT: u 95 ASP cc_start: 0.8257 (m-30) cc_final: 0.8024 (m-30) REVERT: v 57 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7797 (tm-30) REVERT: v 110 GLU cc_start: 0.8514 (tp30) cc_final: 0.8313 (tp30) REVERT: w 102 ILE cc_start: 0.8896 (tp) cc_final: 0.8577 (tt) REVERT: x 112 ASP cc_start: 0.8009 (t0) cc_final: 0.7551 (t0) REVERT: y 14 ASP cc_start: 0.8215 (p0) cc_final: 0.7703 (t0) REVERT: 5 145 ASP cc_start: 0.9082 (t0) cc_final: 0.8824 (t0) REVERT: 7 71 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: 6 84 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8394 (t80) REVERT: 3 80 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: 8 80 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: 0 145 ASP cc_start: 0.9101 (t0) cc_final: 0.8792 (t0) REVERT: 2 71 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: 1 84 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8367 (t80) outliers start: 154 outliers final: 75 residues processed: 872 average time/residue: 1.1083 time to fit residues: 1390.2451 Evaluate side-chains 837 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 745 time to evaluate : 5.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 166 THR Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 426 LEU Chi-restraints excluded: chain b residue 478 VAL Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 173 PHE Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain l residue 12 GLU Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 271 ASP Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 74 ASP Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain 8 residue 80 TYR Chi-restraints excluded: chain 8 residue 146 ILE Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 0 residue 127 ILE Chi-restraints excluded: chain 0 residue 196 ASN Chi-restraints excluded: chain 2 residue 71 TYR Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 104 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 chunk 527 optimal weight: 5.9990 chunk 408 optimal weight: 0.9980 chunk 607 optimal weight: 0.1980 chunk 403 optimal weight: 1.9990 chunk 719 optimal weight: 0.0980 chunk 449 optimal weight: 3.9990 chunk 438 optimal weight: 0.0020 chunk 331 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN U 99 ASN ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN q 126 ASN 5 196 ASN 6 199 ASN P 229 GLN 0 196 ASN 1 199 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 74674 Z= 0.168 Angle : 0.759 24.385 105044 Z= 0.307 Chirality : 0.055 0.961 10022 Planarity : 0.004 0.067 13622 Dihedral : 17.088 179.800 14653 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.11 % Rotamer: Outliers : 2.62 % Allowed : 19.39 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: 0.39 (0.10), residues: 7198 helix: 1.58 (0.08), residues: 3808 sheet: -1.00 (0.32), residues: 256 loop : -1.33 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.010 0.001 HIS 8 69 PHE 0.029 0.001 PHE P 234 TYR 0.013 0.001 TYR q 150 ARG 0.006 0.000 ARG V 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 778 time to evaluate : 5.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8158 (pm20) cc_final: 0.7799 (pm20) REVERT: B 18 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8657 (mtt180) REVERT: B 60 MET cc_start: 0.9216 (mmp) cc_final: 0.8909 (mmt) REVERT: B 208 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8741 (m-80) REVERT: B 426 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9053 (pp) REVERT: B 438 GLU cc_start: 0.7806 (tp30) cc_final: 0.7263 (tm-30) REVERT: C 289 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8352 (t80) REVERT: C 379 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8632 (mttm) REVERT: E 62 GLN cc_start: 0.8502 (pm20) cc_final: 0.8195 (pm20) REVERT: E 77 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7703 (mt-10) REVERT: F 15 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6682 (tt) REVERT: L 14 ASN cc_start: 0.8159 (m110) cc_final: 0.7881 (m-40) REVERT: Q 123 GLU cc_start: 0.8331 (tp30) cc_final: 0.7904 (tp30) REVERT: Q 128 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8694 (tt) REVERT: U 95 ASP cc_start: 0.8202 (m-30) cc_final: 0.7967 (m-30) REVERT: V 55 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8439 (p0) REVERT: V 57 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7775 (tm-30) REVERT: V 110 GLU cc_start: 0.8517 (tp30) cc_final: 0.8303 (tp30) REVERT: W 102 ILE cc_start: 0.8882 (tp) cc_final: 0.8531 (tt) REVERT: X 112 ASP cc_start: 0.7761 (t0) cc_final: 0.7203 (t0) REVERT: Y 14 ASP cc_start: 0.8241 (p0) cc_final: 0.7707 (t0) REVERT: b 60 MET cc_start: 0.9210 (mmp) cc_final: 0.8918 (mmt) REVERT: b 81 THR cc_start: 0.9649 (OUTLIER) cc_final: 0.9294 (p) REVERT: b 438 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7749 (tm-30) REVERT: c 173 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: c 289 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8326 (t80) REVERT: e 77 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7630 (mt-10) REVERT: f 15 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6671 (tt) REVERT: o 257 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8050 (ptp) REVERT: q 123 GLU cc_start: 0.8340 (tp30) cc_final: 0.7923 (tp30) REVERT: q 128 LEU cc_start: 0.8773 (tp) cc_final: 0.8531 (tt) REVERT: u 19 TYR cc_start: 0.9002 (m-80) cc_final: 0.8559 (m-80) REVERT: u 60 SER cc_start: 0.9640 (OUTLIER) cc_final: 0.9426 (p) REVERT: u 95 ASP cc_start: 0.8207 (m-30) cc_final: 0.8000 (m-30) REVERT: v 55 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8409 (p0) REVERT: v 57 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7757 (tm-30) REVERT: w 102 ILE cc_start: 0.8856 (tp) cc_final: 0.8520 (tt) REVERT: x 112 ASP cc_start: 0.7979 (t0) cc_final: 0.7533 (t0) REVERT: y 14 ASP cc_start: 0.8240 (p0) cc_final: 0.7683 (t0) REVERT: 5 145 ASP cc_start: 0.9086 (t0) cc_final: 0.8838 (t0) REVERT: 7 71 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: 6 84 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8280 (t80) REVERT: 3 80 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: 8 80 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: 0 145 ASP cc_start: 0.9099 (t0) cc_final: 0.8775 (t0) REVERT: 2 71 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: 1 84 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8274 (t80) outliers start: 134 outliers final: 74 residues processed: 851 average time/residue: 1.1301 time to fit residues: 1371.1008 Evaluate side-chains 853 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 758 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 440 ASP Chi-restraints excluded: chain b residue 444 ARG Chi-restraints excluded: chain b residue 478 VAL Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain b residue 480 THR Chi-restraints excluded: chain c residue 173 PHE Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 257 MET Chi-restraints excluded: chain o residue 271 ASP Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 67 PHE Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain u residue 60 SER Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain 8 residue 80 TYR Chi-restraints excluded: chain 8 residue 146 ILE Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 2 residue 71 TYR Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 104 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 0.6980 chunk 287 optimal weight: 0.5980 chunk 429 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 457 optimal weight: 0.7980 chunk 489 optimal weight: 8.9990 chunk 355 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 565 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 228 GLN U 99 ASN ** d 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN p 229 GLN P 229 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 74674 Z= 0.171 Angle : 0.756 24.164 105044 Z= 0.307 Chirality : 0.055 0.961 10022 Planarity : 0.004 0.054 13622 Dihedral : 16.801 179.998 14651 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 2.60 % Allowed : 19.79 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: 0.46 (0.10), residues: 7198 helix: 1.63 (0.08), residues: 3806 sheet: -0.99 (0.32), residues: 256 loop : -1.29 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 114 HIS 0.010 0.001 HIS 3 69 PHE 0.021 0.001 PHE p 234 TYR 0.014 0.001 TYR q 150 ARG 0.006 0.000 ARG V 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 766 time to evaluate : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8888 (mtp) REVERT: A 243 GLU cc_start: 0.8158 (pm20) cc_final: 0.7794 (pm20) REVERT: B 18 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8673 (mtt180) REVERT: B 60 MET cc_start: 0.9216 (mmp) cc_final: 0.8908 (mmt) REVERT: B 208 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: B 438 GLU cc_start: 0.7879 (tp30) cc_final: 0.7418 (tm-30) REVERT: C 289 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8319 (t80) REVERT: E 62 GLN cc_start: 0.8511 (pm20) cc_final: 0.8209 (pm20) REVERT: E 77 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7607 (mt-10) REVERT: F 15 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6615 (tt) REVERT: H 69 ASN cc_start: 0.8884 (m-40) cc_final: 0.8406 (t0) REVERT: L 14 ASN cc_start: 0.8088 (m110) cc_final: 0.7842 (m-40) REVERT: Q 69 LEU cc_start: 0.8104 (tp) cc_final: 0.7891 (tm) REVERT: Q 123 GLU cc_start: 0.8384 (tp30) cc_final: 0.7959 (tp30) REVERT: Q 128 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (tt) REVERT: U 95 ASP cc_start: 0.8197 (m-30) cc_final: 0.7969 (m-30) REVERT: V 55 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8421 (p0) REVERT: V 57 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7762 (tm-30) REVERT: V 110 GLU cc_start: 0.8526 (tp30) cc_final: 0.8319 (tp30) REVERT: W 102 ILE cc_start: 0.8870 (tp) cc_final: 0.8529 (tt) REVERT: X 112 ASP cc_start: 0.7753 (t0) cc_final: 0.7280 (t0) REVERT: Y 14 ASP cc_start: 0.8239 (p0) cc_final: 0.7666 (t0) REVERT: b 18 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8151 (mmt180) REVERT: b 60 MET cc_start: 0.9196 (mmp) cc_final: 0.8893 (mmt) REVERT: b 81 THR cc_start: 0.9644 (OUTLIER) cc_final: 0.9288 (p) REVERT: b 438 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7773 (tm-30) REVERT: c 173 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: c 289 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8261 (t80) REVERT: e 77 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7616 (mt-10) REVERT: f 15 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6670 (tt) REVERT: h 69 ASN cc_start: 0.8848 (m110) cc_final: 0.8397 (t0) REVERT: q 123 GLU cc_start: 0.8362 (tp30) cc_final: 0.7927 (tp30) REVERT: q 128 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8541 (tt) REVERT: u 19 TYR cc_start: 0.9002 (m-80) cc_final: 0.8545 (m-80) REVERT: v 57 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7733 (tm-30) REVERT: v 100 ILE cc_start: 0.9276 (mm) cc_final: 0.9063 (mt) REVERT: w 102 ILE cc_start: 0.8877 (tp) cc_final: 0.8542 (tt) REVERT: x 112 ASP cc_start: 0.7995 (t0) cc_final: 0.7556 (t0) REVERT: y 14 ASP cc_start: 0.8239 (p0) cc_final: 0.7647 (t0) REVERT: 5 145 ASP cc_start: 0.9078 (t0) cc_final: 0.8812 (t0) REVERT: 7 71 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: 6 84 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8257 (t80) REVERT: 3 80 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: 8 80 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: 0 145 ASP cc_start: 0.9095 (t0) cc_final: 0.8767 (t0) REVERT: 2 71 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: 1 84 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8256 (t80) outliers start: 133 outliers final: 79 residues processed: 840 average time/residue: 1.1348 time to fit residues: 1357.3728 Evaluate side-chains 853 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 755 time to evaluate : 5.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 108 ILE Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 18 ARG Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 444 ARG Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain b residue 480 THR Chi-restraints excluded: chain c residue 173 PHE Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain j residue 27 LEU Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 271 ASP Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 67 PHE Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 74 ASP Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain p residue 64 SER Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain 8 residue 80 TYR Chi-restraints excluded: chain 8 residue 146 ILE Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 2 residue 71 TYR Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 104 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 30.0000 chunk 688 optimal weight: 6.9990 chunk 628 optimal weight: 50.0000 chunk 670 optimal weight: 20.0000 chunk 403 optimal weight: 5.9990 chunk 291 optimal weight: 0.7980 chunk 526 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 605 optimal weight: 9.9990 chunk 633 optimal weight: 20.0000 chunk 667 optimal weight: 50.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 267 ASN C 74 HIS M 24 ASN O 219 ASN U 99 ASN V 78 ASN a 75 ASN c 74 HIS o 219 ASN o 228 GLN u 99 ASN w 96 ASN 5 196 ASN p 229 GLN P 229 GLN 8 61 GLN 0 196 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 74674 Z= 0.612 Angle : 0.939 25.280 105044 Z= 0.399 Chirality : 0.061 0.971 10022 Planarity : 0.006 0.058 13622 Dihedral : 17.453 175.320 14649 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.75 % Rotamer: Outliers : 2.87 % Allowed : 19.36 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % 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: -0.06 (0.10), residues: 7198 helix: 1.13 (0.08), residues: 3816 sheet: -0.92 (0.33), residues: 244 loop : -1.48 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP W 114 HIS 0.010 0.002 HIS 6 73 PHE 0.035 0.002 PHE p 234 TYR 0.022 0.002 TYR h 61 ARG 0.011 0.001 ARG C 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 736 time to evaluate : 5.209 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8236 (pm20) cc_final: 0.7803 (pm20) REVERT: B 60 MET cc_start: 0.9213 (mmp) cc_final: 0.8848 (mmp) REVERT: B 438 GLU cc_start: 0.8020 (tp30) cc_final: 0.7548 (tm-30) REVERT: C 289 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8550 (t80) REVERT: E 62 GLN cc_start: 0.8603 (pm20) cc_final: 0.8296 (pm20) REVERT: F 15 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6834 (tp) REVERT: H 69 ASN cc_start: 0.8846 (m-40) cc_final: 0.8354 (t0) REVERT: L 14 ASN cc_start: 0.8488 (m110) cc_final: 0.8277 (m-40) REVERT: Q 123 GLU cc_start: 0.8376 (tp30) cc_final: 0.7603 (tp30) REVERT: Q 128 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8592 (tt) REVERT: Q 153 GLU cc_start: 0.8038 (mp0) cc_final: 0.7826 (mp0) REVERT: U 95 ASP cc_start: 0.8330 (m-30) cc_final: 0.8066 (m-30) REVERT: V 57 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7962 (tm-30) REVERT: V 110 GLU cc_start: 0.8578 (tp30) cc_final: 0.8315 (tp30) REVERT: W 102 ILE cc_start: 0.8918 (tp) cc_final: 0.8596 (tt) REVERT: X 112 ASP cc_start: 0.8143 (t0) cc_final: 0.7603 (t0) REVERT: Y 14 ASP cc_start: 0.8333 (p0) cc_final: 0.7802 (p0) REVERT: Z 32 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6787 (tm-30) REVERT: b 18 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8021 (mmt180) REVERT: b 60 MET cc_start: 0.9184 (mmp) cc_final: 0.8813 (mmp) REVERT: b 81 THR cc_start: 0.9665 (OUTLIER) cc_final: 0.9305 (p) REVERT: c 289 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8567 (t80) REVERT: c 339 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8822 (ptmm) REVERT: f 15 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6963 (tp) REVERT: h 69 ASN cc_start: 0.8874 (m110) cc_final: 0.8394 (t0) REVERT: l 14 ASN cc_start: 0.8501 (m110) cc_final: 0.8300 (m-40) REVERT: o 94 GLN cc_start: 0.8907 (mt0) cc_final: 0.8654 (mt0) REVERT: o 257 MET cc_start: 0.9118 (ptp) cc_final: 0.8554 (ptp) REVERT: q 67 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: q 123 GLU cc_start: 0.8353 (tp30) cc_final: 0.7795 (tp30) REVERT: q 128 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8535 (tt) REVERT: v 57 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7915 (tm-30) REVERT: w 102 ILE cc_start: 0.8944 (tp) cc_final: 0.8631 (tt) REVERT: x 112 ASP cc_start: 0.8213 (t0) cc_final: 0.7864 (t0) REVERT: y 14 ASP cc_start: 0.8355 (p0) cc_final: 0.7822 (p0) REVERT: z 32 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6775 (tm-30) REVERT: 7 71 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: 6 84 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8285 (t80) REVERT: 6 153 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8588 (mmt90) REVERT: 3 80 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: 8 80 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: 0 145 ASP cc_start: 0.9133 (t0) cc_final: 0.8929 (t0) REVERT: 2 71 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: 1 84 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8246 (t80) REVERT: 1 153 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8979 (mmt90) outliers start: 147 outliers final: 80 residues processed: 817 average time/residue: 1.1506 time to fit residues: 1336.8656 Evaluate side-chains 817 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 720 time to evaluate : 5.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 78 ASN Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 18 ARG Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 444 ARG Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain c residue 384 ILE Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 325 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 271 ASP Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 67 PHE Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain t residue 2 GLU Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain u residue 33 ILE Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 74 ASP Chi-restraints excluded: chain v residue 114 SER Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 153 ARG Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain 8 residue 80 TYR Chi-restraints excluded: chain 8 residue 146 ILE Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 0 residue 101 ASP Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 0 residue 128 SER Chi-restraints excluded: chain 2 residue 71 TYR Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 104 ASP Chi-restraints excluded: chain 1 residue 153 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 0.9980 chunk 708 optimal weight: 4.9990 chunk 432 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 chunk 492 optimal weight: 4.9990 chunk 743 optimal weight: 0.9980 chunk 684 optimal weight: 50.0000 chunk 591 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 457 optimal weight: 0.8980 chunk 362 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 219 ASN O 228 GLN ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 219 ASN o 228 GLN v 78 ASN ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 229 GLN P 229 GLN 0 196 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.196 74674 Z= 0.431 Angle : 0.966 59.180 105044 Z= 0.426 Chirality : 0.060 0.976 10022 Planarity : 0.006 0.057 13622 Dihedral : 17.376 175.290 14649 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 2.46 % Allowed : 19.80 % Favored : 77.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.05 % 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: -0.05 (0.10), residues: 7198 helix: 1.15 (0.08), residues: 3804 sheet: -0.98 (0.33), residues: 242 loop : -1.47 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP W 114 HIS 0.011 0.002 HIS B 466 PHE 0.023 0.002 PHE W 120 TYR 0.041 0.002 TYR w 106 ARG 0.005 0.001 ARG C 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14396 Ramachandran restraints generated. 7198 Oldfield, 0 Emsley, 7198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 722 time to evaluate : 5.226 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8234 (pm20) cc_final: 0.7800 (pm20) REVERT: B 60 MET cc_start: 0.9218 (mmp) cc_final: 0.8860 (mmp) REVERT: B 438 GLU cc_start: 0.8024 (tp30) cc_final: 0.7542 (tm-30) REVERT: C 289 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.8557 (t80) REVERT: E 62 GLN cc_start: 0.8595 (pm20) cc_final: 0.8289 (pm20) REVERT: F 15 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6826 (tp) REVERT: H 69 ASN cc_start: 0.8839 (m-40) cc_final: 0.8344 (t0) REVERT: L 14 ASN cc_start: 0.8473 (m110) cc_final: 0.8245 (m-40) REVERT: Q 123 GLU cc_start: 0.8370 (tp30) cc_final: 0.7665 (tp30) REVERT: Q 128 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8588 (tt) REVERT: U 95 ASP cc_start: 0.8318 (m-30) cc_final: 0.8056 (m-30) REVERT: V 55 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (p0) REVERT: V 57 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7989 (tm-30) REVERT: V 110 GLU cc_start: 0.8567 (tp30) cc_final: 0.8307 (tp30) REVERT: W 102 ILE cc_start: 0.8906 (tp) cc_final: 0.8584 (tt) REVERT: X 112 ASP cc_start: 0.8129 (t0) cc_final: 0.7588 (t0) REVERT: Y 14 ASP cc_start: 0.8330 (p0) cc_final: 0.7795 (p0) REVERT: Z 32 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6768 (tm-30) REVERT: b 18 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7998 (mmt180) REVERT: b 60 MET cc_start: 0.9176 (mmp) cc_final: 0.8802 (mmp) REVERT: b 81 THR cc_start: 0.9657 (OUTLIER) cc_final: 0.9304 (p) REVERT: c 289 TYR cc_start: 0.9373 (OUTLIER) cc_final: 0.8551 (t80) REVERT: c 339 LYS cc_start: 0.9106 (ptpp) cc_final: 0.8815 (ptmm) REVERT: f 15 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6956 (tp) REVERT: h 69 ASN cc_start: 0.8867 (m110) cc_final: 0.8389 (t0) REVERT: l 14 ASN cc_start: 0.8492 (m110) cc_final: 0.8273 (m-40) REVERT: o 94 GLN cc_start: 0.8907 (mt0) cc_final: 0.8652 (mt0) REVERT: o 257 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8543 (ptp) REVERT: q 123 GLU cc_start: 0.8351 (tp30) cc_final: 0.7785 (tp30) REVERT: q 128 LEU cc_start: 0.8731 (tp) cc_final: 0.8489 (tt) REVERT: v 55 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (p0) REVERT: v 57 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7900 (tm-30) REVERT: w 102 ILE cc_start: 0.8932 (tp) cc_final: 0.8620 (tt) REVERT: x 112 ASP cc_start: 0.8203 (t0) cc_final: 0.7853 (t0) REVERT: y 14 ASP cc_start: 0.8351 (p0) cc_final: 0.7816 (p0) REVERT: z 32 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6750 (tm-30) REVERT: 7 71 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: 6 84 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8277 (t80) REVERT: 6 153 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8603 (mmt90) REVERT: 3 80 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: 8 80 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: 0 145 ASP cc_start: 0.9128 (t0) cc_final: 0.8925 (t0) REVERT: 2 71 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: 1 84 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8237 (t80) REVERT: 1 153 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8979 (mmt90) outliers start: 126 outliers final: 93 residues processed: 787 average time/residue: 1.1533 time to fit residues: 1291.5439 Evaluate side-chains 827 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 716 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain O residue 284 ILE Chi-restraints excluded: chain O residue 291 MET Chi-restraints excluded: chain O residue 327 THR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain b residue 18 ARG Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 444 ARG Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 79 LYS Chi-restraints excluded: chain c residue 289 TYR Chi-restraints excluded: chain c residue 360 ASP Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 325 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain h residue 42 ILE Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 36 ASP Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain o residue 93 SER Chi-restraints excluded: chain o residue 177 VAL Chi-restraints excluded: chain o residue 257 MET Chi-restraints excluded: chain o residue 271 ASP Chi-restraints excluded: chain o residue 284 ILE Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 327 THR Chi-restraints excluded: chain o residue 335 VAL Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain t residue 2 GLU Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 26 VAL Chi-restraints excluded: chain u residue 87 THR Chi-restraints excluded: chain v residue 4 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain v residue 74 ASP Chi-restraints excluded: chain v residue 78 ASN Chi-restraints excluded: chain v residue 114 SER Chi-restraints excluded: chain w residue 96 ASN Chi-restraints excluded: chain x residue 85 SER Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain 5 residue 100 ASP Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 116 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 104 ASP Chi-restraints excluded: chain 6 residue 153 ARG Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain 8 residue 80 TYR Chi-restraints excluded: chain 8 residue 146 ILE Chi-restraints excluded: chain 0 residue 100 ASP Chi-restraints excluded: chain 0 residue 101 ASP Chi-restraints excluded: chain 0 residue 116 ASP Chi-restraints excluded: chain 0 residue 196 ASN Chi-restraints excluded: chain 2 residue 71 TYR Chi-restraints excluded: chain 2 residue 91 ASP Chi-restraints excluded: chain 1 residue 84 TYR Chi-restraints excluded: chain 1 residue 104 ASP Chi-restraints excluded: chain 1 residue 153 ARG Chi-restraints excluded: chain 1 residue 176 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 470 optimal weight: 6.9990 chunk 630 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 545 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 592 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 608 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 219 ASN O 228 GLN U 99 ASN o 219 ASN o 228 GLN ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 229 GLN P 229 GLN ** 1 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062112 restraints weight = 162957.349| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.06 r_work: 0.2705 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 74674 Z= 0.389 Angle : 0.997 59.190 105044 Z= 0.463 Chirality : 0.059 0.980 10022 Planarity : 0.006 0.111 13622 Dihedral : 17.354 175.285 14649 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 2.48 % Allowed : 19.79 % Favored : 77.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.05 % 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: -0.04 (0.10), residues: 7198 helix: 1.16 (0.08), residues: 3804 sheet: -0.97 (0.33), residues: 242 loop : -1.46 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP W 114 HIS 0.010 0.002 HIS B 466 PHE 0.023 0.002 PHE c 436 TYR 0.041 0.002 TYR w 106 ARG 0.006 0.000 ARG B 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22743.37 seconds wall clock time: 395 minutes 47.20 seconds (23747.20 seconds total)