Starting phenix.real_space_refine on Tue Mar 19 22:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j40_9777/03_2024/6j40_9777_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j40_9777/03_2024/6j40_9777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j40_9777/03_2024/6j40_9777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j40_9777/03_2024/6j40_9777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j40_9777/03_2024/6j40_9777_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j40_9777/03_2024/6j40_9777_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.006 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: 9 Type Number sf(0) Gaussians Ca 2 9.91 5 Mn 8 7.51 5 Fe 6 7.16 5 P 8 5.49 5 Mg 290 5.21 5 S 278 5.16 5 C 66920 2.51 5 N 13196 2.21 5 O 15682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 136": "NH1" <-> "NH2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "I TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "Q ARG 122": "NH1" <-> "NH2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 154": "NH1" <-> "NH2" Residue "a ARG 136": "NH1" <-> "NH2" Residue "b PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 272": "NH1" <-> "NH2" Residue "b PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 378": "NH1" <-> "NH2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b ARG 385": "NH1" <-> "NH2" Residue "b PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 447": "NH1" <-> "NH2" Residue "c PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 459": "NH1" <-> "NH2" Residue "c ARG 468": "NH1" <-> "NH2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 179": "NH1" <-> "NH2" Residue "d ARG 250": "NH1" <-> "NH2" Residue "d ARG 264": "NH1" <-> "NH2" Residue "d ARG 293": "NH1" <-> "NH2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "i TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "l ARG 15": "NH1" <-> "NH2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "o TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 150": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "q ARG 122": "NH1" <-> "NH2" Residue "q ARG 144": "NH1" <-> "NH2" Residue "q ARG 154": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 96390 Number of models: 1 Model: "" Number of chains: 120 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3812 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 28, 'TRANS': 455} Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3504 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain: "D" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2697 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 228 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "H" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 513 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "I" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 287 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "J" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 254 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "K" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "M" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 316 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1845 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 250 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "U" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 713 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 86} Chain: "V" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1037 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "Y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "X" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 263 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 447 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "Q" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "W" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "0" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "1" 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: "2" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "b" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3812 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 28, 'TRANS': 455} Chain: "c" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3504 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain: "d" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2697 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "e" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "f" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 228 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "h" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 513 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "i" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 287 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "j" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 254 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "k" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "l" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "m" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 316 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1845 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "t" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 250 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "u" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 713 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 86} Chain: "v" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1037 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "x" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 263 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 447 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "q" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "w" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "5" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "6" 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: "7" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "11" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "12" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "13" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "14" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "15" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "16" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "17" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "18" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "19" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1075 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'TRANS': 214} Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 215 Planarities with less than four sites: {'UNK:plan-1': 215} Unresolved non-hydrogen planarities: 215 Chain: "20" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 715 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'TRANS': 142} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 143 Planarities with less than four sites: {'UNK:plan-1': 143} Unresolved non-hydrogen planarities: 143 Chain: "21" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 775 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'TRANS': 154} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 155 Planarities with less than four sites: {'UNK:plan-1': 155} Unresolved non-hydrogen planarities: 155 Chain: "31" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "32" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "33" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "34" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "35" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "36" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "37" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "38" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "39" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1075 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'TRANS': 214} Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 215 Planarities with less than four sites: {'UNK:plan-1': 215} Unresolved non-hydrogen planarities: 215 Chain: "40" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 715 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'TRANS': 142} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 143 Planarities with less than four sites: {'UNK:plan-1': 143} Unresolved non-hydrogen planarities: 143 Chain: "41" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 775 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'TRANS': 154} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 155 Planarities with less than four sites: {'UNK:plan-1': 155} Unresolved non-hydrogen planarities: 155 Chain: "A" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 379 Unusual residues: {'BCR': 2, 'BCT': 1, 'CLA': 2, 'FE2': 1, 'LHG': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1388 Unusual residues: {'BCR': 4, 'CLA': 16, 'LHG': 1, 'LMG': 2, 'SQD': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "C" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1254 Unusual residues: {'BCR': 2, 'CLA': 16, 'DGD': 2, 'OEX': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 485 Unusual residues: {'CLA': 4, 'LMG': 1, 'PHO': 1, 'PL9': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'LHG': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CLA': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 315 Unusual residues: {'BCR': 2, 'BCT': 1, 'CLA': 2, 'FE2': 1, 'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "b" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1348 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 2, 'SQD': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "c" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1385 Unusual residues: {'BCR': 4, 'CLA': 16, 'DGD': 2, 'LMG': 1, 'OEX': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "d" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 598 Unusual residues: {'CLA': 4, 'LHG': 1, 'LMG': 1, 'PHO': 2, 'PL9': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCR': 1, 'CLA': 1, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: "z" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "11" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 818 Unusual residues: {'A86': 6, 'CLA': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "12" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 954 Unusual residues: {'A86': 6, 'CLA': 11, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "13" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 849 Unusual residues: {'A86': 8, 'CLA': 9} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "14" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 722 Unusual residues: {'A86': 4, 'CLA': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "15" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 801 Unusual residues: {'A86': 7, 'CLA': 9} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "16" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 657 Unusual residues: {'A86': 4, 'CLA': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "17" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 821 Unusual residues: {'A86': 7, 'CLA': 9} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "18" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 787 Unusual residues: {'A86': 4, 'CLA': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "19" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 544 Unusual residues: {'A86': 3, 'CLA': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "20" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 660 Unusual residues: {'A86': 5, 'CLA': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "21" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 725 Unusual residues: {'A86': 5, 'CLA': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "31" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 818 Unusual residues: {'A86': 6, 'CLA': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "32" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 937 Unusual residues: {'A86': 7, 'CLA': 10, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "33" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 866 Unusual residues: {'A86': 7, 'CLA': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "34" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 722 Unusual residues: {'A86': 4, 'CLA': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "35" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 801 Unusual residues: {'A86': 7, 'CLA': 9} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "36" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 657 Unusual residues: {'A86': 4, 'CLA': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "37" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 821 Unusual residues: {'A86': 7, 'CLA': 9} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "38" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 787 Unusual residues: {'A86': 4, 'CLA': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "39" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 544 Unusual residues: {'A86': 3, 'CLA': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "40" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 660 Unusual residues: {'A86': 5, 'CLA': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "41" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 725 Unusual residues: {'A86': 5, 'CLA': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 40.36, per 1000 atoms: 0.42 Number of scatterers: 96390 At special positions: 0 Unit cell: (332.64, 292.32, 125.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 6 26.01 Mn 8 24.99 Ca 2 19.99 S 278 16.00 P 8 15.00 Mg 290 11.99 O 15682 8.00 N 13196 7.00 C 66920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 44 " distance=2.04 Simple disulfide: pdb=" SG CYS o 23 " - pdb=" SG CYS o 44 " distance=2.04 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 Atom "HETATM91904 O1 A8635 310 .*. O " rejected from bonding due to valence issues. Atom "HETATM83566 O1 A8615 310 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=251, symmetry=0 Number of additional bonds: simple=251, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.97 Conformation dependent library (CDL) restraints added in 10.2 seconds 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 374 helices and 20 sheets defined 56.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.44 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.893A pdb=" N TRP A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 Proline residue: A 39 - end of helix removed outlier: 3.830A pdb=" N ILE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 removed outlier: 3.741A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.552A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 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 177 through 190 Processing helix chain 'A' and resid 199 through 221 removed outlier: 3.738A pdb=" N GLY A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) 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 294 removed outlier: 4.221A pdb=" N ALA A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.917A pdb=" N THR A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.991A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 removed outlier: 3.579A pdb=" N ILE B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 No H-bonds generated for 'chain 'B' and resid 63 through 66' 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: 3.544A pdb=" N SER B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 196 through 218 removed outlier: 3.537A pdb=" N GLY B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 235 through 257 removed outlier: 3.643A pdb=" N SER B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 No H-bonds generated for 'chain 'B' and resid 273 through 276' Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.934A pdb=" N SER B 291 " --> pdb=" O GLN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.711A pdb=" N ARG B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) 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 330 through 334 removed outlier: 3.974A pdb=" N ASP B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.757A pdb=" N LYS B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.822A pdb=" N ALA B 459 " --> pdb=" O HIS B 455 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 45 through 71 removed outlier: 3.502A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.612A pdb=" N ALA C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 129 removed outlier: 3.685A pdb=" N LEU C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER C 120 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 153 through 178 removed outlier: 3.530A pdb=" N LEU C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 211 removed outlier: 4.097A pdb=" N VAL C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 251 removed outlier: 3.846A pdb=" N TRP C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.509A pdb=" N ARG C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 261 " --> pdb=" O TRP C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 266 through 290 removed outlier: 3.751A pdb=" N LEU C 270 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 304 through 320 removed outlier: 3.688A pdb=" N SER C 308 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 384 through 395 removed outlier: 3.517A pdb=" N GLU C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 428 through 451 removed outlier: 3.793A pdb=" N PHE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 32 through 52 removed outlier: 3.638A pdb=" N LEU D 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE D 37 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Proline residue: D 38 - end of helix removed outlier: 3.765A pdb=" N TYR D 41 " --> pdb=" O PRO D 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 42 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 44 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY D 45 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 46 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET D 48 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR D 49 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR D 51 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 135 removed outlier: 3.656A pdb=" N ALA D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 156 removed outlier: 3.701A pdb=" N SER D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Proline residue: D 148 - end of helix removed outlier: 3.592A pdb=" N SER D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.723A pdb=" N GLY D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 162' Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.589A pdb=" N PHE D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 194 through 217 removed outlier: 3.503A pdb=" N ALA D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 202 " --> pdb=" O MET D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.772A pdb=" N GLN D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 289 removed outlier: 3.578A pdb=" N LEU D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Proline residue: D 274 - end of helix removed outlier: 3.627A pdb=" N GLY D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 281 " --> pdb=" O GLY D 277 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.575A pdb=" N ARG D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 327 removed outlier: 3.664A pdb=" N HIS D 318 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 319 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 332 No H-bonds generated for 'chain 'D' and resid 329 through 332' Processing helix chain 'E' and resid 11 through 15 removed outlier: 3.582A pdb=" N ILE E 15 " --> pdb=" O PHE E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 11 through 15' Processing helix chain 'E' and resid 18 through 40 removed outlier: 4.279A pdb=" N ILE E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix removed outlier: 3.887A pdb=" N SER E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 47 No H-bonds generated for 'chain 'E' and resid 44 through 47' Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'F' and resid 17 through 35 removed outlier: 4.364A pdb=" N ILE F 21 " --> pdb=" O TRP F 18 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS F 22 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY F 23 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA F 25 " --> pdb=" O HIS F 22 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE F 26 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Proline residue: F 27 - end of helix removed outlier: 3.527A pdb=" N ILE F 35 " --> pdb=" O LEU F 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.721A pdb=" N ILE H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Proline residue: H 13 - end of helix Processing helix chain 'H' and resid 28 through 49 removed outlier: 3.592A pdb=" N ILE H 33 " --> pdb=" O PRO H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 23 removed outlier: 3.510A pdb=" N PHE I 23 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.704A pdb=" N LEU J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 13 No H-bonds generated for 'chain 'K' and resid 11 through 13' Processing helix chain 'K' and resid 15 through 40 Proline residue: K 18 - end of helix Proline residue: K 24 - end of helix Proline residue: K 27 - end of helix removed outlier: 3.741A pdb=" N LEU K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 36 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 37 removed outlier: 3.604A pdb=" N TYR L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 37 Proline residue: M 18 - end of helix removed outlier: 3.548A pdb=" N ASN M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 8 No H-bonds generated for 'chain 'O' and resid 5 through 8' Processing helix chain 'O' and resid 11 through 14 No H-bonds generated for 'chain 'O' and resid 11 through 14' Processing helix chain 'O' and resid 183 through 188 removed outlier: 3.510A pdb=" N PHE O 186 " --> pdb=" O ALA O 183 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY O 187 " --> pdb=" O GLU O 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 22 removed outlier: 3.701A pdb=" N VAL T 16 " --> pdb=" O GLY T 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 34 through 37 removed outlier: 3.685A pdb=" N LYS U 37 " --> pdb=" O ALA U 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 34 through 37' Processing helix chain 'U' and resid 44 through 51 removed outlier: 3.512A pdb=" N ILE U 49 " --> pdb=" O VAL U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 71 through 77 removed outlier: 3.752A pdb=" N ILE U 75 " --> pdb=" O GLU U 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 36 removed outlier: 3.608A pdb=" N LYS V 30 " --> pdb=" O VAL V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 44 No H-bonds generated for 'chain 'V' and resid 42 through 44' Processing helix chain 'V' and resid 56 through 60 Processing helix chain 'V' and resid 69 through 77 Processing helix chain 'V' and resid 102 through 104 No H-bonds generated for 'chain 'V' and resid 102 through 104' Processing helix chain 'V' and resid 109 through 125 Proline residue: V 123 - end of helix Processing helix chain 'Y' and resid 4 through 30 removed outlier: 3.502A pdb=" N GLY Y 20 " --> pdb=" O ILE Y 16 " (cutoff:3.500A) Proline residue: Y 21 - end of helix removed outlier: 3.756A pdb=" N ILE Y 24 " --> pdb=" O GLY Y 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 32 removed outlier: 3.633A pdb=" N VAL X 19 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE X 22 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER X 32 " --> pdb=" O VAL X 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 25 removed outlier: 3.689A pdb=" N ALA Z 7 " --> pdb=" O THR Z 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU Z 11 " --> pdb=" O ALA Z 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Z 12 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Z 17 " --> pdb=" O SER Z 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL Z 18 " --> pdb=" O LEU Z 14 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR Z 19 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) Proline residue: Z 21 - end of helix Processing helix chain 'Z' and resid 29 through 32 No H-bonds generated for 'chain 'Z' and resid 29 through 32' Processing helix chain 'Z' and resid 35 through 57 removed outlier: 3.756A pdb=" N ARG Z 39 " --> pdb=" O GLY Z 35 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE Z 40 " --> pdb=" O LYS Z 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL Z 48 " --> pdb=" O TRP Z 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 123 removed outlier: 3.546A pdb=" N VAL Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN Q 121 " --> pdb=" O ALA Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 131 removed outlier: 3.503A pdb=" N VAL Q 130 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 144 removed outlier: 3.793A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU Q 142 " --> pdb=" O VAL Q 138 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR Q 143 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 156 removed outlier: 4.202A pdb=" N ARG Q 150 " --> pdb=" O TYR Q 147 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY Q 151 " --> pdb=" O GLU Q 148 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL Q 153 " --> pdb=" O ARG Q 150 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG Q 154 " --> pdb=" O GLY Q 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Q 156 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 180 removed outlier: 3.581A pdb=" N GLU Q 164 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA Q 166 " --> pdb=" O GLN Q 162 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU Q 167 " --> pdb=" O LYS Q 163 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL Q 168 " --> pdb=" O GLU Q 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE Q 169 " --> pdb=" O LYS Q 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 205 removed outlier: 3.703A pdb=" N ASP Q 193 " --> pdb=" O LYS Q 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA Q 198 " --> pdb=" O LYS Q 194 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR Q 205 " --> pdb=" O ALA Q 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 28 No H-bonds generated for 'chain 'W' and resid 26 through 28' Processing helix chain 'W' and resid 32 through 51 removed outlier: 3.533A pdb=" N ALA W 36 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE W 39 " --> pdb=" O ALA W 36 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU W 40 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS W 42 " --> pdb=" O PHE W 39 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP W 43 " --> pdb=" O LEU W 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA W 44 " --> pdb=" O GLY W 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE W 45 " --> pdb=" O HIS W 42 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER W 47 " --> pdb=" O ALA W 44 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU W 50 " --> pdb=" O SER W 47 " (cutoff:3.500A) Processing helix chain '0' and resid 10 through 24 removed outlier: 3.922A pdb=" N UNK 0 15 " --> pdb=" O UNK 0 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK 0 16 " --> pdb=" O UNK 0 12 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 27 removed outlier: 3.729A pdb=" N UNK 1 11 " --> pdb=" O UNK 1 7 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK 1 12 " --> pdb=" O UNK 1 8 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK 1 21 " --> pdb=" O UNK 1 17 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK 1 25 " --> pdb=" O UNK 1 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 21 removed outlier: 3.893A pdb=" N TRP a 20 " --> pdb=" O ARG a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 53 Proline residue: a 39 - end of helix removed outlier: 3.831A pdb=" N ILE a 50 " --> pdb=" O SER a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 110 through 136 removed outlier: 3.741A pdb=" N LEU a 114 " --> pdb=" O GLY a 110 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY a 128 " --> pdb=" O SER a 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER a 134 " --> pdb=" O GLU a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 146 No H-bonds generated for 'chain 'a' and resid 143 through 146' Processing helix chain 'a' and resid 148 through 158 removed outlier: 3.552A pdb=" N VAL a 157 " --> pdb=" O ALA a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 160 through 164 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 177 through 190 Processing helix chain 'a' and resid 199 through 221 removed outlier: 3.738A pdb=" N GLY a 204 " --> pdb=" O ALA a 200 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER a 217 " --> pdb=" O ALA a 213 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU a 218 " --> pdb=" O MET a 214 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR a 220 " --> pdb=" O GLY a 216 " (cutoff:3.500A) 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 294 removed outlier: 4.220A pdb=" N ALA a 276 " --> pdb=" O HIS a 272 " (cutoff:3.500A) Proline residue: a 279 - end of helix removed outlier: 3.917A pdb=" N THR a 292 " --> pdb=" O MET a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 329 Processing helix chain 'b' and resid 5 through 10 removed outlier: 3.990A pdb=" N VAL b 8 " --> pdb=" O TRP b 5 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS b 9 " --> pdb=" O TYR b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 44 removed outlier: 3.581A pdb=" N ILE b 20 " --> pdb=" O PRO b 16 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL b 44 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 63 through 66 No H-bonds generated for 'chain 'b' and resid 63 through 66' 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: 3.545A pdb=" N SER b 146 " --> pdb=" O HIS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 190 Processing helix chain 'b' and resid 196 through 218 removed outlier: 3.536A pdb=" N GLY b 213 " --> pdb=" O GLY b 209 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR b 218 " --> pdb=" O ILE b 214 " (cutoff:3.500A) Processing helix chain 'b' and resid 223 through 228 Processing helix chain 'b' and resid 235 through 257 removed outlier: 3.645A pdb=" N SER b 240 " --> pdb=" O THR b 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER b 243 " --> pdb=" O SER b 239 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE b 247 " --> pdb=" O SER b 243 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA b 248 " --> pdb=" O ALA b 244 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 251 " --> pdb=" O PHE b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 273 through 276 No H-bonds generated for 'chain 'b' and resid 273 through 276' Processing helix chain 'b' and resid 281 through 293 removed outlier: 3.934A pdb=" N SER b 291 " --> pdb=" O GLN b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 304 removed outlier: 3.712A pdb=" N ARG b 304 " --> pdb=" O GLN b 300 " (cutoff:3.500A) 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 330 through 334 removed outlier: 3.976A pdb=" N ASP b 334 " --> pdb=" O ASN b 331 " (cutoff:3.500A) Processing helix chain 'b' and resid 392 through 395 No H-bonds generated for 'chain 'b' and resid 392 through 395' Processing helix chain 'b' and resid 404 through 406 No H-bonds generated for 'chain 'b' and resid 404 through 406' Processing helix chain 'b' and resid 414 through 422 removed outlier: 3.757A pdb=" N LYS b 419 " --> pdb=" O PRO b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 447 through 474 removed outlier: 3.821A pdb=" N ALA b 459 " --> pdb=" O HIS b 455 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU b 460 " --> pdb=" O ALA b 456 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE b 464 " --> pdb=" O LEU b 460 " (cutoff:3.500A) Processing helix chain 'b' and resid 476 through 478 No H-bonds generated for 'chain 'b' and resid 476 through 478' Processing helix chain 'c' and resid 37 through 40 Processing helix chain 'c' and resid 45 through 71 removed outlier: 3.503A pdb=" N VAL c 66 " --> pdb=" O ALA c 62 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 93 removed outlier: 3.613A pdb=" N ALA c 91 " --> pdb=" O ILE c 87 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR c 92 " --> pdb=" O GLN c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 129 removed outlier: 3.683A pdb=" N LEU c 117 " --> pdb=" O GLY c 113 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER c 120 " --> pdb=" O HIS c 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA c 121 " --> pdb=" O LEU c 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE c 122 " --> pdb=" O ILE c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 138 through 141 No H-bonds generated for 'chain 'c' and resid 138 through 141' Processing helix chain 'c' and resid 153 through 178 removed outlier: 3.529A pdb=" N LEU c 165 " --> pdb=" O ILE c 161 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER c 170 " --> pdb=" O LEU c 166 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU c 173 " --> pdb=" O GLY c 169 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL c 174 " --> pdb=" O SER c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 204 through 211 removed outlier: 4.095A pdb=" N VAL c 211 " --> pdb=" O ILE c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 228 through 251 removed outlier: 3.847A pdb=" N TRP c 237 " --> pdb=" O GLY c 233 " (cutoff:3.500A) Processing helix chain 'c' and resid 256 through 261 removed outlier: 3.508A pdb=" N ARG c 260 " --> pdb=" O ALA c 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA c 261 " --> pdb=" O TRP c 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 256 through 261' Processing helix chain 'c' and resid 266 through 290 removed outlier: 3.751A pdb=" N LEU c 270 " --> pdb=" O GLY c 266 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA c 275 " --> pdb=" O SER c 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER c 278 " --> pdb=" O LEU c 274 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP c 289 " --> pdb=" O ALA c 285 " (cutoff:3.500A) Processing helix chain 'c' and resid 297 through 300 No H-bonds generated for 'chain 'c' and resid 297 through 300' Processing helix chain 'c' and resid 304 through 320 removed outlier: 3.689A pdb=" N SER c 308 " --> pdb=" O GLY c 304 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN c 311 " --> pdb=" O ALA c 307 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA c 312 " --> pdb=" O SER c 308 " (cutoff:3.500A) Processing helix chain 'c' and resid 352 through 354 No H-bonds generated for 'chain 'c' and resid 352 through 354' Processing helix chain 'c' and resid 365 through 367 No H-bonds generated for 'chain 'c' and resid 365 through 367' Processing helix chain 'c' and resid 375 through 380 Processing helix chain 'c' and resid 384 through 395 removed outlier: 3.518A pdb=" N GLU c 392 " --> pdb=" O ARG c 388 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR c 395 " --> pdb=" O ALA c 391 " (cutoff:3.500A) Processing helix chain 'c' and resid 420 through 424 Processing helix chain 'c' and resid 428 through 451 removed outlier: 3.794A pdb=" N PHE c 434 " --> pdb=" O PHE c 430 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU c 436 " --> pdb=" O ALA c 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA c 451 " --> pdb=" O ARG c 447 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 21 Processing helix chain 'd' and resid 32 through 52 removed outlier: 3.637A pdb=" N LEU d 36 " --> pdb=" O GLY d 33 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE d 37 " --> pdb=" O LEU d 34 " (cutoff:3.500A) Proline residue: d 38 - end of helix removed outlier: 3.764A pdb=" N TYR d 41 " --> pdb=" O PRO d 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU d 42 " --> pdb=" O THR d 39 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA d 44 " --> pdb=" O TYR d 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY d 45 " --> pdb=" O LEU d 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY d 46 " --> pdb=" O ALA d 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET d 48 " --> pdb=" O GLY d 45 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR d 49 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR d 51 " --> pdb=" O MET d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 106 Processing helix chain 'd' and resid 108 through 135 removed outlier: 3.656A pdb=" N ALA d 132 " --> pdb=" O GLN d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 156 removed outlier: 3.699A pdb=" N SER d 146 " --> pdb=" O ALA d 142 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY d 147 " --> pdb=" O ILE d 143 " (cutoff:3.500A) Proline residue: d 148 - end of helix removed outlier: 3.592A pdb=" N SER d 154 " --> pdb=" O ALA d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 158 through 162 removed outlier: 3.723A pdb=" N GLY d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 158 through 162' Processing helix chain 'd' and resid 166 through 168 No H-bonds generated for 'chain 'd' and resid 166 through 168' Processing helix chain 'd' and resid 174 through 186 removed outlier: 3.587A pdb=" N PHE d 180 " --> pdb=" O ALA d 176 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN d 185 " --> pdb=" O LEU d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 192 No H-bonds generated for 'chain 'd' and resid 190 through 192' Processing helix chain 'd' and resid 194 through 217 removed outlier: 3.502A pdb=" N ALA d 201 " --> pdb=" O MET d 197 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY d 202 " --> pdb=" O MET d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 255 removed outlier: 3.772A pdb=" N GLN d 254 " --> pdb=" O ARG d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 289 removed outlier: 3.577A pdb=" N LEU d 271 " --> pdb=" O HIS d 267 " (cutoff:3.500A) Proline residue: d 274 - end of helix removed outlier: 3.627A pdb=" N GLY d 277 " --> pdb=" O VAL d 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU d 278 " --> pdb=" O PRO d 274 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER d 281 " --> pdb=" O GLY d 277 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY d 284 " --> pdb=" O THR d 280 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE d 285 " --> pdb=" O SER d 281 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL d 286 " --> pdb=" O SER d 282 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 306 removed outlier: 3.573A pdb=" N ARG d 303 " --> pdb=" O SER d 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 327 removed outlier: 3.663A pdb=" N HIS d 318 " --> pdb=" O TYR d 314 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU d 319 " --> pdb=" O THR d 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY d 323 " --> pdb=" O LEU d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 329 through 332 No H-bonds generated for 'chain 'd' and resid 329 through 332' Processing helix chain 'e' and resid 11 through 15 removed outlier: 3.583A pdb=" N ILE e 15 " --> pdb=" O PHE e 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 11 through 15' Processing helix chain 'e' and resid 18 through 40 removed outlier: 4.280A pdb=" N ILE e 26 " --> pdb=" O ILE e 22 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE e 28 " --> pdb=" O HIS e 24 " (cutoff:3.500A) Proline residue: e 29 - end of helix removed outlier: 3.887A pdb=" N SER e 34 " --> pdb=" O SER e 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE e 39 " --> pdb=" O GLY e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 47 No H-bonds generated for 'chain 'e' and resid 44 through 47' Processing helix chain 'e' and resid 73 through 80 Processing helix chain 'f' and resid 17 through 35 removed outlier: 4.363A pdb=" N ILE f 21 " --> pdb=" O TRP f 18 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS f 22 " --> pdb=" O LEU f 19 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY f 23 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA f 25 " --> pdb=" O HIS f 22 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE f 26 " --> pdb=" O GLY f 23 " (cutoff:3.500A) Proline residue: f 27 - end of helix removed outlier: 3.526A pdb=" N ILE f 35 " --> pdb=" O LEU f 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 15 removed outlier: 3.719A pdb=" N ILE h 10 " --> pdb=" O ARG h 6 " (cutoff:3.500A) Proline residue: h 13 - end of helix Processing helix chain 'h' and resid 28 through 49 removed outlier: 3.592A pdb=" N ILE h 33 " --> pdb=" O PRO h 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 23 removed outlier: 3.509A pdb=" N PHE i 23 " --> pdb=" O PHE i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 29 No H-bonds generated for 'chain 'i' and resid 27 through 29' Processing helix chain 'j' and resid 9 through 29 removed outlier: 3.704A pdb=" N LEU j 26 " --> pdb=" O THR j 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 13 No H-bonds generated for 'chain 'k' and resid 11 through 13' Processing helix chain 'k' and resid 15 through 40 Proline residue: k 18 - end of helix Proline residue: k 24 - end of helix Proline residue: k 27 - end of helix removed outlier: 3.742A pdb=" N LEU k 32 " --> pdb=" O PHE k 29 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL k 36 " --> pdb=" O LEU k 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 15 through 37 removed outlier: 3.603A pdb=" N TYR l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR l 35 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 37 Proline residue: m 18 - end of helix removed outlier: 3.546A pdb=" N ASN m 24 " --> pdb=" O LEU m 20 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE m 26 " --> pdb=" O LEU m 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 8 No H-bonds generated for 'chain 'o' and resid 5 through 8' Processing helix chain 'o' and resid 11 through 14 No H-bonds generated for 'chain 'o' and resid 11 through 14' Processing helix chain 'o' and resid 183 through 188 removed outlier: 3.510A pdb=" N PHE o 186 " --> pdb=" O ALA o 183 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY o 187 " --> pdb=" O GLU o 184 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 22 removed outlier: 3.700A pdb=" N VAL t 16 " --> pdb=" O GLY t 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 17 through 20 No H-bonds generated for 'chain 'u' and resid 17 through 20' Processing helix chain 'u' and resid 34 through 37 removed outlier: 3.684A pdb=" N LYS u 37 " --> pdb=" O ALA u 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 34 through 37' Processing helix chain 'u' and resid 44 through 51 removed outlier: 3.512A pdb=" N ILE u 49 " --> pdb=" O VAL u 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 59 through 63 Processing helix chain 'u' and resid 71 through 77 removed outlier: 3.753A pdb=" N ILE u 75 " --> pdb=" O GLU u 71 " (cutoff:3.500A) Processing helix chain 'v' and resid 25 through 36 removed outlier: 3.608A pdb=" N LYS v 30 " --> pdb=" O VAL v 26 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 44 No H-bonds generated for 'chain 'v' and resid 42 through 44' Processing helix chain 'v' and resid 56 through 60 Processing helix chain 'v' and resid 69 through 77 Processing helix chain 'v' and resid 102 through 104 No H-bonds generated for 'chain 'v' and resid 102 through 104' Processing helix chain 'v' and resid 109 through 125 Proline residue: v 123 - end of helix Processing helix chain 'y' and resid 4 through 30 removed outlier: 3.504A pdb=" N GLY y 20 " --> pdb=" O ILE y 16 " (cutoff:3.500A) Proline residue: y 21 - end of helix removed outlier: 3.755A pdb=" N ILE y 24 " --> pdb=" O GLY y 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 3 through 32 removed outlier: 3.631A pdb=" N VAL x 19 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE x 22 " --> pdb=" O VAL x 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER x 32 " --> pdb=" O VAL x 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 25 removed outlier: 3.689A pdb=" N ALA z 7 " --> pdb=" O THR z 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU z 11 " --> pdb=" O ALA z 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE z 12 " --> pdb=" O LEU z 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL z 17 " --> pdb=" O SER z 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL z 18 " --> pdb=" O LEU z 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR z 19 " --> pdb=" O GLY z 15 " (cutoff:3.500A) Proline residue: z 21 - end of helix Processing helix chain 'z' and resid 29 through 32 No H-bonds generated for 'chain 'z' and resid 29 through 32' Processing helix chain 'z' and resid 35 through 57 removed outlier: 3.757A pdb=" N ARG z 39 " --> pdb=" O GLY z 35 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE z 40 " --> pdb=" O LYS z 36 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL z 48 " --> pdb=" O TRP z 44 " (cutoff:3.500A) Processing helix chain 'q' and resid 106 through 123 removed outlier: 3.545A pdb=" N VAL q 115 " --> pdb=" O ARG q 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS q 120 " --> pdb=" O LEU q 116 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN q 121 " --> pdb=" O ALA q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 126 through 131 removed outlier: 3.501A pdb=" N VAL q 130 " --> pdb=" O ILE q 126 " (cutoff:3.500A) Processing helix chain 'q' and resid 136 through 144 removed outlier: 3.793A pdb=" N ASP q 140 " --> pdb=" O PHE q 136 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU q 142 " --> pdb=" O VAL q 138 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR q 143 " --> pdb=" O LYS q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 146 through 156 removed outlier: 4.200A pdb=" N ARG q 150 " --> pdb=" O TYR q 147 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY q 151 " --> pdb=" O GLU q 148 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL q 153 " --> pdb=" O ARG q 150 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG q 154 " --> pdb=" O GLY q 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU q 156 " --> pdb=" O VAL q 153 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 180 removed outlier: 3.581A pdb=" N GLU q 164 " --> pdb=" O VAL q 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU q 167 " --> pdb=" O LYS q 163 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL q 168 " --> pdb=" O GLU q 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE q 169 " --> pdb=" O LYS q 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP q 175 " --> pdb=" O ARG q 171 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR q 176 " --> pdb=" O ALA q 172 " (cutoff:3.500A) Processing helix chain 'q' and resid 185 through 205 removed outlier: 3.703A pdb=" N ASP q 193 " --> pdb=" O LYS q 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA q 198 " --> pdb=" O LYS q 194 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR q 205 " --> pdb=" O ALA q 201 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 28 No H-bonds generated for 'chain 'w' and resid 26 through 28' Processing helix chain 'w' and resid 32 through 51 removed outlier: 3.534A pdb=" N ALA w 36 " --> pdb=" O ARG w 33 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE w 39 " --> pdb=" O ALA w 36 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU w 40 " --> pdb=" O VAL w 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS w 42 " --> pdb=" O PHE w 39 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TRP w 43 " --> pdb=" O LEU w 40 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA w 44 " --> pdb=" O GLY w 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE w 45 " --> pdb=" O HIS w 42 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER w 47 " --> pdb=" O ALA w 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU w 50 " --> pdb=" O SER w 47 " (cutoff:3.500A) Processing helix chain '5' and resid 10 through 24 removed outlier: 3.945A pdb=" N UNK 5 15 " --> pdb=" O UNK 5 11 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK 5 16 " --> pdb=" O UNK 5 12 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 27 removed outlier: 3.722A pdb=" N UNK 6 11 " --> pdb=" O UNK 6 7 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK 6 12 " --> pdb=" O UNK 6 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK 6 21 " --> pdb=" O UNK 6 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N UNK 6 25 " --> pdb=" O UNK 6 21 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 35 No H-bonds generated for 'chain '11' and resid 33 through 35' Processing helix chain '11' and resid 49 through 52 No H-bonds generated for 'chain '11' and resid 49 through 52' Processing helix chain '11' and resid 56 through 82 removed outlier: 4.368A pdb=" N ARG11 61 " --> pdb=" O GLU11 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG11 65 " --> pdb=" O ALA11 62 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS11 67 " --> pdb=" O GLU11 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL11 70 " --> pdb=" O HIS11 67 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET11 72 " --> pdb=" O ARG11 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL11 75 " --> pdb=" O MET11 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL11 76 " --> pdb=" O ALA11 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL11 80 " --> pdb=" O GLY11 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS11 81 " --> pdb=" O THR11 78 " (cutoff:3.500A) Processing helix chain '11' and resid 106 through 111 removed outlier: 4.098A pdb=" N ILE11 109 " --> pdb=" O VAL11 106 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG11 110 " --> pdb=" O ASP11 107 " (cutoff:3.500A) Processing helix chain '11' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU11 126 " --> pdb=" O ALA11 122 " (cutoff:3.500A) Processing helix chain '11' and resid 145 through 147 No H-bonds generated for 'chain '11' and resid 145 through 147' Processing helix chain '11' and resid 153 through 180 removed outlier: 4.189A pdb=" N ASN11 161 " --> pdb=" O ALA11 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA11 180 " --> pdb=" O GLY11 176 " (cutoff:3.500A) Processing helix chain '11' and resid 188 through 194 Processing helix chain '12' and resid 33 through 35 No H-bonds generated for 'chain '12' and resid 33 through 35' Processing helix chain '12' and resid 49 through 52 No H-bonds generated for 'chain '12' and resid 49 through 52' Processing helix chain '12' and resid 56 through 82 removed outlier: 4.367A pdb=" N ARG12 61 " --> pdb=" O GLU12 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG12 65 " --> pdb=" O ALA12 62 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS12 67 " --> pdb=" O GLU12 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL12 70 " --> pdb=" O HIS12 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET12 72 " --> pdb=" O ARG12 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL12 75 " --> pdb=" O MET12 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL12 76 " --> pdb=" O ALA12 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL12 80 " --> pdb=" O GLY12 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS12 81 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing helix chain '12' and resid 106 through 111 removed outlier: 4.100A pdb=" N ILE12 109 " --> pdb=" O VAL12 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG12 110 " --> pdb=" O ASP12 107 " (cutoff:3.500A) Processing helix chain '12' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU12 126 " --> pdb=" O ALA12 122 " (cutoff:3.500A) Processing helix chain '12' and resid 145 through 147 No H-bonds generated for 'chain '12' and resid 145 through 147' Processing helix chain '12' and resid 153 through 180 removed outlier: 4.189A pdb=" N ASN12 161 " --> pdb=" O ALA12 157 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA12 180 " --> pdb=" O GLY12 176 " (cutoff:3.500A) Processing helix chain '12' and resid 188 through 194 Processing helix chain '13' and resid 33 through 35 No H-bonds generated for 'chain '13' and resid 33 through 35' Processing helix chain '13' and resid 49 through 52 No H-bonds generated for 'chain '13' and resid 49 through 52' Processing helix chain '13' and resid 56 through 82 removed outlier: 4.369A pdb=" N ARG13 61 " --> pdb=" O GLU13 58 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG13 65 " --> pdb=" O ALA13 62 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS13 67 " --> pdb=" O GLU13 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL13 70 " --> pdb=" O HIS13 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET13 72 " --> pdb=" O ARG13 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL13 75 " --> pdb=" O MET13 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL13 76 " --> pdb=" O ALA13 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL13 80 " --> pdb=" O GLY13 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS13 81 " --> pdb=" O THR13 78 " (cutoff:3.500A) Processing helix chain '13' and resid 106 through 111 removed outlier: 4.098A pdb=" N ILE13 109 " --> pdb=" O VAL13 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG13 110 " --> pdb=" O ASP13 107 " (cutoff:3.500A) Processing helix chain '13' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU13 126 " --> pdb=" O ALA13 122 " (cutoff:3.500A) Processing helix chain '13' and resid 145 through 147 No H-bonds generated for 'chain '13' and resid 145 through 147' Processing helix chain '13' and resid 153 through 180 removed outlier: 4.189A pdb=" N ASN13 161 " --> pdb=" O ALA13 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA13 180 " --> pdb=" O GLY13 176 " (cutoff:3.500A) Processing helix chain '13' and resid 188 through 194 Processing helix chain '14' and resid 33 through 35 No H-bonds generated for 'chain '14' and resid 33 through 35' Processing helix chain '14' and resid 49 through 52 No H-bonds generated for 'chain '14' and resid 49 through 52' Processing helix chain '14' and resid 56 through 82 removed outlier: 4.368A pdb=" N ARG14 61 " --> pdb=" O GLU14 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG14 65 " --> pdb=" O ALA14 62 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS14 67 " --> pdb=" O GLU14 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL14 70 " --> pdb=" O HIS14 67 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET14 72 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL14 75 " --> pdb=" O MET14 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL14 76 " --> pdb=" O ALA14 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL14 80 " --> pdb=" O GLY14 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS14 81 " --> pdb=" O THR14 78 " (cutoff:3.500A) Processing helix chain '14' and resid 106 through 111 removed outlier: 4.099A pdb=" N ILE14 109 " --> pdb=" O VAL14 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG14 110 " --> pdb=" O ASP14 107 " (cutoff:3.500A) Processing helix chain '14' and resid 114 through 129 removed outlier: 3.722A pdb=" N LEU14 126 " --> pdb=" O ALA14 122 " (cutoff:3.500A) Processing helix chain '14' and resid 145 through 147 No H-bonds generated for 'chain '14' and resid 145 through 147' Processing helix chain '14' and resid 153 through 180 removed outlier: 4.189A pdb=" N ASN14 161 " --> pdb=" O ALA14 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA14 180 " --> pdb=" O GLY14 176 " (cutoff:3.500A) Processing helix chain '14' and resid 188 through 194 Processing helix chain '15' and resid 32 through 35 removed outlier: 3.536A pdb=" N LEU15 35 " --> pdb=" O GLU15 32 " (cutoff:3.500A) No H-bonds generated for 'chain '15' and resid 32 through 35' Processing helix chain '15' and resid 49 through 52 No H-bonds generated for 'chain '15' and resid 49 through 52' Processing helix chain '15' and resid 57 through 82 removed outlier: 3.868A pdb=" N LYS15 66 " --> pdb=" O ALA15 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA15 73 " --> pdb=" O ARG15 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL15 76 " --> pdb=" O MET15 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS15 81 " --> pdb=" O GLY15 77 " (cutoff:3.500A) Processing helix chain '15' and resid 114 through 129 removed outlier: 3.571A pdb=" N ALA15 122 " --> pdb=" O ALA15 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE15 123 " --> pdb=" O GLN15 119 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU15 126 " --> pdb=" O ALA15 122 " (cutoff:3.500A) Processing helix chain '15' and resid 153 through 182 removed outlier: 3.591A pdb=" N ASN15 161 " --> pdb=" O ALA15 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL15 162 " --> pdb=" O ARG15 158 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU15 164 " --> pdb=" O LEU15 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL15 179 " --> pdb=" O MET15 175 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA15 180 " --> pdb=" O GLY15 176 " (cutoff:3.500A) Processing helix chain '15' and resid 188 through 193 removed outlier: 3.646A pdb=" N TYR15 192 " --> pdb=" O MET15 188 " (cutoff:3.500A) Processing helix chain '16' and resid 57 through 82 removed outlier: 3.544A pdb=" N VAL16 63 " --> pdb=" O ARG16 59 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA16 71 " --> pdb=" O HIS16 67 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA16 73 " --> pdb=" O ARG16 69 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL16 76 " --> pdb=" O MET16 72 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY16 77 " --> pdb=" O ALA16 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS16 81 " --> pdb=" O GLY16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 106 through 111 removed outlier: 4.245A pdb=" N ILE16 109 " --> pdb=" O VAL16 106 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG16 110 " --> pdb=" O ASP16 107 " (cutoff:3.500A) Processing helix chain '16' and resid 114 through 129 removed outlier: 4.088A pdb=" N GLN16 119 " --> pdb=" O ALA16 115 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE16 123 " --> pdb=" O GLN16 119 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU16 126 " --> pdb=" O ALA16 122 " (cutoff:3.500A) Processing helix chain '16' and resid 153 through 182 removed outlier: 3.653A pdb=" N ALA16 157 " --> pdb=" O PRO16 153 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG16 158 " --> pdb=" O GLU16 154 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN16 161 " --> pdb=" O ALA16 157 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL16 162 " --> pdb=" O ARG16 158 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU16 164 " --> pdb=" O LEU16 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA16 169 " --> pdb=" O ASN16 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET16 171 " --> pdb=" O GLY16 167 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET16 172 " --> pdb=" O ARG16 168 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY16 173 " --> pdb=" O ALA16 169 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA16 180 " --> pdb=" O GLY16 176 " (cutoff:3.500A) Processing helix chain '16' and resid 188 through 194 removed outlier: 3.581A pdb=" N TYR16 192 " --> pdb=" O MET16 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA16 193 " --> pdb=" O TYR16 189 " (cutoff:3.500A) Processing helix chain '17' and resid 33 through 35 No H-bonds generated for 'chain '17' and resid 33 through 35' Processing helix chain '17' and resid 49 through 52 No H-bonds generated for 'chain '17' and resid 49 through 52' Processing helix chain '17' and resid 55 through 82 removed outlier: 3.896A pdb=" N GLU17 58 " --> pdb=" O GLU17 55 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG17 61 " --> pdb=" O GLU17 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU17 64 " --> pdb=" O ARG17 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N HIS17 67 " --> pdb=" O GLU17 64 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL17 70 " --> pdb=" O HIS17 67 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET17 72 " --> pdb=" O ARG17 69 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL17 76 " --> pdb=" O ALA17 73 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL17 80 " --> pdb=" O GLY17 77 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS17 81 " --> pdb=" O THR17 78 " (cutoff:3.500A) Processing helix chain '17' and resid 106 through 111 removed outlier: 4.218A pdb=" N ILE17 109 " --> pdb=" O VAL17 106 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG17 110 " --> pdb=" O ASP17 107 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA17 111 " --> pdb=" O GLY17 108 " (cutoff:3.500A) No H-bonds generated for 'chain '17' and resid 106 through 111' Processing helix chain '17' and resid 114 through 129 removed outlier: 3.692A pdb=" N LEU17 126 " --> pdb=" O ALA17 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU17 128 " --> pdb=" O PHE17 124 " (cutoff:3.500A) Processing helix chain '17' and resid 154 through 182 removed outlier: 3.995A pdb=" N ARG17 158 " --> pdb=" O GLU17 154 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA17 170 " --> pdb=" O ASN17 166 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET17 171 " --> pdb=" O GLY17 167 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET17 172 " --> pdb=" O ARG17 168 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY17 173 " --> pdb=" O ALA17 169 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET17 175 " --> pdb=" O MET17 171 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA17 180 " --> pdb=" O GLY17 176 " (cutoff:3.500A) Processing helix chain '17' and resid 188 through 194 Processing helix chain '18' and resid 49 through 52 No H-bonds generated for 'chain '18' and resid 49 through 52' Processing helix chain '18' and resid 57 through 82 removed outlier: 3.725A pdb=" N VAL18 63 " --> pdb=" O ARG18 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL18 76 " --> pdb=" O MET18 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS18 81 " --> pdb=" O GLY18 77 " (cutoff:3.500A) Processing helix chain '18' and resid 106 through 111 removed outlier: 4.055A pdb=" N ILE18 109 " --> pdb=" O VAL18 106 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG18 110 " --> pdb=" O ASP18 107 " (cutoff:3.500A) Processing helix chain '18' and resid 114 through 128 removed outlier: 3.577A pdb=" N LEU18 126 " --> pdb=" O ALA18 122 " (cutoff:3.500A) Processing helix chain '18' and resid 145 through 147 No H-bonds generated for 'chain '18' and resid 145 through 147' Processing helix chain '18' and resid 153 through 182 removed outlier: 3.875A pdb=" N VAL18 162 " --> pdb=" O ARG18 158 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU18 163 " --> pdb=" O LYS18 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET18 172 " --> pdb=" O ARG18 168 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA18 180 " --> pdb=" O GLY18 176 " (cutoff:3.500A) Processing helix chain '18' and resid 188 through 194 removed outlier: 3.547A pdb=" N TYR18 192 " --> pdb=" O MET18 188 " (cutoff:3.500A) Processing helix chain '19' and resid 3 through 6 No H-bonds generated for 'chain '19' and resid 3 through 6' Processing helix chain '19' and resid 20 through 22 No H-bonds generated for 'chain '19' and resid 20 through 22' Processing helix chain '19' and resid 58 through 67 removed outlier: 3.577A pdb=" N UNK19 63 " --> pdb=" O UNK19 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N UNK19 64 " --> pdb=" O UNK19 60 " (cutoff:3.500A) Processing helix chain '19' and resid 69 through 72 No H-bonds generated for 'chain '19' and resid 69 through 72' Processing helix chain '19' and resid 77 through 80 No H-bonds generated for 'chain '19' and resid 77 through 80' Processing helix chain '19' and resid 106 through 109 No H-bonds generated for 'chain '19' and resid 106 through 109' Processing helix chain '19' and resid 112 through 134 removed outlier: 3.651A pdb=" N UNK19 116 " --> pdb=" O UNK19 112 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N UNK19 125 " --> pdb=" O UNK19 121 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N UNK19 128 " --> pdb=" O UNK19 124 " (cutoff:3.500A) Processing helix chain '19' and resid 157 through 187 removed outlier: 3.923A pdb=" N UNK19 161 " --> pdb=" O UNK19 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK19 162 " --> pdb=" O UNK19 158 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N UNK19 174 " --> pdb=" O UNK19 170 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK19 176 " --> pdb=" O UNK19 172 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNK19 177 " --> pdb=" O UNK19 173 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N UNK19 179 " --> pdb=" O UNK19 175 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N UNK19 180 " --> pdb=" O UNK19 176 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK19 183 " --> pdb=" O UNK19 179 " (cutoff:3.500A) Processing helix chain '19' and resid 191 through 194 No H-bonds generated for 'chain '19' and resid 191 through 194' Processing helix chain '20' and resid 59 through 82 removed outlier: 3.982A pdb=" N UNK20 76 " --> pdb=" O UNK20 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N UNK20 77 " --> pdb=" O UNK20 73 " (cutoff:3.500A) Processing helix chain '20' and resid 114 through 129 removed outlier: 3.533A pdb=" N UNK20 127 " --> pdb=" O UNK20 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N UNK20 128 " --> pdb=" O UNK20 124 " (cutoff:3.500A) Processing helix chain '20' and resid 156 through 182 removed outlier: 3.836A pdb=" N UNK20 169 " --> pdb=" O UNK20 165 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N UNK20 170 " --> pdb=" O UNK20 166 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N UNK20 172 " --> pdb=" O UNK20 168 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK20 173 " --> pdb=" O UNK20 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N UNK20 175 " --> pdb=" O UNK20 171 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK20 178 " --> pdb=" O UNK20 174 " (cutoff:3.500A) Processing helix chain '21' and resid 49 through 52 No H-bonds generated for 'chain '21' and resid 49 through 52' Processing helix chain '21' and resid 55 through 82 removed outlier: 3.798A pdb=" N UNK21 58 " --> pdb=" O UNK21 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK21 59 " --> pdb=" O UNK21 56 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK21 61 " --> pdb=" O UNK21 58 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N UNK21 62 " --> pdb=" O UNK21 59 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK21 63 " --> pdb=" O UNK21 60 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N UNK21 65 " --> pdb=" O UNK21 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N UNK21 66 " --> pdb=" O UNK21 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK21 68 " --> pdb=" O UNK21 65 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N UNK21 69 " --> pdb=" O UNK21 66 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N UNK21 70 " --> pdb=" O UNK21 67 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK21 72 " --> pdb=" O UNK21 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK21 73 " --> pdb=" O UNK21 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N UNK21 75 " --> pdb=" O UNK21 72 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N UNK21 76 " --> pdb=" O UNK21 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK21 79 " --> pdb=" O UNK21 76 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N UNK21 80 " --> pdb=" O UNK21 77 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N UNK21 81 " --> pdb=" O UNK21 78 " (cutoff:3.500A) Processing helix chain '21' and resid 106 through 111 removed outlier: 4.090A pdb=" N UNK21 109 " --> pdb=" O UNK21 106 " (cutoff:3.500A) Processing helix chain '21' and resid 114 through 129 removed outlier: 3.502A pdb=" N UNK21 118 " --> pdb=" O UNK21 114 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK21 119 " --> pdb=" O UNK21 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N UNK21 122 " --> pdb=" O UNK21 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N UNK21 128 " --> pdb=" O UNK21 124 " (cutoff:3.500A) Processing helix chain '21' and resid 153 through 183 removed outlier: 3.602A pdb=" N UNK21 157 " --> pdb=" O UNK21 153 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N UNK21 166 " --> pdb=" O UNK21 162 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK21 167 " --> pdb=" O UNK21 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK21 169 " --> pdb=" O UNK21 165 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N UNK21 170 " --> pdb=" O UNK21 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK21 172 " --> pdb=" O UNK21 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK21 175 " --> pdb=" O UNK21 171 " (cutoff:3.500A) Processing helix chain '31' and resid 32 through 35 removed outlier: 3.512A pdb=" N LEU31 35 " --> pdb=" O GLU31 32 " (cutoff:3.500A) No H-bonds generated for 'chain '31' and resid 32 through 35' Processing helix chain '31' and resid 49 through 52 No H-bonds generated for 'chain '31' and resid 49 through 52' Processing helix chain '31' and resid 56 through 82 removed outlier: 4.327A pdb=" N ARG31 61 " --> pdb=" O GLU31 58 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG31 65 " --> pdb=" O ALA31 62 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS31 67 " --> pdb=" O GLU31 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL31 70 " --> pdb=" O HIS31 67 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET31 72 " --> pdb=" O ARG31 69 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL31 75 " --> pdb=" O MET31 72 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL31 76 " --> pdb=" O ALA31 73 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL31 80 " --> pdb=" O GLY31 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS31 81 " --> pdb=" O THR31 78 " (cutoff:3.500A) Processing helix chain '31' and resid 106 through 111 removed outlier: 4.099A pdb=" N ILE31 109 " --> pdb=" O VAL31 106 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG31 110 " --> pdb=" O ASP31 107 " (cutoff:3.500A) Processing helix chain '31' and resid 114 through 129 removed outlier: 3.725A pdb=" N LEU31 126 " --> pdb=" O ALA31 122 " (cutoff:3.500A) Processing helix chain '31' and resid 145 through 147 No H-bonds generated for 'chain '31' and resid 145 through 147' Processing helix chain '31' and resid 153 through 180 removed outlier: 3.994A pdb=" N ASN31 161 " --> pdb=" O ALA31 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA31 180 " --> pdb=" O GLY31 176 " (cutoff:3.500A) Processing helix chain '31' and resid 188 through 194 Processing helix chain '32' and resid 32 through 35 removed outlier: 3.514A pdb=" N LEU32 35 " --> pdb=" O GLU32 32 " (cutoff:3.500A) No H-bonds generated for 'chain '32' and resid 32 through 35' Processing helix chain '32' and resid 49 through 52 No H-bonds generated for 'chain '32' and resid 49 through 52' Processing helix chain '32' and resid 56 through 82 removed outlier: 4.328A pdb=" N ARG32 61 " --> pdb=" O GLU32 58 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG32 65 " --> pdb=" O ALA32 62 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS32 67 " --> pdb=" O GLU32 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL32 70 " --> pdb=" O HIS32 67 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET32 72 " --> pdb=" O ARG32 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL32 75 " --> pdb=" O MET32 72 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL32 76 " --> pdb=" O ALA32 73 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL32 80 " --> pdb=" O GLY32 77 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS32 81 " --> pdb=" O THR32 78 " (cutoff:3.500A) Processing helix chain '32' and resid 106 through 111 removed outlier: 4.100A pdb=" N ILE32 109 " --> pdb=" O VAL32 106 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG32 110 " --> pdb=" O ASP32 107 " (cutoff:3.500A) Processing helix chain '32' and resid 114 through 129 removed outlier: 3.724A pdb=" N LEU32 126 " --> pdb=" O ALA32 122 " (cutoff:3.500A) Processing helix chain '32' and resid 145 through 147 No H-bonds generated for 'chain '32' and resid 145 through 147' Processing helix chain '32' and resid 153 through 180 removed outlier: 3.994A pdb=" N ASN32 161 " --> pdb=" O ALA32 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA32 180 " --> pdb=" O GLY32 176 " (cutoff:3.500A) Processing helix chain '32' and resid 188 through 194 Processing helix chain '33' and resid 32 through 35 removed outlier: 3.513A pdb=" N LEU33 35 " --> pdb=" O GLU33 32 " (cutoff:3.500A) No H-bonds generated for 'chain '33' and resid 32 through 35' Processing helix chain '33' and resid 49 through 52 No H-bonds generated for 'chain '33' and resid 49 through 52' Processing helix chain '33' and resid 56 through 82 removed outlier: 4.327A pdb=" N ARG33 61 " --> pdb=" O GLU33 58 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG33 65 " --> pdb=" O ALA33 62 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS33 67 " --> pdb=" O GLU33 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL33 70 " --> pdb=" O HIS33 67 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET33 72 " --> pdb=" O ARG33 69 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL33 75 " --> pdb=" O MET33 72 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL33 76 " --> pdb=" O ALA33 73 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL33 80 " --> pdb=" O GLY33 77 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS33 81 " --> pdb=" O THR33 78 " (cutoff:3.500A) Processing helix chain '33' and resid 106 through 111 removed outlier: 4.100A pdb=" N ILE33 109 " --> pdb=" O VAL33 106 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG33 110 " --> pdb=" O ASP33 107 " (cutoff:3.500A) Processing helix chain '33' and resid 114 through 129 removed outlier: 3.725A pdb=" N LEU33 126 " --> pdb=" O ALA33 122 " (cutoff:3.500A) Processing helix chain '33' and resid 145 through 147 No H-bonds generated for 'chain '33' and resid 145 through 147' Processing helix chain '33' and resid 153 through 180 removed outlier: 3.995A pdb=" N ASN33 161 " --> pdb=" O ALA33 157 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA33 180 " --> pdb=" O GLY33 176 " (cutoff:3.500A) Processing helix chain '33' and resid 188 through 194 Processing helix chain '34' and resid 32 through 35 removed outlier: 3.513A pdb=" N LEU34 35 " --> pdb=" O GLU34 32 " (cutoff:3.500A) No H-bonds generated for 'chain '34' and resid 32 through 35' Processing helix chain '34' and resid 49 through 52 No H-bonds generated for 'chain '34' and resid 49 through 52' Processing helix chain '34' and resid 56 through 82 removed outlier: 4.326A pdb=" N ARG34 61 " --> pdb=" O GLU34 58 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG34 65 " --> pdb=" O ALA34 62 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS34 67 " --> pdb=" O GLU34 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL34 70 " --> pdb=" O HIS34 67 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET34 72 " --> pdb=" O ARG34 69 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL34 75 " --> pdb=" O MET34 72 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL34 76 " --> pdb=" O ALA34 73 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL34 80 " --> pdb=" O GLY34 77 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS34 81 " --> pdb=" O THR34 78 " (cutoff:3.500A) Processing helix chain '34' and resid 106 through 111 removed outlier: 4.101A pdb=" N ILE34 109 " --> pdb=" O VAL34 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG34 110 " --> pdb=" O ASP34 107 " (cutoff:3.500A) Processing helix chain '34' and resid 114 through 129 removed outlier: 3.726A pdb=" N LEU34 126 " --> pdb=" O ALA34 122 " (cutoff:3.500A) Processing helix chain '34' and resid 145 through 147 No H-bonds generated for 'chain '34' and resid 145 through 147' Processing helix chain '34' and resid 153 through 180 removed outlier: 3.994A pdb=" N ASN34 161 " --> pdb=" O ALA34 157 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA34 180 " --> pdb=" O GLY34 176 " (cutoff:3.500A) Processing helix chain '34' and resid 188 through 194 Processing helix chain '35' and resid 32 through 35 removed outlier: 3.536A pdb=" N LEU35 35 " --> pdb=" O GLU35 32 " (cutoff:3.500A) No H-bonds generated for 'chain '35' and resid 32 through 35' Processing helix chain '35' and resid 49 through 52 No H-bonds generated for 'chain '35' and resid 49 through 52' Processing helix chain '35' and resid 57 through 82 removed outlier: 3.868A pdb=" N LYS35 66 " --> pdb=" O ALA35 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA35 73 " --> pdb=" O ARG35 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL35 76 " --> pdb=" O MET35 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS35 81 " --> pdb=" O GLY35 77 " (cutoff:3.500A) Processing helix chain '35' and resid 114 through 129 removed outlier: 3.572A pdb=" N ALA35 122 " --> pdb=" O ALA35 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE35 123 " --> pdb=" O GLN35 119 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU35 126 " --> pdb=" O ALA35 122 " (cutoff:3.500A) Processing helix chain '35' and resid 153 through 182 removed outlier: 3.591A pdb=" N ASN35 161 " --> pdb=" O ALA35 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL35 162 " --> pdb=" O ARG35 158 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU35 164 " --> pdb=" O LEU35 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL35 179 " --> pdb=" O MET35 175 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA35 180 " --> pdb=" O GLY35 176 " (cutoff:3.500A) Processing helix chain '35' and resid 188 through 193 removed outlier: 3.646A pdb=" N TYR35 192 " --> pdb=" O MET35 188 " (cutoff:3.500A) Processing helix chain '36' and resid 57 through 82 removed outlier: 3.544A pdb=" N VAL36 63 " --> pdb=" O ARG36 59 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA36 71 " --> pdb=" O HIS36 67 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA36 73 " --> pdb=" O ARG36 69 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL36 76 " --> pdb=" O MET36 72 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY36 77 " --> pdb=" O ALA36 73 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS36 81 " --> pdb=" O GLY36 77 " (cutoff:3.500A) Processing helix chain '36' and resid 106 through 111 removed outlier: 4.245A pdb=" N ILE36 109 " --> pdb=" O VAL36 106 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG36 110 " --> pdb=" O ASP36 107 " (cutoff:3.500A) Processing helix chain '36' and resid 114 through 129 removed outlier: 4.089A pdb=" N GLN36 119 " --> pdb=" O ALA36 115 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE36 123 " --> pdb=" O GLN36 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU36 126 " --> pdb=" O ALA36 122 " (cutoff:3.500A) Processing helix chain '36' and resid 153 through 182 removed outlier: 3.652A pdb=" N ALA36 157 " --> pdb=" O PRO36 153 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG36 158 " --> pdb=" O GLU36 154 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN36 161 " --> pdb=" O ALA36 157 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL36 162 " --> pdb=" O ARG36 158 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU36 164 " --> pdb=" O LEU36 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA36 169 " --> pdb=" O ASN36 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET36 171 " --> pdb=" O GLY36 167 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET36 172 " --> pdb=" O ARG36 168 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY36 173 " --> pdb=" O ALA36 169 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA36 180 " --> pdb=" O GLY36 176 " (cutoff:3.500A) Processing helix chain '36' and resid 188 through 194 removed outlier: 3.581A pdb=" N TYR36 192 " --> pdb=" O MET36 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA36 193 " --> pdb=" O TYR36 189 " (cutoff:3.500A) Processing helix chain '37' and resid 33 through 35 No H-bonds generated for 'chain '37' and resid 33 through 35' Processing helix chain '37' and resid 49 through 52 No H-bonds generated for 'chain '37' and resid 49 through 52' Processing helix chain '37' and resid 55 through 82 removed outlier: 3.896A pdb=" N GLU37 58 " --> pdb=" O GLU37 55 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG37 61 " --> pdb=" O GLU37 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU37 64 " --> pdb=" O ARG37 61 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS37 67 " --> pdb=" O GLU37 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL37 70 " --> pdb=" O HIS37 67 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET37 72 " --> pdb=" O ARG37 69 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL37 76 " --> pdb=" O ALA37 73 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL37 80 " --> pdb=" O GLY37 77 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS37 81 " --> pdb=" O THR37 78 " (cutoff:3.500A) Processing helix chain '37' and resid 106 through 108 No H-bonds generated for 'chain '37' and resid 106 through 108' Processing helix chain '37' and resid 114 through 129 removed outlier: 3.692A pdb=" N LEU37 126 " --> pdb=" O ALA37 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU37 128 " --> pdb=" O PHE37 124 " (cutoff:3.500A) Processing helix chain '37' and resid 154 through 182 removed outlier: 3.997A pdb=" N ARG37 158 " --> pdb=" O GLU37 154 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA37 170 " --> pdb=" O ASN37 166 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET37 171 " --> pdb=" O GLY37 167 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET37 172 " --> pdb=" O ARG37 168 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY37 173 " --> pdb=" O ALA37 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET37 175 " --> pdb=" O MET37 171 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA37 180 " --> pdb=" O GLY37 176 " (cutoff:3.500A) Processing helix chain '37' and resid 188 through 194 Processing helix chain '38' and resid 49 through 52 No H-bonds generated for 'chain '38' and resid 49 through 52' Processing helix chain '38' and resid 57 through 82 removed outlier: 3.725A pdb=" N VAL38 63 " --> pdb=" O ARG38 59 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL38 76 " --> pdb=" O MET38 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS38 81 " --> pdb=" O GLY38 77 " (cutoff:3.500A) Processing helix chain '38' and resid 106 through 111 removed outlier: 4.054A pdb=" N ILE38 109 " --> pdb=" O VAL38 106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG38 110 " --> pdb=" O ASP38 107 " (cutoff:3.500A) Processing helix chain '38' and resid 114 through 128 removed outlier: 3.577A pdb=" N LEU38 126 " --> pdb=" O ALA38 122 " (cutoff:3.500A) Processing helix chain '38' and resid 145 through 147 No H-bonds generated for 'chain '38' and resid 145 through 147' Processing helix chain '38' and resid 153 through 182 removed outlier: 3.875A pdb=" N VAL38 162 " --> pdb=" O ARG38 158 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU38 163 " --> pdb=" O LYS38 159 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET38 172 " --> pdb=" O ARG38 168 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA38 180 " --> pdb=" O GLY38 176 " (cutoff:3.500A) Processing helix chain '38' and resid 188 through 194 removed outlier: 3.548A pdb=" N TYR38 192 " --> pdb=" O MET38 188 " (cutoff:3.500A) Processing helix chain '39' and resid 3 through 6 No H-bonds generated for 'chain '39' and resid 3 through 6' Processing helix chain '39' and resid 20 through 22 No H-bonds generated for 'chain '39' and resid 20 through 22' Processing helix chain '39' and resid 58 through 67 removed outlier: 3.578A pdb=" N UNK39 63 " --> pdb=" O UNK39 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK39 64 " --> pdb=" O UNK39 60 " (cutoff:3.500A) Processing helix chain '39' and resid 69 through 72 No H-bonds generated for 'chain '39' and resid 69 through 72' Processing helix chain '39' and resid 77 through 80 No H-bonds generated for 'chain '39' and resid 77 through 80' Processing helix chain '39' and resid 106 through 109 No H-bonds generated for 'chain '39' and resid 106 through 109' Processing helix chain '39' and resid 112 through 134 removed outlier: 3.651A pdb=" N UNK39 116 " --> pdb=" O UNK39 112 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N UNK39 125 " --> pdb=" O UNK39 121 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N UNK39 128 " --> pdb=" O UNK39 124 " (cutoff:3.500A) Processing helix chain '39' and resid 157 through 187 removed outlier: 3.922A pdb=" N UNK39 161 " --> pdb=" O UNK39 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK39 162 " --> pdb=" O UNK39 158 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N UNK39 174 " --> pdb=" O UNK39 170 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK39 176 " --> pdb=" O UNK39 172 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNK39 177 " --> pdb=" O UNK39 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK39 179 " --> pdb=" O UNK39 175 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N UNK39 180 " --> pdb=" O UNK39 176 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK39 183 " --> pdb=" O UNK39 179 " (cutoff:3.500A) Processing helix chain '39' and resid 191 through 194 No H-bonds generated for 'chain '39' and resid 191 through 194' Processing helix chain '40' and resid 59 through 82 removed outlier: 3.982A pdb=" N UNK40 76 " --> pdb=" O UNK40 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK40 77 " --> pdb=" O UNK40 73 " (cutoff:3.500A) Processing helix chain '40' and resid 114 through 129 removed outlier: 3.533A pdb=" N UNK40 127 " --> pdb=" O UNK40 123 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNK40 128 " --> pdb=" O UNK40 124 " (cutoff:3.500A) Processing helix chain '40' and resid 156 through 182 removed outlier: 3.836A pdb=" N UNK40 169 " --> pdb=" O UNK40 165 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N UNK40 170 " --> pdb=" O UNK40 166 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N UNK40 172 " --> pdb=" O UNK40 168 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK40 173 " --> pdb=" O UNK40 169 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N UNK40 175 " --> pdb=" O UNK40 171 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK40 178 " --> pdb=" O UNK40 174 " (cutoff:3.500A) Processing helix chain '41' and resid 49 through 52 No H-bonds generated for 'chain '41' and resid 49 through 52' Processing helix chain '41' and resid 55 through 82 removed outlier: 3.798A pdb=" N UNK41 58 " --> pdb=" O UNK41 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N UNK41 59 " --> pdb=" O UNK41 56 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK41 61 " --> pdb=" O UNK41 58 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N UNK41 62 " --> pdb=" O UNK41 59 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK41 63 " --> pdb=" O UNK41 60 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N UNK41 65 " --> pdb=" O UNK41 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N UNK41 66 " --> pdb=" O UNK41 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK41 68 " --> pdb=" O UNK41 65 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N UNK41 69 " --> pdb=" O UNK41 66 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N UNK41 70 " --> pdb=" O UNK41 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK41 72 " --> pdb=" O UNK41 69 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N UNK41 73 " --> pdb=" O UNK41 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N UNK41 75 " --> pdb=" O UNK41 72 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N UNK41 76 " --> pdb=" O UNK41 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK41 79 " --> pdb=" O UNK41 76 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N UNK41 80 " --> pdb=" O UNK41 77 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N UNK41 81 " --> pdb=" O UNK41 78 " (cutoff:3.500A) Processing helix chain '41' and resid 106 through 111 removed outlier: 4.090A pdb=" N UNK41 109 " --> pdb=" O UNK41 106 " (cutoff:3.500A) Processing helix chain '41' and resid 114 through 129 removed outlier: 3.502A pdb=" N UNK41 118 " --> pdb=" O UNK41 114 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK41 119 " --> pdb=" O UNK41 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N UNK41 122 " --> pdb=" O UNK41 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N UNK41 128 " --> pdb=" O UNK41 124 " (cutoff:3.500A) Processing helix chain '41' and resid 153 through 183 removed outlier: 3.602A pdb=" N UNK41 157 " --> pdb=" O UNK41 153 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N UNK41 166 " --> pdb=" O UNK41 162 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK41 167 " --> pdb=" O UNK41 163 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N UNK41 169 " --> pdb=" O UNK41 165 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N UNK41 170 " --> pdb=" O UNK41 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N UNK41 172 " --> pdb=" O UNK41 168 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK41 175 " --> pdb=" O UNK41 171 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 345 through 347 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.807A 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 183 through 185 Processing sheet with id= F, first strand: chain 'C' and resid 339 through 341 Processing sheet with id= G, first strand: chain 'O' and resid 64 through 68 removed outlier: 6.794A pdb=" N LYS O 239 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TRP O 50 " --> pdb=" O LEU O 237 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU O 237 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL O 52 " --> pdb=" O LYS O 235 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS O 235 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY O 240 " --> pdb=" O PHE O 218 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY O 216 " --> pdb=" O PHE O 242 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL O 217 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL O 204 " --> pdb=" O VAL O 217 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL O 219 " --> pdb=" O MET O 202 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET O 202 " --> pdb=" O VAL O 219 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR O 221 " --> pdb=" O ILE O 200 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE O 200 " --> pdb=" O THR O 221 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU O 223 " --> pdb=" O GLY O 198 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLY O 198 " --> pdb=" O LEU O 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 92 through 96 Processing sheet with id= I, first strand: chain 'O' and resid 103 through 109 Processing sheet with id= J, first strand: chain 'V' and resid 9 through 11 Processing sheet with id= K, first strand: chain 'b' and resid 166 through 169 Processing sheet with id= L, first strand: chain 'b' and resid 345 through 347 Processing sheet with id= M, first strand: chain 'b' and resid 336 through 340 removed outlier: 6.809A pdb=" N GLU b 431 " --> pdb=" O GLU b 338 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'b' and resid 369 through 371 Processing sheet with id= O, first strand: chain 'c' and resid 183 through 185 Processing sheet with id= P, first strand: chain 'c' and resid 339 through 341 Processing sheet with id= Q, first strand: chain 'o' and resid 64 through 68 removed outlier: 6.793A pdb=" N LYS o 239 " --> pdb=" O LYS o 48 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP o 50 " --> pdb=" O LEU o 237 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU o 237 " --> pdb=" O TRP o 50 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL o 52 " --> pdb=" O LYS o 235 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS o 235 " --> pdb=" O VAL o 52 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY o 240 " --> pdb=" O PHE o 218 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY o 216 " --> pdb=" O PHE o 242 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL o 217 " --> pdb=" O VAL o 204 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL o 204 " --> pdb=" O VAL o 217 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL o 219 " --> pdb=" O MET o 202 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET o 202 " --> pdb=" O VAL o 219 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR o 221 " --> pdb=" O ILE o 200 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE o 200 " --> pdb=" O THR o 221 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU o 223 " --> pdb=" O GLY o 198 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY o 198 " --> pdb=" O LEU o 223 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'o' and resid 92 through 96 Processing sheet with id= S, first strand: chain 'o' and resid 103 through 109 Processing sheet with id= T, first strand: chain 'v' and resid 9 through 11 2704 hydrogen bonds defined for protein. 7248 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: 29.45 Time building geometry restraints manager: 36.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.68: 98984 1.68 - 2.19: 1712 2.19 - 2.70: 12 2.70 - 3.22: 0 3.22 - 3.73: 8 Bond restraints: 100716 Sorted by residual: bond pdb=" C4 A8640 201 " pdb=" C5 A8640 201 " ideal model delta sigma weight residual 1.431 1.669 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4 A8620 201 " pdb=" C5 A8620 201 " ideal model delta sigma weight residual 1.431 1.669 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4 A8620 212 " pdb=" C5 A8620 212 " ideal model delta sigma weight residual 1.431 1.665 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C4 A8639 310 " pdb=" C5 A8639 310 " ideal model delta sigma weight residual 1.431 1.664 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4 A8619 310 " pdb=" C5 A8619 310 " ideal model delta sigma weight residual 1.431 1.664 -0.233 2.00e-02 2.50e+03 1.36e+02 ... (remaining 100711 not shown) Histogram of bond angle deviations from ideal: 59.41 - 83.46: 360 83.46 - 107.50: 10380 107.50 - 131.54: 129030 131.54 - 155.59: 1638 155.59 - 179.63: 710 Bond angle restraints: 142118 Sorted by residual: angle pdb=" C19 A8637 315 " pdb=" C20 A8637 315 " pdb=" O1 A8637 315 " ideal model delta sigma weight residual 115.66 154.96 -39.30 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C19 A8617 311 " pdb=" C20 A8617 311 " pdb=" O1 A8617 311 " ideal model delta sigma weight residual 115.66 154.95 -39.29 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C19 A8617 315 " pdb=" C20 A8617 315 " pdb=" O1 A8617 315 " ideal model delta sigma weight residual 115.66 154.95 -39.29 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C19 A8637 311 " pdb=" C20 A8637 311 " pdb=" O1 A8637 311 " ideal model delta sigma weight residual 115.66 154.93 -39.27 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C19 A8618 313 " pdb=" C20 A8618 313 " pdb=" O1 A8618 313 " ideal model delta sigma weight residual 115.66 154.76 -39.10 3.00e+00 1.11e-01 1.70e+02 ... (remaining 142113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 48984 31.11 - 62.22: 2957 62.22 - 93.33: 777 93.33 - 124.44: 266 124.44 - 155.56: 86 Dihedral angle restraints: 53070 sinusoidal: 25928 harmonic: 27142 Sorted by residual: dihedral pdb=" CA UNK40 146 " pdb=" C UNK40 146 " pdb=" N UNK40 147 " pdb=" CA UNK40 147 " ideal model delta harmonic sigma weight residual -180.00 -134.08 -45.92 0 5.00e+00 4.00e-02 8.43e+01 dihedral pdb=" CA UNK20 146 " pdb=" C UNK20 146 " pdb=" N UNK20 147 " pdb=" CA UNK20 147 " ideal model delta harmonic sigma weight residual -180.00 -134.15 -45.85 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 44 " pdb=" CB CYS O 44 " ideal model delta sinusoidal sigma weight residual 93.00 167.32 -74.32 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 53067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 12847 0.337 - 0.673: 112 0.673 - 1.010: 9 1.010 - 1.346: 2 1.346 - 1.683: 118 Chirality restraints: 13088 Sorted by residual: chirality pdb=" C20 A8640 201 " pdb=" C15 A8640 201 " pdb=" C19 A8640 201 " pdb=" C21 A8640 201 " both_signs ideal model delta sigma weight residual True 1.08 2.76 -1.68 2.00e-01 2.50e+01 7.08e+01 chirality pdb=" C20 A8620 201 " pdb=" C15 A8620 201 " pdb=" C19 A8620 201 " pdb=" C21 A8620 201 " both_signs ideal model delta sigma weight residual True 1.08 2.76 -1.68 2.00e-01 2.50e+01 7.07e+01 chirality pdb=" C20 A8618 313 " pdb=" C15 A8618 313 " pdb=" C19 A8618 313 " pdb=" C21 A8618 313 " both_signs ideal model delta sigma weight residual True 1.08 2.76 -1.68 2.00e-01 2.50e+01 7.03e+01 ... (remaining 13085 not shown) Planarity restraints: 18582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR b 623 " 0.011 2.00e-02 2.50e+03 2.65e-01 7.00e+02 pdb=" C11 BCR b 623 " -0.242 2.00e-02 2.50e+03 pdb=" C12 BCR b 623 " 0.427 2.00e-02 2.50e+03 pdb=" C13 BCR b 623 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR B 624 " -0.038 2.00e-02 2.50e+03 2.63e-01 6.94e+02 pdb=" C11 BCR B 624 " 0.273 2.00e-02 2.50e+03 pdb=" C12 BCR B 624 " -0.412 2.00e-02 2.50e+03 pdb=" C13 BCR B 624 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 BCR a 404 " -0.252 2.00e-02 2.50e+03 2.23e-01 6.24e+02 pdb=" C17 BCR a 404 " 0.413 2.00e-02 2.50e+03 pdb=" C18 BCR a 404 " -0.033 2.00e-02 2.50e+03 pdb=" C19 BCR a 404 " -0.120 2.00e-02 2.50e+03 pdb=" C36 BCR a 404 " -0.007 2.00e-02 2.50e+03 ... (remaining 18579 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 44 2.08 - 2.79: 21829 2.79 - 3.49: 119617 3.49 - 4.20: 246346 4.20 - 4.90: 410992 Nonbonded interactions: 798828 Sorted by model distance: nonbonded pdb=" O PHE13 146 " pdb=" O5 A8613 301 " model vdw 1.376 3.040 nonbonded pdb=" OE2 GLU c 352 " pdb=" O3 OEX c 501 " model vdw 1.392 3.040 nonbonded pdb=" O PHE11 146 " pdb=" O5 A8611 316 " model vdw 1.468 3.040 nonbonded pdb=" O PHE18 146 " pdb=" O5 A8618 302 " model vdw 1.619 3.040 nonbonded pdb=" OE2 GLU C 352 " pdb=" O3 OEX C 501 " model vdw 1.622 3.040 ... (remaining 798823 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' and resid 2 through 31) selection = chain '1' selection = (chain '5' and resid 2 through 31) selection = chain '6' } ncs_group { reference = (chain '11' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '12' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '13' and (resid 31 through 206 or resid 303 or (resid 305 through 309 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 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 na \ me O1D or name O2A or name O2D or name OBD or name MG )))) selection = (chain '14' and (resid 31 through 206 or resid 303 or (resid 305 through 309 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 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 na \ me O1D or name O2A or name O2D or name OBD or name MG )))) selection = (chain '15' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '16' and (resid 31 through 206 or resid 303 or resid 305 through 309)) selection = (chain '17' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '18' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '31' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '32' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '33' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '34' and (resid 31 through 206 or resid 303 or (resid 305 through 309 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 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 na \ me O1D or name O2A or name O2D or name OBD or name MG )))) selection = (chain '35' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '36' and (resid 31 through 206 or resid 303 or resid 305 through 309)) selection = (chain '37' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) selection = (chain '38' and (resid 31 through 206 or (resid 303 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 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 nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e 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 CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e 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 )))) } ncs_group { reference = chain '19' selection = chain '39' } ncs_group { reference = chain '2' selection = chain '7' } ncs_group { reference = (chain '20' and (resid 42 through 183 or resid 202 through 203 or (resid 204 thr \ ough 208 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 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 na \ me O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 21 \ 0 through 213)) selection = (chain '21' and (resid 44 through 185 or resid 303 through 305 or (resid 306 thr \ ough 309 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 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 na \ me O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 31 \ 1 through 314)) selection = (chain '40' and (resid 42 through 183 or resid 202 through 203 or (resid 204 thr \ ough 208 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 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 na \ me O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 21 \ 0 through 213)) selection = (chain '41' and (resid 44 through 185 or resid 303 through 305 or (resid 306 thr \ ough 309 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 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 na \ me O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 31 \ 1 through 314)) } ncs_group { reference = (chain 'A' and (resid 11 through 344 or resid 401 through 402)) selection = (chain 'a' and (resid 11 through 344 or resid 401 through 402)) } ncs_group { reference = (chain 'B' and (resid 2 through 485 or resid 601 through 617 or resid 619)) selection = (chain 'b' and (resid 2 through 485 or resid 601 through 617 or resid 619)) } ncs_group { reference = (chain 'C' and (resid 21 through 471 or resid 501 through 515 or resid 517)) selection = (chain 'c' and (resid 21 through 471 or resid 501 through 515 or resid 517)) } ncs_group { reference = (chain 'D' and (resid 11 through 351 or resid 401 through 403 or resid 406)) selection = (chain 'd' and (resid 11 through 351 or resid 401 through 403 or resid 406)) } 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' and (resid 1 through 38 or resid 102)) selection = (chain 'l' and (resid 1 through 38 or resid 102)) } ncs_group { reference = chain 'M' selection = (chain 'm' and (resid 2 through 43 or resid 101 through 102)) } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = (chain 'Q' and resid 70 through 206) 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' and resid 1 through 34) selection = chain 'y' } ncs_group { reference = (chain 'Z' and resid 1 through 59) selection = (chain 'z' and resid 1 through 59) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.790 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: 0.120 Extract box with map and model: 29.710 Check model and map are aligned: 1.200 Set scattering table: 0.700 Process input model: 195.130 Find NCS groups from input model: 5.650 Set up NCS constraints: 1.830 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.022 0.249 100716 Z= 1.156 Angle : 1.993 39.297 142118 Z= 0.764 Chirality : 0.176 1.683 13088 Planarity : 0.013 0.265 18582 Dihedral : 22.440 155.556 35724 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 0.33 % Allowed : 2.73 % Favored : 96.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -5.08 (0.07), residues: 8276 helix: -4.08 (0.04), residues: 4330 sheet: -1.77 (0.33), residues: 236 loop : -2.37 (0.09), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP a 142 HIS 0.018 0.004 HIS F 22 PHE 0.041 0.004 PHE c 282 TYR 0.042 0.003 TYR H 49 ARG 0.016 0.001 ARG17 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1061 time to evaluate : 6.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.7025 (ptp) cc_final: 0.6410 (ptt) REVERT: B 60 MET cc_start: 0.9019 (mmt) cc_final: 0.8728 (mmm) REVERT: B 108 PHE cc_start: 0.8154 (t80) cc_final: 0.7881 (t80) REVERT: C 396 HIS cc_start: 0.7554 (m90) cc_final: 0.7005 (m90) REVERT: I 1 MET cc_start: 0.6533 (mpp) cc_final: 0.6142 (mpp) REVERT: I 19 PHE cc_start: 0.8918 (t80) cc_final: 0.8511 (t80) REVERT: I 23 PHE cc_start: 0.8132 (m-80) cc_final: 0.7736 (m-80) REVERT: L 31 LEU cc_start: 0.9339 (tp) cc_final: 0.9043 (tp) REVERT: M 9 LEU cc_start: 0.8795 (mt) cc_final: 0.8519 (mm) REVERT: T 6 TYR cc_start: 0.8576 (m-80) cc_final: 0.8115 (m-80) REVERT: W 34 LEU cc_start: 0.9064 (mt) cc_final: 0.8805 (mp) REVERT: W 45 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8763 (mm) REVERT: b 237 VAL cc_start: 0.8708 (t) cc_final: 0.8461 (t) REVERT: c 396 HIS cc_start: 0.7609 (m90) cc_final: 0.7232 (m90) REVERT: d 198 MET cc_start: 0.8091 (mtm) cc_final: 0.7661 (mtp) REVERT: d 280 THR cc_start: 0.9038 (p) cc_final: 0.8669 (t) REVERT: f 38 MET cc_start: 0.8001 (mtm) cc_final: 0.7788 (mtm) REVERT: i 1 MET cc_start: 0.6310 (mpp) cc_final: 0.6059 (mpp) REVERT: i 2 LEU cc_start: 0.8758 (mt) cc_final: 0.8554 (tp) REVERT: j 18 LEU cc_start: 0.8729 (pp) cc_final: 0.8328 (tt) REVERT: l 32 PHE cc_start: 0.8592 (m-80) cc_final: 0.8343 (m-80) REVERT: m 9 LEU cc_start: 0.8865 (mt) cc_final: 0.8610 (mm) REVERT: 11 72 MET cc_start: 0.7973 (mtp) cc_final: 0.7515 (ttm) REVERT: 11 188 MET cc_start: 0.7633 (ttp) cc_final: 0.7402 (ttm) REVERT: 13 140 ASP cc_start: 0.7208 (p0) cc_final: 0.5676 (p0) REVERT: 14 91 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7885 (tt) REVERT: 16 171 MET cc_start: 0.7049 (mtt) cc_final: 0.6818 (mtm) REVERT: 17 72 MET cc_start: 0.7520 (mtp) cc_final: 0.7180 (mtp) REVERT: 17 171 MET cc_start: 0.7773 (ptp) cc_final: 0.7476 (ptp) REVERT: 18 72 MET cc_start: 0.5156 (mtp) cc_final: 0.4303 (mtp) REVERT: 32 72 MET cc_start: 0.7860 (mtp) cc_final: 0.7517 (mtm) REVERT: 34 91 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (tt) REVERT: 34 145 TYR cc_start: 0.8245 (t80) cc_final: 0.8039 (t80) REVERT: 36 171 MET cc_start: 0.7316 (mtt) cc_final: 0.7006 (mtm) REVERT: 37 171 MET cc_start: 0.8029 (ptp) cc_final: 0.7700 (ptp) outliers start: 22 outliers final: 2 residues processed: 1081 average time/residue: 0.8493 time to fit residues: 1613.9742 Evaluate side-chains 543 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 538 time to evaluate : 6.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain c residue 270 LEU Chi-restraints excluded: chain 14 residue 91 LEU Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 34 residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 780 optimal weight: 10.0000 chunk 700 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 472 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 724 optimal weight: 40.0000 chunk 280 optimal weight: 1.9990 chunk 440 optimal weight: 0.0040 chunk 539 optimal weight: 3.9990 chunk 839 optimal weight: 4.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 72 HIS C 89 HIS C 311 GLN C 325 ASN ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 193 ASN D 219 ASN D 229 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 GLN U 52 HIS V 25 GLN Q 105 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 ASN b 87 ASN b 457 ASN c 72 HIS c 311 GLN ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 ASN d 193 ASN d 219 ASN ** d 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN l 7 ASN l 14 ASN o 222 GLN v 14 ASN v 25 GLN q 105 ASN ** 11 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 83 ASN 13 161 ASN 14 83 ASN 14 161 ASN 15 82 ASN 15 95 ASN 15 96 ASN 16 95 ASN 17 96 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 177 ASN 18 82 ASN 18 96 ASN 18 177 ASN ** 31 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 83 ASN 32 95 ASN ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 83 ASN 33 161 ASN 34 161 ASN 35 82 ASN 35 95 ASN 35 96 ASN 36 177 ASN 37 96 ASN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 37 177 ASN 38 96 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 100716 Z= 0.274 Angle : 0.862 12.562 142118 Z= 0.364 Chirality : 0.047 0.643 13088 Planarity : 0.005 0.057 18582 Dihedral : 22.016 175.560 21224 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 1.74 % Allowed : 7.95 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.08), residues: 8276 helix: -1.95 (0.06), residues: 4442 sheet: -1.46 (0.34), residues: 220 loop : -1.62 (0.10), residues: 3614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 61 HIS 0.009 0.002 HIS b 23 PHE 0.029 0.002 PHE33 124 TYR 0.020 0.002 TYR Q 89 ARG 0.007 0.001 ARG u 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 605 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7226 (tmm) cc_final: 0.6883 (tmm) REVERT: A 77 ILE cc_start: 0.9196 (mm) cc_final: 0.8945 (mm) REVERT: A 286 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8471 (t) REVERT: B 108 PHE cc_start: 0.8265 (t80) cc_final: 0.8008 (t80) REVERT: B 453 TYR cc_start: 0.8310 (t80) cc_final: 0.8051 (t80) REVERT: C 287 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7752 (t80) REVERT: C 354 MET cc_start: 0.7630 (tmm) cc_final: 0.7359 (tmm) REVERT: C 396 HIS cc_start: 0.7733 (m90) cc_final: 0.7059 (m90) REVERT: F 38 MET cc_start: 0.8551 (mtm) cc_final: 0.8316 (mtm) REVERT: J 18 LEU cc_start: 0.8791 (pp) cc_final: 0.8588 (pp) REVERT: Y 34 LEU cc_start: 0.7631 (mt) cc_final: 0.7406 (mp) REVERT: W 45 ILE cc_start: 0.9031 (mp) cc_final: 0.8804 (mm) REVERT: a 286 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8485 (t) REVERT: b 63 MET cc_start: 0.8206 (ttm) cc_final: 0.7981 (ttm) REVERT: b 237 VAL cc_start: 0.8795 (t) cc_final: 0.8489 (t) REVERT: c 287 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7832 (t80) REVERT: c 396 HIS cc_start: 0.7858 (m90) cc_final: 0.7379 (m90) REVERT: d 280 THR cc_start: 0.9186 (p) cc_final: 0.8887 (t) REVERT: o 168 MET cc_start: 0.8785 (pmm) cc_final: 0.8189 (pmm) REVERT: t 6 TYR cc_start: 0.8782 (m-80) cc_final: 0.8504 (m-80) REVERT: q 79 THR cc_start: 0.7628 (p) cc_final: 0.7426 (m) REVERT: w 45 ILE cc_start: 0.9048 (mp) cc_final: 0.8846 (mm) REVERT: 11 178 MET cc_start: 0.7470 (mtp) cc_final: 0.7248 (mtp) REVERT: 13 172 MET cc_start: 0.8728 (mmm) cc_final: 0.8487 (mmp) REVERT: 14 171 MET cc_start: 0.8155 (mtt) cc_final: 0.7618 (mmm) REVERT: 15 188 MET cc_start: 0.6997 (tpt) cc_final: 0.6432 (tpt) REVERT: 17 72 MET cc_start: 0.7815 (mtp) cc_final: 0.7564 (mtp) REVERT: 18 178 MET cc_start: 0.6622 (mmm) cc_final: 0.6330 (mmp) REVERT: 32 172 MET cc_start: 0.8644 (mmm) cc_final: 0.8404 (mpp) REVERT: 33 172 MET cc_start: 0.8855 (mmm) cc_final: 0.8577 (mmp) REVERT: 38 160 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8741 (tp) REVERT: 38 171 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6377 (ttm) outliers start: 117 outliers final: 43 residues processed: 677 average time/residue: 0.8484 time to fit residues: 1018.9869 Evaluate side-chains 539 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 490 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 287 TYR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 296 ASP Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain v residue 14 ASN Chi-restraints excluded: chain v residue 119 ILE Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain 11 residue 88 ASP Chi-restraints excluded: chain 11 residue 174 ILE Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 95 ASN Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 76 VAL Chi-restraints excluded: chain 31 residue 88 ASP Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 31 residue 174 ILE Chi-restraints excluded: chain 32 residue 95 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 38 residue 160 LEU Chi-restraints excluded: chain 38 residue 171 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 466 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 698 optimal weight: 9.9990 chunk 571 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 840 optimal weight: 9.9990 chunk 908 optimal weight: 40.0000 chunk 748 optimal weight: 8.9990 chunk 833 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 674 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN V 14 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 7 ASN u 52 HIS v 68 ASN 11 96 ASN ** 11 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 95 ASN ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 191 GLN 14 96 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 95 ASN 31 96 ASN ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 82 ASN ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 191 GLN 33 191 GLN 35 83 ASN 36 177 ASN 37 95 ASN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 38 95 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 100716 Z= 0.285 Angle : 0.793 14.557 142118 Z= 0.336 Chirality : 0.046 0.415 13088 Planarity : 0.005 0.084 18582 Dihedral : 20.279 179.640 21216 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 2.27 % Allowed : 8.60 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.09), residues: 8276 helix: -0.73 (0.07), residues: 4432 sheet: -1.28 (0.36), residues: 210 loop : -1.16 (0.10), residues: 3634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 61 HIS 0.009 0.002 HIS b 201 PHE 0.031 0.002 PHE15 124 TYR 0.022 0.002 TYR13 192 ARG 0.007 0.001 ARG32 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 508 time to evaluate : 7.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7457 (tmm) cc_final: 0.7093 (tmm) REVERT: A 77 ILE cc_start: 0.9256 (mm) cc_final: 0.8983 (mm) REVERT: B 453 TYR cc_start: 0.8405 (t80) cc_final: 0.8166 (t80) REVERT: C 287 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7649 (t80) REVERT: C 354 MET cc_start: 0.7973 (tmm) cc_final: 0.7682 (tmm) REVERT: C 396 HIS cc_start: 0.7820 (m90) cc_final: 0.7201 (m90) REVERT: H 35 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7802 (mpp) REVERT: H 50 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7882 (m-40) REVERT: T 6 TYR cc_start: 0.8706 (m-80) cc_final: 0.8482 (m-80) REVERT: W 45 ILE cc_start: 0.9056 (mp) cc_final: 0.8825 (mm) REVERT: a 37 MET cc_start: 0.7885 (tmm) cc_final: 0.7613 (tmm) REVERT: a 91 MET cc_start: 0.8429 (mmm) cc_final: 0.8068 (tpp) REVERT: b 63 MET cc_start: 0.8219 (ttm) cc_final: 0.7903 (ttm) REVERT: b 231 MET cc_start: 0.9048 (mpp) cc_final: 0.8765 (mtt) REVERT: b 237 VAL cc_start: 0.8967 (t) cc_final: 0.8682 (t) REVERT: b 330 MET cc_start: 0.7549 (mtp) cc_final: 0.7345 (ttm) REVERT: c 287 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7788 (t80) REVERT: c 396 HIS cc_start: 0.8031 (m90) cc_final: 0.7390 (m90) REVERT: d 321 ASP cc_start: 0.8201 (m-30) cc_final: 0.7817 (t70) REVERT: h 50 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7874 (t0) REVERT: m 9 LEU cc_start: 0.8912 (mp) cc_final: 0.8569 (mt) REVERT: o 168 MET cc_start: 0.8814 (pmm) cc_final: 0.8547 (pmm) REVERT: y 34 LEU cc_start: 0.7122 (mt) cc_final: 0.6847 (mp) REVERT: w 45 ILE cc_start: 0.9150 (mp) cc_final: 0.8940 (mm) REVERT: 12 91 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8626 (tt) REVERT: 14 91 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8171 (tt) REVERT: 15 188 MET cc_start: 0.7191 (tpt) cc_final: 0.6741 (tpp) REVERT: 17 132 MET cc_start: 0.8519 (mpp) cc_final: 0.8309 (mpp) REVERT: 17 166 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8180 (t160) REVERT: 17 171 MET cc_start: 0.7490 (ptt) cc_final: 0.7256 (ptt) REVERT: 18 138 ASP cc_start: 0.7696 (p0) cc_final: 0.7335 (p0) REVERT: 18 178 MET cc_start: 0.6710 (mmm) cc_final: 0.6497 (mmp) REVERT: 32 172 MET cc_start: 0.8835 (mmm) cc_final: 0.8444 (mpp) REVERT: 33 172 MET cc_start: 0.8897 (mmm) cc_final: 0.8677 (mmp) REVERT: 35 172 MET cc_start: 0.8415 (mpp) cc_final: 0.8146 (mpp) REVERT: 35 188 MET cc_start: 0.6580 (mmt) cc_final: 0.6168 (mtt) REVERT: 37 166 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8352 (t160) REVERT: 37 171 MET cc_start: 0.8560 (ptp) cc_final: 0.8353 (ptt) REVERT: 37 172 MET cc_start: 0.8627 (mmm) cc_final: 0.8423 (mmt) REVERT: 38 72 MET cc_start: 0.6387 (ttm) cc_final: 0.6022 (ttt) REVERT: 38 171 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6843 (ttm) outliers start: 153 outliers final: 64 residues processed: 613 average time/residue: 0.9277 time to fit residues: 1021.4444 Evaluate side-chains 524 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 450 time to evaluate : 6.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 14 ASN Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 30 LYS Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 270 LEU Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 287 TYR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 296 ASP Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 50 ASN Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain l residue 14 ASN Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 17 LEU Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain u residue 69 SER Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain 11 residue 88 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 12 residue 91 LEU Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 14 residue 91 LEU Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 91 LEU Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 95 ASN Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 76 VAL Chi-restraints excluded: chain 31 residue 88 ASP Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 33 residue 31 SER Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 36 residue 164 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Chi-restraints excluded: chain 38 residue 171 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 830 optimal weight: 0.9980 chunk 632 optimal weight: 6.9990 chunk 436 optimal weight: 0.0040 chunk 93 optimal weight: 6.9990 chunk 401 optimal weight: 0.1980 chunk 564 optimal weight: 4.9990 chunk 843 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 chunk 799 optimal weight: 0.0060 chunk 240 optimal weight: 4.9990 overall best weight: 0.8410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 179 GLN B 274 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 GLN b 274 GLN ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 349 ASN ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 161 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 191 GLN ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 82 ASN ** 32 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 191 GLN ** 34 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 36 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 100716 Z= 0.152 Angle : 0.676 12.472 142118 Z= 0.283 Chirality : 0.042 0.384 13088 Planarity : 0.004 0.057 18582 Dihedral : 19.279 174.007 21216 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 1.65 % Allowed : 9.74 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.93 (0.09), residues: 8276 helix: -0.20 (0.08), residues: 4440 sheet: -1.15 (0.37), residues: 190 loop : -0.99 (0.10), residues: 3646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 33 HIS 0.008 0.001 HIS C 116 PHE 0.027 0.001 PHE36 123 TYR 0.024 0.001 TYR32 141 ARG 0.006 0.000 ARG U 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 516 time to evaluate : 6.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7307 (tmm) cc_final: 0.7041 (tmm) REVERT: A 77 ILE cc_start: 0.9269 (mm) cc_final: 0.9014 (mm) REVERT: A 286 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8509 (m) REVERT: B 60 MET cc_start: 0.8685 (mmp) cc_final: 0.8467 (mmt) REVERT: B 453 TYR cc_start: 0.8191 (t80) cc_final: 0.7932 (t80) REVERT: C 228 MET cc_start: 0.7744 (mmm) cc_final: 0.7534 (mmt) REVERT: C 287 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7692 (t80) REVERT: C 354 MET cc_start: 0.7847 (tmm) cc_final: 0.7582 (tmm) REVERT: C 396 HIS cc_start: 0.7801 (m90) cc_final: 0.7199 (m90) REVERT: D 184 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9014 (mm) REVERT: D 321 ASP cc_start: 0.8060 (m-30) cc_final: 0.7746 (t70) REVERT: L 1 MET cc_start: 0.6234 (tpt) cc_final: 0.5855 (tpp) REVERT: L 22 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8549 (mm) REVERT: M 20 LEU cc_start: 0.9083 (mm) cc_final: 0.8880 (mm) REVERT: W 45 ILE cc_start: 0.8993 (mp) cc_final: 0.8790 (mm) REVERT: a 37 MET cc_start: 0.7782 (tmm) cc_final: 0.7575 (tmm) REVERT: a 286 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8566 (m) REVERT: b 63 MET cc_start: 0.8215 (ttm) cc_final: 0.7908 (ttm) REVERT: b 231 MET cc_start: 0.9047 (mpp) cc_final: 0.8635 (mtt) REVERT: b 237 VAL cc_start: 0.8812 (t) cc_final: 0.8520 (t) REVERT: b 330 MET cc_start: 0.7549 (mtp) cc_final: 0.7329 (ttm) REVERT: c 287 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (t80) REVERT: c 396 HIS cc_start: 0.7971 (m90) cc_final: 0.7302 (m90) REVERT: d 321 ASP cc_start: 0.8034 (m-30) cc_final: 0.7695 (t70) REVERT: j 18 LEU cc_start: 0.8745 (pp) cc_final: 0.7727 (mp) REVERT: m 9 LEU cc_start: 0.8758 (mp) cc_final: 0.8554 (mm) REVERT: y 34 LEU cc_start: 0.7224 (mt) cc_final: 0.6945 (mp) REVERT: w 45 ILE cc_start: 0.8988 (mp) cc_final: 0.8786 (mm) REVERT: 14 171 MET cc_start: 0.8089 (mtt) cc_final: 0.7809 (mmm) REVERT: 15 188 MET cc_start: 0.6976 (tpt) cc_final: 0.6533 (tpp) REVERT: 17 166 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8116 (t160) REVERT: 17 171 MET cc_start: 0.7411 (ptt) cc_final: 0.6784 (ptp) REVERT: 18 138 ASP cc_start: 0.7511 (p0) cc_final: 0.7252 (p0) REVERT: 18 178 MET cc_start: 0.6753 (mmm) cc_final: 0.6524 (mmp) REVERT: 35 172 MET cc_start: 0.8262 (mpp) cc_final: 0.7999 (mpp) REVERT: 37 166 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8230 (t160) REVERT: 38 72 MET cc_start: 0.6481 (ttm) cc_final: 0.6046 (ttt) outliers start: 111 outliers final: 60 residues processed: 580 average time/residue: 0.8188 time to fit residues: 850.9787 Evaluate side-chains 528 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 460 time to evaluate : 6.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain V residue 14 ASN Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 283 THR Chi-restraints excluded: chain c residue 287 TYR Chi-restraints excluded: chain d residue 296 ASP Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain j residue 9 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain q residue 186 ASP Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 35 LEU Chi-restraints excluded: chain 11 residue 88 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 76 VAL Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 31 residue 88 ASP Chi-restraints excluded: chain 31 residue 174 ILE Chi-restraints excluded: chain 32 residue 88 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 96 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 32 residue 151 LYS Chi-restraints excluded: chain 36 residue 174 ILE Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 743 optimal weight: 4.9990 chunk 506 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 665 optimal weight: 5.9990 chunk 368 optimal weight: 20.0000 chunk 762 optimal weight: 7.9990 chunk 617 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 456 optimal weight: 10.0000 chunk 801 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN Z 38 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 ASN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 38 ASN q 162 GLN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 191 GLN 14 191 GLN 15 83 ASN ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 96 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 191 GLN 34 191 GLN 36 83 ASN 37 96 ASN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 100716 Z= 0.261 Angle : 0.733 12.499 142118 Z= 0.310 Chirality : 0.044 0.359 13088 Planarity : 0.004 0.065 18582 Dihedral : 18.543 170.834 21214 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 2.08 % Allowed : 10.40 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.59 (0.09), residues: 8276 helix: 0.11 (0.08), residues: 4418 sheet: -1.13 (0.37), residues: 188 loop : -0.86 (0.10), residues: 3670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 61 HIS 0.008 0.002 HIS B 201 PHE 0.029 0.002 PHE15 124 TYR 0.022 0.001 TYR32 141 ARG 0.009 0.000 ARG13 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 461 time to evaluate : 6.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7414 (tmm) cc_final: 0.7146 (tmm) REVERT: B 60 MET cc_start: 0.8753 (mmp) cc_final: 0.8463 (mmt) REVERT: B 453 TYR cc_start: 0.8335 (t80) cc_final: 0.8029 (t80) REVERT: C 287 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7670 (t80) REVERT: C 354 MET cc_start: 0.8080 (tmm) cc_final: 0.7872 (tmm) REVERT: C 396 HIS cc_start: 0.7849 (m90) cc_final: 0.7238 (m90) REVERT: H 35 MET cc_start: 0.8138 (mpp) cc_final: 0.7702 (mpp) REVERT: U 38 MET cc_start: 0.8430 (mpp) cc_final: 0.8208 (mtm) REVERT: W 45 ILE cc_start: 0.9063 (mp) cc_final: 0.8847 (mm) REVERT: b 231 MET cc_start: 0.9173 (mpp) cc_final: 0.8754 (mtt) REVERT: b 237 VAL cc_start: 0.9018 (t) cc_final: 0.8763 (t) REVERT: c 287 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7834 (t80) REVERT: c 396 HIS cc_start: 0.8206 (m90) cc_final: 0.7611 (m90) REVERT: h 50 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7923 (m-40) REVERT: m 9 LEU cc_start: 0.8817 (mp) cc_final: 0.8577 (mm) REVERT: y 34 LEU cc_start: 0.7159 (mt) cc_final: 0.6754 (mp) REVERT: w 45 ILE cc_start: 0.9096 (mp) cc_final: 0.8889 (mm) REVERT: 14 171 MET cc_start: 0.8223 (mtt) cc_final: 0.7921 (mmm) REVERT: 15 178 MET cc_start: 0.8136 (mmt) cc_final: 0.7673 (ptm) REVERT: 15 188 MET cc_start: 0.7168 (tpt) cc_final: 0.6750 (tpp) REVERT: 17 166 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8439 (t160) REVERT: 18 178 MET cc_start: 0.6768 (mmm) cc_final: 0.6521 (mmp) REVERT: 32 95 ASN cc_start: 0.7506 (p0) cc_final: 0.7267 (p0) REVERT: 37 171 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7760 (ptp) REVERT: 38 72 MET cc_start: 0.6498 (ttm) cc_final: 0.6125 (ttt) outliers start: 140 outliers final: 92 residues processed: 552 average time/residue: 0.8095 time to fit residues: 803.4300 Evaluate side-chains 529 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 432 time to evaluate : 6.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 477 ASP Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 211 VAL Chi-restraints excluded: chain c residue 270 LEU Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 283 THR Chi-restraints excluded: chain c residue 287 TYR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 198 MET Chi-restraints excluded: chain d residue 296 ASP Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 50 ASN Chi-restraints excluded: chain j residue 9 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 17 LEU Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain u residue 69 SER Chi-restraints excluded: chain z residue 5 LEU Chi-restraints excluded: chain q residue 146 MET Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 35 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 12 residue 91 LEU Chi-restraints excluded: chain 12 residue 151 LYS Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 91 LEU Chi-restraints excluded: chain 15 residue 120 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 95 ASN Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 76 VAL Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 18 residue 132 MET Chi-restraints excluded: chain 18 residue 138 ASP Chi-restraints excluded: chain 31 residue 88 ASP Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 96 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 32 residue 151 LYS Chi-restraints excluded: chain 33 residue 31 SER Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 171 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 300 optimal weight: 2.9990 chunk 804 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 524 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 894 optimal weight: 20.0000 chunk 742 optimal weight: 9.9990 chunk 413 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 469 optimal weight: 10.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 ASN V 14 ASN Q 162 GLN W 57 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** b 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 83 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 191 GLN 34 191 GLN 35 96 ASN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 100716 Z= 0.323 Angle : 0.769 14.228 142118 Z= 0.329 Chirality : 0.046 0.347 13088 Planarity : 0.005 0.070 18582 Dihedral : 18.148 167.510 21214 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 2.42 % Allowed : 10.99 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.59 (0.09), residues: 8276 helix: 0.07 (0.08), residues: 4426 sheet: -1.29 (0.35), residues: 216 loop : -0.81 (0.10), residues: 3634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP38 131 HIS 0.009 0.002 HIS B 201 PHE 0.031 0.002 PHE b 108 TYR 0.028 0.002 TYR32 141 ARG 0.005 0.001 ARG32 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 446 time to evaluate : 7.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7617 (tmm) cc_final: 0.7308 (tmm) REVERT: B 453 TYR cc_start: 0.8379 (t80) cc_final: 0.7955 (t80) REVERT: C 178 MET cc_start: 0.8568 (mmm) cc_final: 0.8268 (mmm) REVERT: C 287 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7736 (t80) REVERT: D 22 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7478 (tptt) REVERT: H 31 MET cc_start: 0.6765 (mmm) cc_final: 0.6243 (mmm) REVERT: H 50 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: M 9 LEU cc_start: 0.8856 (mm) cc_final: 0.8524 (mt) REVERT: O 140 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6881 (ppp) REVERT: Q 131 ASP cc_start: 0.8392 (p0) cc_final: 0.8100 (p0) REVERT: W 45 ILE cc_start: 0.9027 (mp) cc_final: 0.8788 (mm) REVERT: b 55 MET cc_start: 0.7011 (ptt) cc_final: 0.6745 (ttp) REVERT: b 231 MET cc_start: 0.9202 (mpp) cc_final: 0.8781 (mtt) REVERT: b 237 VAL cc_start: 0.9083 (t) cc_final: 0.8821 (t) REVERT: c 287 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7848 (t80) REVERT: c 396 HIS cc_start: 0.8190 (m90) cc_final: 0.7506 (m90) REVERT: j 18 LEU cc_start: 0.8759 (pp) cc_final: 0.7857 (mp) REVERT: l 22 LEU cc_start: 0.9035 (mm) cc_final: 0.8821 (mm) REVERT: m 21 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8557 (t80) REVERT: v 104 MET cc_start: 0.8333 (pmm) cc_final: 0.8047 (pmm) REVERT: y 34 LEU cc_start: 0.7005 (mt) cc_final: 0.6642 (mp) REVERT: 12 95 ASN cc_start: 0.7779 (p0) cc_final: 0.7319 (p0) REVERT: 12 171 MET cc_start: 0.8094 (mmm) cc_final: 0.7810 (mmm) REVERT: 14 171 MET cc_start: 0.8300 (mtt) cc_final: 0.8060 (mmm) REVERT: 15 178 MET cc_start: 0.8149 (mmt) cc_final: 0.7724 (ptm) REVERT: 15 188 MET cc_start: 0.7272 (tpt) cc_final: 0.6743 (mmt) REVERT: 17 171 MET cc_start: 0.8087 (ptt) cc_final: 0.7877 (ptt) REVERT: 18 178 MET cc_start: 0.6825 (mmm) cc_final: 0.6567 (mmp) REVERT: 32 140 ASP cc_start: 0.7731 (p0) cc_final: 0.7428 (p0) REVERT: 32 171 MET cc_start: 0.8340 (mmm) cc_final: 0.7991 (mmm) REVERT: 37 166 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8575 (t160) REVERT: 37 171 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7687 (ptp) REVERT: 38 72 MET cc_start: 0.6533 (ttm) cc_final: 0.6195 (ttt) REVERT: 38 178 MET cc_start: 0.7537 (mmp) cc_final: 0.7262 (mmp) outliers start: 163 outliers final: 95 residues processed: 554 average time/residue: 0.8186 time to fit residues: 812.7447 Evaluate side-chains 523 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 420 time to evaluate : 6.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain O residue 140 MET Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 14 ASN Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 31 ASP Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 477 ASP Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 270 LEU Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain c residue 287 TYR Chi-restraints excluded: chain d residue 198 MET Chi-restraints excluded: chain d residue 296 ASP Chi-restraints excluded: chain h residue 33 ILE Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 17 LEU Chi-restraints excluded: chain m residue 21 PHE Chi-restraints excluded: chain m residue 36 LYS Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain u residue 69 SER Chi-restraints excluded: chain z residue 5 LEU Chi-restraints excluded: chain q residue 146 MET Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 35 LEU Chi-restraints excluded: chain 11 residue 88 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 11 residue 197 ILE Chi-restraints excluded: chain 12 residue 96 ASN Chi-restraints excluded: chain 12 residue 151 LYS Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 14 residue 33 ILE Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 91 LEU Chi-restraints excluded: chain 15 residue 120 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 95 ASN Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 31 residue 88 ASP Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 31 residue 197 ILE Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 96 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 32 residue 151 LYS Chi-restraints excluded: chain 33 residue 31 SER Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 36 residue 174 ILE Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 38 THR Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Chi-restraints excluded: chain 37 residue 171 MET Chi-restraints excluded: chain 38 residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 861 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 509 optimal weight: 0.9990 chunk 652 optimal weight: 9.9990 chunk 505 optimal weight: 4.9990 chunk 752 optimal weight: 0.9990 chunk 499 optimal weight: 6.9990 chunk 890 optimal weight: 10.0000 chunk 557 optimal weight: 1.9990 chunk 542 optimal weight: 0.7980 chunk 411 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 331 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN 11 83 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31 83 ASN ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31 191 GLN ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 191 GLN 35 96 ASN ** 35 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 38 177 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 100716 Z= 0.157 Angle : 0.665 15.304 142118 Z= 0.281 Chirality : 0.042 0.345 13088 Planarity : 0.004 0.055 18582 Dihedral : 17.446 170.881 21214 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 1.72 % Allowed : 12.00 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.30 (0.09), residues: 8276 helix: 0.34 (0.08), residues: 4480 sheet: -1.31 (0.36), residues: 198 loop : -0.70 (0.11), residues: 3598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 33 HIS 0.013 0.001 HIS c 116 PHE 0.029 0.001 PHE36 123 TYR 0.033 0.001 TYR16 189 ARG 0.006 0.000 ARG32 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 466 time to evaluate : 6.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7331 (tmm) cc_final: 0.7097 (tmm) REVERT: A 139 MET cc_start: 0.7642 (mtp) cc_final: 0.7379 (tpp) REVERT: B 453 TYR cc_start: 0.8306 (t80) cc_final: 0.7853 (t80) REVERT: C 178 MET cc_start: 0.8561 (mmm) cc_final: 0.8356 (mmm) REVERT: C 287 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7715 (t80) REVERT: D 184 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8917 (mm) REVERT: J 18 LEU cc_start: 0.8790 (pp) cc_final: 0.8498 (pt) REVERT: U 38 MET cc_start: 0.8510 (mpp) cc_final: 0.8286 (mtm) REVERT: a 151 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8979 (p) REVERT: b 231 MET cc_start: 0.9100 (mpp) cc_final: 0.8695 (mtt) REVERT: b 237 VAL cc_start: 0.8922 (t) cc_final: 0.8639 (t) REVERT: b 453 TYR cc_start: 0.8166 (t80) cc_final: 0.7949 (t80) REVERT: c 396 HIS cc_start: 0.8128 (m90) cc_final: 0.7466 (m90) REVERT: j 18 LEU cc_start: 0.8821 (pp) cc_final: 0.7935 (mp) REVERT: l 22 LEU cc_start: 0.8994 (mm) cc_final: 0.8708 (mm) REVERT: u 38 MET cc_start: 0.8654 (pmm) cc_final: 0.7956 (pmm) REVERT: v 104 MET cc_start: 0.8466 (pmm) cc_final: 0.7897 (pmm) REVERT: y 1 MET cc_start: 0.6387 (ppp) cc_final: 0.5988 (tmm) REVERT: y 34 LEU cc_start: 0.7043 (mt) cc_final: 0.6640 (mp) REVERT: 11 117 LEU cc_start: 0.9253 (mt) cc_final: 0.9040 (tt) REVERT: 12 95 ASN cc_start: 0.7606 (p0) cc_final: 0.7319 (p0) REVERT: 14 171 MET cc_start: 0.8254 (mtt) cc_final: 0.7972 (mmm) REVERT: 15 120 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8121 (mm) REVERT: 15 188 MET cc_start: 0.7184 (tpt) cc_final: 0.6628 (mmt) REVERT: 17 166 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8411 (t160) REVERT: 17 171 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7529 (ptp) REVERT: 18 72 MET cc_start: 0.6447 (tmm) cc_final: 0.6178 (tmm) REVERT: 18 178 MET cc_start: 0.6827 (mmm) cc_final: 0.6600 (mmp) REVERT: 32 67 HIS cc_start: 0.9214 (OUTLIER) cc_final: 0.7813 (m90) REVERT: 32 171 MET cc_start: 0.8117 (mmm) cc_final: 0.7794 (mmm) REVERT: 37 166 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8448 (t160) REVERT: 38 72 MET cc_start: 0.6560 (ttm) cc_final: 0.6228 (ttt) outliers start: 116 outliers final: 72 residues processed: 539 average time/residue: 0.8087 time to fit residues: 781.6743 Evaluate side-chains 507 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 427 time to evaluate : 6.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain y residue 16 ILE Chi-restraints excluded: chain q residue 146 MET Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 30 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 91 LEU Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 91 LEU Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 120 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 38 THR Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 171 MET Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 18 residue 174 ILE Chi-restraints excluded: chain 31 residue 188 MET Chi-restraints excluded: chain 32 residue 67 HIS Chi-restraints excluded: chain 32 residue 88 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 33 residue 31 SER Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 35 residue 91 LEU Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 38 THR Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Chi-restraints excluded: chain 38 residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 550 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 531 optimal weight: 0.5980 chunk 268 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 566 optimal weight: 0.9990 chunk 606 optimal weight: 2.9990 chunk 440 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 700 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN 11 82 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 196 HIS 13 83 ASN ** 13 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 177 ASN ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 191 GLN 35 96 ASN ** 35 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 35 191 GLN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 100716 Z= 0.159 Angle : 0.649 14.238 142118 Z= 0.274 Chirality : 0.041 0.318 13088 Planarity : 0.004 0.051 18582 Dihedral : 16.901 169.774 21214 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.66 % Allowed : 12.60 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.16 (0.09), residues: 8276 helix: 0.46 (0.08), residues: 4484 sheet: -1.29 (0.36), residues: 200 loop : -0.66 (0.11), residues: 3592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 97 HIS 0.015 0.001 HIS c 116 PHE 0.032 0.001 PHE D 180 TYR 0.021 0.001 TYR33 192 ARG 0.005 0.000 ARG12 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 464 time to evaluate : 6.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.7766 (mtp) cc_final: 0.7517 (tpp) REVERT: A 199 MET cc_start: 0.8190 (ptp) cc_final: 0.7948 (mpp) REVERT: B 330 MET cc_start: 0.8090 (mmm) cc_final: 0.7780 (tpp) REVERT: B 453 TYR cc_start: 0.8303 (t80) cc_final: 0.7827 (t80) REVERT: I 1 MET cc_start: 0.6417 (mpp) cc_final: 0.6215 (mpp) REVERT: J 18 LEU cc_start: 0.8784 (pp) cc_final: 0.8479 (pt) REVERT: U 38 MET cc_start: 0.8443 (mpp) cc_final: 0.8215 (mtm) REVERT: a 151 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8953 (p) REVERT: b 231 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8694 (mtt) REVERT: b 237 VAL cc_start: 0.8895 (t) cc_final: 0.8609 (t) REVERT: b 453 TYR cc_start: 0.8195 (t80) cc_final: 0.7917 (t80) REVERT: c 396 HIS cc_start: 0.8050 (m90) cc_final: 0.7351 (m90) REVERT: j 18 LEU cc_start: 0.8851 (pp) cc_final: 0.7915 (mp) REVERT: l 22 LEU cc_start: 0.8980 (mm) cc_final: 0.8752 (mt) REVERT: m 9 LEU cc_start: 0.8709 (mm) cc_final: 0.8334 (mt) REVERT: o 167 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7684 (p0) REVERT: u 38 MET cc_start: 0.8708 (pmm) cc_final: 0.8015 (pmm) REVERT: v 104 MET cc_start: 0.8508 (pmm) cc_final: 0.8204 (pmm) REVERT: v 137 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6766 (m-10) REVERT: y 34 LEU cc_start: 0.7030 (mt) cc_final: 0.6610 (mp) REVERT: 11 117 LEU cc_start: 0.9269 (mt) cc_final: 0.9044 (tt) REVERT: 12 95 ASN cc_start: 0.7641 (p0) cc_final: 0.7330 (p0) REVERT: 15 178 MET cc_start: 0.8252 (mmt) cc_final: 0.7683 (ptm) REVERT: 15 188 MET cc_start: 0.7155 (tpt) cc_final: 0.6603 (mmt) REVERT: 17 166 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8384 (t160) REVERT: 18 72 MET cc_start: 0.6408 (tmm) cc_final: 0.6079 (tmm) REVERT: 31 145 TYR cc_start: 0.7358 (t80) cc_final: 0.6908 (t80) REVERT: 32 67 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.7873 (m90) REVERT: 32 171 MET cc_start: 0.8224 (mmm) cc_final: 0.7880 (mmm) REVERT: 37 166 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (t160) REVERT: 37 171 MET cc_start: 0.8084 (ptt) cc_final: 0.7543 (ptt) REVERT: 38 72 MET cc_start: 0.6689 (ttm) cc_final: 0.6373 (ttt) REVERT: 38 171 MET cc_start: 0.7722 (tpp) cc_final: 0.7265 (tpp) outliers start: 112 outliers final: 75 residues processed: 536 average time/residue: 0.9164 time to fit residues: 889.9080 Evaluate side-chains 521 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 439 time to evaluate : 6.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain V residue 14 ASN Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 231 MET Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 226 ASN Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 283 THR Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 255 ILE Chi-restraints excluded: chain h residue 33 ILE Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain m residue 17 LEU Chi-restraints excluded: chain o residue 167 ASP Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain v residue 137 TYR Chi-restraints excluded: chain y residue 16 ILE Chi-restraints excluded: chain q residue 146 MET Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 30 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 11 residue 197 ILE Chi-restraints excluded: chain 12 residue 91 LEU Chi-restraints excluded: chain 12 residue 151 LYS Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 120 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 38 THR Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 18 residue 138 ASP Chi-restraints excluded: chain 18 residue 174 ILE Chi-restraints excluded: chain 31 residue 197 ILE Chi-restraints excluded: chain 32 residue 67 HIS Chi-restraints excluded: chain 32 residue 88 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 96 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 38 THR Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Chi-restraints excluded: chain 38 residue 138 ASP Chi-restraints excluded: chain 38 residue 174 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 810 optimal weight: 9.9990 chunk 853 optimal weight: 10.0000 chunk 778 optimal weight: 8.9990 chunk 829 optimal weight: 4.9990 chunk 852 optimal weight: 2.9990 chunk 499 optimal weight: 7.9990 chunk 361 optimal weight: 0.9980 chunk 651 optimal weight: 1.9990 chunk 254 optimal weight: 20.0000 chunk 749 optimal weight: 8.9990 chunk 784 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** b 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 188 HIS d 291 ASN w 57 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 196 HIS ** 13 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 96 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 83 ASN 33 191 GLN ** 34 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 191 GLN 35 96 ASN ** 35 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 35 191 GLN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 100716 Z= 0.287 Angle : 0.734 14.884 142118 Z= 0.314 Chirality : 0.044 0.306 13088 Planarity : 0.004 0.063 18582 Dihedral : 16.914 167.150 21214 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.72 % Allowed : 12.88 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.23 (0.09), residues: 8276 helix: 0.40 (0.08), residues: 4470 sheet: -1.19 (0.35), residues: 216 loop : -0.68 (0.11), residues: 3590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 20 HIS 0.014 0.002 HIS c 116 PHE 0.038 0.002 PHE d 180 TYR 0.039 0.001 TYR34 145 ARG 0.004 0.000 ARG W 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 430 time to evaluate : 6.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8560 (mmm) cc_final: 0.7738 (tpp) REVERT: B 330 MET cc_start: 0.8147 (mmm) cc_final: 0.7893 (tpp) REVERT: B 453 TYR cc_start: 0.8349 (t80) cc_final: 0.7851 (t80) REVERT: D 22 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7419 (tptt) REVERT: U 38 MET cc_start: 0.8494 (mpp) cc_final: 0.8272 (mtm) REVERT: Q 131 ASP cc_start: 0.8464 (p0) cc_final: 0.8191 (p0) REVERT: b 231 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8707 (mtt) REVERT: b 237 VAL cc_start: 0.9064 (t) cc_final: 0.8807 (t) REVERT: b 453 TYR cc_start: 0.8309 (t80) cc_final: 0.8018 (t80) REVERT: c 396 HIS cc_start: 0.8175 (m90) cc_final: 0.7431 (m90) REVERT: l 1 MET cc_start: 0.5945 (tpt) cc_final: 0.5286 (tpt) REVERT: l 22 LEU cc_start: 0.9066 (mm) cc_final: 0.8787 (mm) REVERT: m 9 LEU cc_start: 0.8781 (mm) cc_final: 0.8340 (mt) REVERT: u 38 MET cc_start: 0.8795 (pmm) cc_final: 0.7986 (pmm) REVERT: v 104 MET cc_start: 0.8439 (pmm) cc_final: 0.7992 (pmm) REVERT: v 137 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6834 (m-10) REVERT: y 34 LEU cc_start: 0.7007 (mt) cc_final: 0.6657 (mp) REVERT: 12 95 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7445 (p0) REVERT: 12 171 MET cc_start: 0.7322 (mmm) cc_final: 0.7042 (tpp) REVERT: 14 171 MET cc_start: 0.8260 (mtt) cc_final: 0.7964 (mmm) REVERT: 15 178 MET cc_start: 0.8277 (mmt) cc_final: 0.7717 (ptm) REVERT: 15 188 MET cc_start: 0.7311 (tpt) cc_final: 0.6704 (mmt) REVERT: 17 166 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8489 (t160) REVERT: 17 171 MET cc_start: 0.8049 (ptt) cc_final: 0.7691 (ptt) REVERT: 18 72 MET cc_start: 0.6542 (tmm) cc_final: 0.6079 (tmm) REVERT: 18 178 MET cc_start: 0.7328 (mmp) cc_final: 0.6954 (mmp) REVERT: 32 67 HIS cc_start: 0.9335 (OUTLIER) cc_final: 0.8211 (m90) REVERT: 34 72 MET cc_start: 0.8422 (mmm) cc_final: 0.7884 (tpt) REVERT: 35 171 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7495 (ptt) REVERT: 35 178 MET cc_start: 0.8009 (mmt) cc_final: 0.7414 (mmm) REVERT: 37 166 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8557 (t160) REVERT: 37 171 MET cc_start: 0.8316 (ptt) cc_final: 0.8012 (ptt) REVERT: 38 72 MET cc_start: 0.6775 (ttm) cc_final: 0.6454 (ttt) REVERT: 38 136 LYS cc_start: 0.8698 (ptpp) cc_final: 0.8494 (ptpp) REVERT: 38 171 MET cc_start: 0.7720 (tpp) cc_final: 0.7351 (tpp) outliers start: 116 outliers final: 92 residues processed: 504 average time/residue: 0.8149 time to fit residues: 737.6677 Evaluate side-chains 525 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 425 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 14 ASN Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 321 LEU Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 231 MET Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 226 ASN Chi-restraints excluded: chain c residue 247 ILE Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 280 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 255 ILE Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain m residue 17 LEU Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain v residue 137 TYR Chi-restraints excluded: chain y residue 16 ILE Chi-restraints excluded: chain q residue 146 MET Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 30 ASP Chi-restraints excluded: chain 11 residue 88 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 11 residue 197 ILE Chi-restraints excluded: chain 12 residue 91 LEU Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 151 LYS Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 14 residue 72 MET Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 91 LEU Chi-restraints excluded: chain 15 residue 120 ILE Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 38 THR Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 18 residue 132 MET Chi-restraints excluded: chain 18 residue 138 ASP Chi-restraints excluded: chain 18 residue 174 ILE Chi-restraints excluded: chain 31 residue 188 MET Chi-restraints excluded: chain 31 residue 197 ILE Chi-restraints excluded: chain 32 residue 67 HIS Chi-restraints excluded: chain 32 residue 88 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 96 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 33 residue 31 SER Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 35 residue 91 LEU Chi-restraints excluded: chain 35 residue 171 MET Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 34 GLU Chi-restraints excluded: chain 37 residue 38 THR Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Chi-restraints excluded: chain 38 residue 138 ASP Chi-restraints excluded: chain 38 residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 827 optimal weight: 2.9990 chunk 544 optimal weight: 0.9980 chunk 877 optimal weight: 20.0000 chunk 535 optimal weight: 0.3980 chunk 416 optimal weight: 0.8980 chunk 610 optimal weight: 0.3980 chunk 920 optimal weight: 40.0000 chunk 847 optimal weight: 9.9990 chunk 733 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 566 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** c 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 196 HIS 13 191 GLN 15 96 ASN ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 34 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 191 GLN 35 96 ASN 35 177 ASN 35 191 GLN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 100716 Z= 0.151 Angle : 0.665 15.289 142118 Z= 0.282 Chirality : 0.041 0.294 13088 Planarity : 0.004 0.054 18582 Dihedral : 16.569 169.272 21214 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.28 % Allowed : 13.50 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % 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: -0.08 (0.09), residues: 8276 helix: 0.54 (0.08), residues: 4524 sheet: -1.22 (0.36), residues: 200 loop : -0.66 (0.11), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 33 HIS 0.014 0.001 HIS c 116 PHE 0.045 0.001 PHE d 180 TYR 0.025 0.001 TYR34 145 ARG 0.006 0.000 ARG12 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16552 Ramachandran restraints generated. 8276 Oldfield, 0 Emsley, 8276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 451 time to evaluate : 6.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8423 (mmm) cc_final: 0.7754 (tpp) REVERT: A 199 MET cc_start: 0.8177 (ptp) cc_final: 0.7731 (mpp) REVERT: B 330 MET cc_start: 0.8094 (mmm) cc_final: 0.7824 (tpp) REVERT: D 197 MET cc_start: 0.8290 (ptp) cc_final: 0.7901 (ptp) REVERT: M 17 LEU cc_start: 0.8852 (mm) cc_final: 0.8589 (mt) REVERT: Q 131 ASP cc_start: 0.8405 (p0) cc_final: 0.8091 (p0) REVERT: Q 146 MET cc_start: 0.8338 (mmm) cc_final: 0.8078 (mmm) REVERT: a 151 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8995 (p) REVERT: b 231 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8632 (mtt) REVERT: b 237 VAL cc_start: 0.8913 (t) cc_final: 0.8634 (t) REVERT: b 453 TYR cc_start: 0.8176 (t80) cc_final: 0.7890 (t80) REVERT: c 396 HIS cc_start: 0.7996 (m90) cc_final: 0.7254 (m90) REVERT: j 18 LEU cc_start: 0.8720 (pp) cc_final: 0.7896 (mp) REVERT: l 1 MET cc_start: 0.5791 (tpt) cc_final: 0.5492 (tpt) REVERT: l 22 LEU cc_start: 0.8966 (mm) cc_final: 0.8699 (mt) REVERT: m 9 LEU cc_start: 0.8785 (mm) cc_final: 0.8325 (mt) REVERT: t 1 MET cc_start: 0.7442 (ppp) cc_final: 0.7206 (ppp) REVERT: u 38 MET cc_start: 0.8643 (pmm) cc_final: 0.7904 (pmm) REVERT: v 104 MET cc_start: 0.8500 (pmm) cc_final: 0.8270 (pmm) REVERT: v 137 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6657 (m-10) REVERT: y 34 LEU cc_start: 0.7000 (mt) cc_final: 0.6609 (mp) REVERT: 11 117 LEU cc_start: 0.9257 (mt) cc_final: 0.9042 (tt) REVERT: 12 95 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7345 (p0) REVERT: 15 178 MET cc_start: 0.8230 (mmt) cc_final: 0.7687 (ptm) REVERT: 15 188 MET cc_start: 0.7005 (tpt) cc_final: 0.6457 (mmt) REVERT: 16 188 MET cc_start: 0.7983 (tpp) cc_final: 0.7683 (tpp) REVERT: 17 166 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8304 (t160) REVERT: 17 171 MET cc_start: 0.7875 (ptt) cc_final: 0.7140 (ptp) REVERT: 18 72 MET cc_start: 0.6432 (tmm) cc_final: 0.6022 (tmm) REVERT: 31 145 TYR cc_start: 0.7329 (t80) cc_final: 0.6994 (t80) REVERT: 32 172 MET cc_start: 0.8639 (mmt) cc_final: 0.8369 (mmt) REVERT: 34 72 MET cc_start: 0.8249 (mmm) cc_final: 0.7878 (tpt) REVERT: 34 171 MET cc_start: 0.8377 (mtp) cc_final: 0.8025 (mmm) REVERT: 35 171 MET cc_start: 0.7787 (ptm) cc_final: 0.7329 (ptt) REVERT: 35 178 MET cc_start: 0.7997 (mmt) cc_final: 0.7335 (mmm) REVERT: 36 171 MET cc_start: 0.7760 (mtp) cc_final: 0.7431 (ptp) REVERT: 37 166 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8337 (t160) REVERT: 37 171 MET cc_start: 0.8051 (ptt) cc_final: 0.7710 (ptt) REVERT: 38 72 MET cc_start: 0.6787 (ttm) cc_final: 0.6458 (ttt) REVERT: 38 171 MET cc_start: 0.7690 (tpp) cc_final: 0.7335 (tpp) outliers start: 86 outliers final: 73 residues processed: 508 average time/residue: 0.8203 time to fit residues: 748.4797 Evaluate side-chains 515 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 436 time to evaluate : 6.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 13 TYR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 331 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 231 MET Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 205 ILE Chi-restraints excluded: chain c residue 226 ASN Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain j residue 21 ILE Chi-restraints excluded: chain k residue 13 TYR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 219 VAL Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain v residue 137 TYR Chi-restraints excluded: chain y residue 16 ILE Chi-restraints excluded: chain q residue 146 MET Chi-restraints excluded: chain w residue 30 ASP Chi-restraints excluded: chain 11 residue 88 ASP Chi-restraints excluded: chain 11 residue 120 ILE Chi-restraints excluded: chain 12 residue 91 LEU Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 151 LYS Chi-restraints excluded: chain 13 residue 140 ASP Chi-restraints excluded: chain 13 residue 141 TYR Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 91 LEU Chi-restraints excluded: chain 17 residue 34 GLU Chi-restraints excluded: chain 17 residue 38 THR Chi-restraints excluded: chain 17 residue 72 MET Chi-restraints excluded: chain 17 residue 151 LYS Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 126 LEU Chi-restraints excluded: chain 18 residue 138 ASP Chi-restraints excluded: chain 18 residue 174 ILE Chi-restraints excluded: chain 31 residue 197 ILE Chi-restraints excluded: chain 32 residue 88 ASP Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 96 ASN Chi-restraints excluded: chain 32 residue 148 THR Chi-restraints excluded: chain 33 residue 91 LEU Chi-restraints excluded: chain 35 residue 33 ILE Chi-restraints excluded: chain 36 residue 183 LEU Chi-restraints excluded: chain 37 residue 38 THR Chi-restraints excluded: chain 37 residue 72 MET Chi-restraints excluded: chain 37 residue 151 LYS Chi-restraints excluded: chain 37 residue 160 LEU Chi-restraints excluded: chain 37 residue 166 ASN Chi-restraints excluded: chain 38 residue 126 LEU Chi-restraints excluded: chain 38 residue 138 ASP Chi-restraints excluded: chain 38 residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 449 optimal weight: 0.9980 chunk 582 optimal weight: 7.9990 chunk 780 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 675 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 734 optimal weight: 50.0000 chunk 307 optimal weight: 6.9990 chunk 753 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 317 ASN ** b 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 15 ASN w 57 ASN ** 12 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 96 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 96 ASN ** 31 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 34 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 191 GLN 37 82 ASN ** 37 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 38 96 ASN ** 38 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.049546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.041251 restraints weight = 740639.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.042246 restraints weight = 620995.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.043041 restraints weight = 332218.740| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 100716 Z= 0.411 Angle : 0.870 20.463 142118 Z= 0.373 Chirality : 0.049 0.380 13088 Planarity : 0.005 0.076 18582 Dihedral : 17.097 165.349 21214 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.56 % Allowed : 13.44 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.09), residues: 8276 helix: 0.15 (0.08), residues: 4462 sheet: -1.51 (0.32), residues: 238 loop : -0.80 (0.11), residues: 3576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 440 HIS 0.013 0.002 HIS c 116 PHE 0.048 0.002 PHE d 180 TYR 0.035 0.002 TYR34 145 ARG 0.007 0.001 ARG C 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16182.05 seconds wall clock time: 289 minutes 20.28 seconds (17360.28 seconds total)