Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 10:47:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/04_2023/6j3z_9776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/04_2023/6j3z_9776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/04_2023/6j3z_9776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/04_2023/6j3z_9776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/04_2023/6j3z_9776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/04_2023/6j3z_9776_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 184 5.21 5 S 222 5.16 5 C 51517 2.51 5 N 10435 2.21 5 O 12237 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 74619 Number of models: 1 Model: "" Number of chains: 97 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: "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: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 1420 Unusual residues: {'BCR': 4, 'CLA': 16, 'LHG': 1, 'LMG': 2, 'LMU': 1, 'SQD': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "C" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1189 Unusual residues: {'BCR': 2, 'CLA': 15, 'DGD': 2, 'OEX': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} 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: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'BCR': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 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: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1190 Unusual residues: {'BCR': 4, 'CLA': 13, 'DGD': 2, 'LMG': 1, 'OEX': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} 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: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'BCR': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 753 Unusual residues: {'A86': 6, 'CLA': 9} 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: "14" 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: "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: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 609 Unusual residues: {'A86': 3, 'CLA': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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 Time building chain proxies: 28.30, per 1000 atoms: 0.38 Number of scatterers: 74619 At special positions: 0 Unit cell: (224, 248.64, 129.92, 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 222 16.00 P 8 15.00 Mg 184 11.99 O 12237 8.00 N 10435 7.00 C 51517 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 "HETATM70068 O1 A8615 310 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=166, symmetry=0 Number of additional bonds: simple=166, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.67 Conformation dependent library (CDL) restraints added in 6.3 seconds 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 300 helices and 20 sheets defined 54.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.892A 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: 3.725A pdb=" N GLY A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.739A 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: 3.594A 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: 3.919A 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: 3.605A 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: 3.620A 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: 3.935A 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: 3.975A 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: 3.613A 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: 3.685A 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: 3.529A 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: 3.520A 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: 4.190A 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: 3.593A 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: 3.792A 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: 5.161A 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: 3.534A 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: 3.700A 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: 3.724A 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: 3.588A 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: 3.753A 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: 3.568A 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: 3.546A pdb=" N VAL D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.574A 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: 4.160A pdb=" N GLY F 23 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA F 25 " --> pdb=" O HIS F 22 " (cutoff:3.500A) removed outlier: 5.407A 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: 3.720A 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: 3.591A 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: 3.692A 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: 3.547A pdb=" N ASN M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.576A 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: 3.509A 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: 3.685A 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: 3.511A 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: 3.535A 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: 3.522A 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: 3.502A 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: 4.151A 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: 4.513A pdb=" N ARG Q 154 " --> pdb=" O GLY Q 151 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU Q 156 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 180 removed outlier: 3.582A pdb=" N GLU Q 164 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 3.719A 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: 4.459A 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: 3.663A 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: 3.535A 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: 3.780A pdb=" N HIS W 42 " --> pdb=" O PHE W 39 " (cutoff:3.500A) removed outlier: 4.596A 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: 3.542A pdb=" N ILE W 45 " --> pdb=" O HIS W 42 " (cutoff:3.500A) removed outlier: 4.241A 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 '0' and resid 10 through 24 removed outlier: 3.921A 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: 3.535A pdb=" N UNK 1 21 " --> pdb=" O UNK 1 17 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.832A 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: 3.532A 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: 3.991A 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: 3.580A 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: 3.537A 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: 3.604A 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: 3.824A 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: 3.500A 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: 4.904A 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: 3.644A 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: 3.528A 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: 3.789A pdb=" N ALA c 275 " --> pdb=" O SER c 271 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.688A 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: 3.500A 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: 3.638A 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: 3.764A 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: 3.972A 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: 3.534A pdb=" N MET d 48 " --> pdb=" O GLY d 45 " (cutoff:3.500A) removed outlier: 3.914A 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: 3.700A 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: 3.503A 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: 3.771A 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: 3.627A pdb=" N ILE d 285 " --> pdb=" O SER d 281 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.664A 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: 4.364A 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: 4.161A 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: 3.526A 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: 3.591A 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: 4.752A 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: 3.685A 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: 3.753A 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: 3.632A pdb=" N VAL x 19 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.559A 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: 3.655A 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: 3.870A 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: 3.546A 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: 3.851A 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: 3.502A pdb=" N VAL q 130 " --> pdb=" O ILE q 126 " (cutoff:3.500A) Processing helix chain 'q' and resid 136 through 144 removed outlier: 3.792A pdb=" N ASP q 140 " --> pdb=" O PHE q 136 " (cutoff:3.500A) removed outlier: 4.151A 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: 3.721A 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: 3.988A 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: 3.663A 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: 3.533A 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: 3.655A pdb=" N LEU w 40 " --> pdb=" O VAL w 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS w 42 " --> pdb=" O PHE w 39 " (cutoff:3.500A) removed outlier: 4.597A 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: 3.541A pdb=" N ILE w 45 " --> pdb=" O HIS w 42 " (cutoff:3.500A) removed outlier: 4.240A 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 '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: 3.617A 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: 4.631A 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: 3.781A pdb=" N VAL11 70 " --> pdb=" O HIS11 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET11 72 " --> pdb=" O ARG11 69 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.687A 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: 4.190A 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: 4.368A 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: 4.216A pdb=" N HIS12 67 " --> pdb=" O GLU12 64 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.798A 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: 3.689A 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: 4.190A pdb=" N ASN12 161 " --> pdb=" O ALA12 157 " (cutoff:3.500A) removed outlier: 3.704A 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: 4.215A pdb=" N HIS13 67 " --> pdb=" O GLU13 64 " (cutoff:3.500A) removed outlier: 3.781A 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: 4.099A 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: 4.190A 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: 3.782A 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: 3.687A 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: 3.535A 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: 3.572A pdb=" N ALA15 122 " --> pdb=" O ALA15 118 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE15 123 " --> pdb=" O GLN15 119 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.502A 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: 3.645A 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: 3.810A 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: 3.894A 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: 4.030A pdb=" N LEU16 164 " --> pdb=" O LEU16 160 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA16 169 " --> pdb=" O ASN16 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET16 171 " --> pdb=" O GLY16 167 " (cutoff:3.500A) removed outlier: 4.062A 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: 3.893A 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: 3.562A 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: 3.897A pdb=" N GLU17 58 " --> pdb=" O GLU17 55 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG17 61 " --> pdb=" O GLU17 58 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.794A 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: 4.694A pdb=" N VAL17 76 " --> pdb=" O ALA17 73 " (cutoff:3.500A) removed outlier: 5.033A 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 108 No H-bonds generated for 'chain '17' and resid 106 through 108' Processing helix chain '17' and resid 114 through 129 removed outlier: 3.693A 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: 3.997A 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: 3.658A pdb=" N MET17 171 " --> pdb=" O GLY17 167 " (cutoff:3.500A) removed outlier: 3.836A 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: 3.526A 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: 4.007A 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: 3.693A 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: 3.548A 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: 3.909A pdb=" N UNK20 77 " --> pdb=" O UNK20 73 " (cutoff:3.500A) Processing helix chain '20' and resid 114 through 129 removed outlier: 3.534A pdb=" N UNK20 127 " --> pdb=" O UNK20 123 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNK20 128 " --> pdb=" O UNK20 124 " (cutoff:3.500A) Processing helix chain '20' and resid 156 through 182 removed outlier: 3.835A 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: 3.833A pdb=" N UNK20 175 " --> pdb=" O UNK20 171 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.586A 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: 4.715A 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: 3.728A 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: 3.969A 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: 3.501A 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: 3.703A pdb=" N UNK21 128 " --> pdb=" O UNK21 124 " (cutoff:3.500A) Processing helix chain '21' and resid 153 through 183 removed outlier: 3.601A 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: 3.562A pdb=" N UNK21 172 " --> pdb=" O UNK21 168 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK21 175 " --> pdb=" O UNK21 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: 7.174A 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: 3.517A pdb=" N GLY O 216 " --> pdb=" O PHE O 242 " (cutoff:3.500A) removed outlier: 6.464A 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: 7.660A 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: 6.921A 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: 6.464A 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: 6.832A 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: 7.661A 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 2182 hydrogen bonds defined for protein. 5958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.64 Time building geometry restraints manager: 27.94 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: 76547 1.68 - 2.19: 1175 2.19 - 2.71: 12 2.71 - 3.22: 0 3.22 - 3.73: 8 Bond restraints: 77742 Sorted by residual: 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 1.36e+02 bond pdb=" C4 A8619 311 " pdb=" C5 A8619 311 " ideal model delta sigma weight residual 1.431 1.664 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4 A8620 210 " pdb=" C5 A8620 210 " ideal model delta sigma weight residual 1.431 1.663 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C4 A8617 315 " pdb=" C5 A8617 315 " ideal model delta sigma weight residual 1.431 1.663 -0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 77737 not shown) Histogram of bond angle deviations from ideal: 59.42 - 83.46: 183 83.46 - 107.50: 7517 107.50 - 131.54: 99446 131.54 - 155.58: 1113 155.58 - 179.61: 439 Bond angle restraints: 108698 Sorted by residual: 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 115.66 154.94 -39.28 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 115.66 154.75 -39.09 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C19 A8620 210 " pdb=" C20 A8620 210 " pdb=" O1 A8620 210 " ideal model delta sigma weight residual 115.66 154.74 -39.08 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C19 A8611 310 " pdb=" C20 A8611 310 " pdb=" O1 A8611 310 " ideal model delta sigma weight residual 115.66 154.72 -39.06 3.00e+00 1.11e-01 1.70e+02 ... (remaining 108693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 36676 31.11 - 62.22: 1696 62.22 - 93.34: 285 93.34 - 124.45: 52 124.45 - 155.56: 23 Dihedral angle restraints: 38732 sinusoidal: 17062 harmonic: 21670 Sorted by residual: 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 -134.10 -45.90 0 5.00e+00 4.00e-02 8.43e+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 93.00 167.29 -74.29 1 1.00e+01 1.00e-02 7.00e+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 93.00 167.26 -74.26 1 1.00e+01 1.00e-02 7.00e+01 ... (remaining 38729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 10155 0.336 - 0.672: 57 0.672 - 1.008: 4 1.008 - 1.344: 1 1.344 - 1.679: 59 Chirality restraints: 10276 Sorted by residual: 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 7.05e+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 7.04e+01 chirality pdb=" C20 A8613 311 " pdb=" C15 A8613 311 " pdb=" C19 A8613 311 " pdb=" C21 A8613 311 " both_signs ideal model delta sigma weight residual True 1.08 2.75 -1.67 2.00e-01 2.50e+01 6.99e+01 ... (remaining 10273 not shown) Planarity restraints: 13979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR b 623 " 0.011 2.00e-02 2.50e+03 2.64e-01 6.99e+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 " -0.037 2.00e-02 2.50e+03 2.64e-01 6.95e+02 pdb=" C11 BCR B 624 " 0.272 2.00e-02 2.50e+03 pdb=" C12 BCR B 624 " -0.413 2.00e-02 2.50e+03 pdb=" C13 BCR B 624 " 0.178 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 " -0.034 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 13976 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 27 2.09 - 2.80: 18535 2.80 - 3.50: 92902 3.50 - 4.20: 191889 4.20 - 4.90: 323030 Nonbonded interactions: 626383 Sorted by model distance: nonbonded pdb=" OE2 GLU c 352 " pdb=" O3 OEX c 501 " model vdw 1.392 3.040 nonbonded pdb=" O PHE18 146 " pdb=" O5 A8618 302 " model vdw 1.590 3.040 nonbonded pdb=" O PHE11 146 " pdb=" O5 A8611 316 " model vdw 1.619 3.040 nonbonded pdb=" OE2 GLU C 352 " pdb=" O3 OEX C 501 " model vdw 1.622 3.040 nonbonded pdb=" O PHE13 146 " pdb=" O5 A8613 301 " model vdw 1.632 3.040 ... (remaining 626378 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 30) selection = (chain '1' and resid 2 through 30) selection = (chain '5' and resid 2 through 30) selection = (chain '6' and resid 1 through 29) } 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 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 '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 )))) } 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)) } 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: 11.950 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: 0.070 Extract box with map and model: 29.880 Check model and map are aligned: 0.850 Set scattering table: 0.490 Process input model: 134.270 Find NCS groups from input model: 3.750 Set up NCS constraints: 1.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.019 0.249 77742 Z= 1.039 Angle : 1.821 39.293 108698 Z= 0.722 Chirality : 0.146 1.679 10276 Planarity : 0.014 0.264 13979 Dihedral : 17.987 155.560 24892 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.31 % Favored : 95.67 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.07), residues: 6884 helix: -4.10 (0.04), residues: 3588 sheet: -1.77 (0.33), residues: 236 loop : -2.37 (0.10), residues: 3060 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1801 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1785 time to evaluate : 5.291 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 outliers start: 16 outliers final: 0 residues processed: 1798 average time/residue: 0.8106 time to fit residues: 2472.4709 Evaluate side-chains 919 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 919 time to evaluate : 5.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 5.9990 chunk 559 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 377 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 chunk 578 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 351 optimal weight: 0.3980 chunk 430 optimal weight: 0.9990 chunk 670 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 303 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 330 GLN C 380 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 229 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 50 ASN O 190 ASN U 52 HIS V 118 HIS Y 5 GLN Q 121 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 ASN b 87 ASN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 457 ASN c 325 ASN c 413 ASN c 416 ASN d 60 HIS d 185 GLN d 219 ASN d 229 ASN d 349 ASN ** o 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN o 222 GLN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN 11 83 ASN ** 11 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 161 ASN 11 177 ASN 12 83 ASN 12 161 ASN 12 177 ASN 13 82 ASN 13 83 ASN 13 161 ASN 14 82 ASN 14 161 ASN 15 82 ASN 15 177 ASN 15 196 HIS 16 96 ASN 16 191 GLN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 177 ASN 18 177 ASN 18 196 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 77742 Z= 0.217 Angle : 0.783 17.681 108698 Z= 0.341 Chirality : 0.046 0.566 10276 Planarity : 0.005 0.062 13979 Dihedral : 19.870 177.833 12846 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.51 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -2.94 (0.09), residues: 6884 helix: -2.02 (0.07), residues: 3611 sheet: -1.37 (0.34), residues: 224 loop : -1.73 (0.10), residues: 3049 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1084 time to evaluate : 5.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 85 residues processed: 1175 average time/residue: 0.7495 time to fit residues: 1540.0253 Evaluate side-chains 977 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 892 time to evaluate : 5.188 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.6183 time to fit residues: 107.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 557 optimal weight: 0.9990 chunk 456 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 671 optimal weight: 3.9990 chunk 725 optimal weight: 10.0000 chunk 597 optimal weight: 0.2980 chunk 665 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 538 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** C 416 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** M 4 GLN Y 5 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 311 GLN c 413 ASN ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN w 24 ASN w 57 ASN 11 96 ASN 11 191 GLN 12 177 ASN 13 191 GLN 15 95 ASN 15 177 ASN ** 16 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 177 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 77742 Z= 0.191 Angle : 0.686 14.933 108698 Z= 0.297 Chirality : 0.043 0.322 10276 Planarity : 0.004 0.059 13979 Dihedral : 18.449 169.338 12846 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.34 % Favored : 96.64 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -1.69 (0.09), residues: 6884 helix: -0.85 (0.08), residues: 3605 sheet: -1.01 (0.35), residues: 224 loop : -1.34 (0.11), residues: 3055 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 978 time to evaluate : 5.466 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 outliers start: 101 outliers final: 49 residues processed: 1033 average time/residue: 0.7126 time to fit residues: 1287.6732 Evaluate side-chains 898 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 849 time to evaluate : 5.383 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5857 time to fit residues: 61.8521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 1.9990 chunk 504 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 450 optimal weight: 0.9990 chunk 673 optimal weight: 10.0000 chunk 713 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 638 optimal weight: 0.5980 chunk 192 optimal weight: 0.0570 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** 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** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN V 68 ASN Y 5 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 309 GLN c 413 ASN d 105 GLN d 185 GLN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 335 HIS ** o 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 15 ASN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 82 ASN 13 82 ASN 13 191 GLN ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 177 ASN ** 16 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 77742 Z= 0.255 Angle : 0.693 13.178 108698 Z= 0.303 Chirality : 0.045 0.325 10276 Planarity : 0.004 0.061 13979 Dihedral : 17.802 161.595 12846 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.53 % Favored : 96.46 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -1.04 (0.10), residues: 6884 helix: -0.27 (0.08), residues: 3625 sheet: -0.62 (0.38), residues: 192 loop : -1.11 (0.11), residues: 3067 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 913 time to evaluate : 5.329 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 outliers start: 134 outliers final: 70 residues processed: 982 average time/residue: 0.7236 time to fit residues: 1251.2978 Evaluate side-chains 907 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 837 time to evaluate : 5.206 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.5725 time to fit residues: 83.8670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 4.9990 chunk 404 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 531 optimal weight: 10.0000 chunk 294 optimal weight: 0.9980 chunk 608 optimal weight: 1.9990 chunk 493 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 640 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 291 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN O 189 ASN Y 5 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 335 HIS ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 189 ASN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN 11 177 ASN 11 186 GLN 13 191 GLN 13 196 HIS ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 177 ASN ** 16 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 82 ASN 17 83 ASN ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 77742 Z= 0.212 Angle : 0.651 11.341 108698 Z= 0.286 Chirality : 0.043 0.298 10276 Planarity : 0.004 0.060 13979 Dihedral : 17.392 162.564 12846 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.27 % Favored : 96.72 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.70 (0.10), residues: 6884 helix: 0.03 (0.08), residues: 3633 sheet: -0.55 (0.37), residues: 196 loop : -0.96 (0.11), residues: 3055 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 910 time to evaluate : 5.297 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 outliers start: 95 outliers final: 47 residues processed: 969 average time/residue: 0.7087 time to fit residues: 1200.9938 Evaluate side-chains 866 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 819 time to evaluate : 5.245 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5731 time to fit residues: 58.0956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 3.9990 chunk 642 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 418 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 714 optimal weight: 9.9990 chunk 592 optimal weight: 0.0870 chunk 330 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 374 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 416 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** L 7 ASN ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 335 HIS ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 189 ASN u 52 HIS z 38 ASN q 162 GLN 11 177 ASN 13 196 HIS ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 177 ASN ** 16 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 177 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 77742 Z= 0.177 Angle : 0.630 10.636 108698 Z= 0.277 Chirality : 0.042 0.283 10276 Planarity : 0.004 0.058 13979 Dihedral : 16.989 162.252 12846 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.45 (0.10), residues: 6884 helix: 0.27 (0.09), residues: 3627 sheet: -0.51 (0.36), residues: 204 loop : -0.89 (0.11), residues: 3053 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 885 time to evaluate : 5.404 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 outliers start: 76 outliers final: 40 residues processed: 922 average time/residue: 0.7033 time to fit residues: 1136.0916 Evaluate side-chains 866 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 826 time to evaluate : 5.213 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5673 time to fit residues: 49.9613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 406 optimal weight: 0.0030 chunk 521 optimal weight: 0.7980 chunk 404 optimal weight: 5.9990 chunk 601 optimal weight: 3.9990 chunk 398 optimal weight: 3.9990 chunk 711 optimal weight: 10.0000 chunk 445 optimal weight: 0.0980 chunk 433 optimal weight: 0.7980 chunk 328 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Y 5 GLN ** Q 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 189 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 196 HIS 14 196 HIS ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 177 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** ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 177 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 77742 Z= 0.160 Angle : 0.622 13.770 108698 Z= 0.273 Chirality : 0.042 0.299 10276 Planarity : 0.004 0.058 13979 Dihedral : 16.639 160.871 12846 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.22 (0.10), residues: 6884 helix: 0.49 (0.09), residues: 3597 sheet: -0.47 (0.36), residues: 206 loop : -0.80 (0.11), residues: 3081 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 881 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 909 average time/residue: 0.7193 time to fit residues: 1147.9661 Evaluate side-chains 841 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 812 time to evaluate : 5.324 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.6209 time to fit residues: 39.6574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 4.9990 chunk 284 optimal weight: 0.0670 chunk 424 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 452 optimal weight: 0.7980 chunk 484 optimal weight: 0.4980 chunk 351 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 559 optimal weight: 0.0040 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 416 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Y 5 GLN a 261 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 189 ASN q 162 GLN ** 11 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 196 HIS 15 82 ASN ** 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** ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 77742 Z= 0.157 Angle : 0.617 14.520 108698 Z= 0.271 Chirality : 0.041 0.290 10276 Planarity : 0.004 0.057 13979 Dihedral : 16.336 158.518 12846 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.09 (0.10), residues: 6884 helix: 0.60 (0.09), residues: 3611 sheet: -0.40 (0.39), residues: 184 loop : -0.77 (0.11), residues: 3089 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 874 time to evaluate : 5.238 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 outliers start: 39 outliers final: 20 residues processed: 891 average time/residue: 0.7107 time to fit residues: 1115.0242 Evaluate side-chains 833 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 813 time to evaluate : 5.425 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.6056 time to fit residues: 30.0487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 0.3980 chunk 681 optimal weight: 1.9990 chunk 621 optimal weight: 0.9990 chunk 662 optimal weight: 0.0030 chunk 398 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 520 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 598 optimal weight: 4.9990 chunk 626 optimal weight: 4.9990 chunk 660 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Y 5 GLN a 261 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 349 ASN h 50 ASN ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 95 ASN 13 196 HIS ** 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** ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 77742 Z= 0.174 Angle : 0.630 16.654 108698 Z= 0.278 Chirality : 0.042 0.296 10276 Planarity : 0.004 0.057 13979 Dihedral : 16.199 155.903 12846 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 6884 helix: 0.61 (0.09), residues: 3616 sheet: -0.38 (0.38), residues: 184 loop : -0.76 (0.11), residues: 3084 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 840 time to evaluate : 5.262 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 outliers start: 27 outliers final: 12 residues processed: 851 average time/residue: 0.7171 time to fit residues: 1074.5492 Evaluate side-chains 828 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 816 time to evaluate : 5.287 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5672 time to fit residues: 19.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.7980 chunk 700 optimal weight: 6.9990 chunk 427 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 487 optimal weight: 7.9990 chunk 735 optimal weight: 20.0000 chunk 676 optimal weight: 3.9990 chunk 585 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 358 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 GLN ** 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** L 7 ASN Y 5 GLN a 261 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN ** 11 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 196 HIS 13 196 HIS 14 96 ASN ** 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** ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 77742 Z= 0.218 Angle : 0.661 18.630 108698 Z= 0.293 Chirality : 0.043 0.300 10276 Planarity : 0.004 0.057 13979 Dihedral : 16.170 153.681 12846 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % 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: -0.09 (0.10), residues: 6884 helix: 0.60 (0.09), residues: 3618 sheet: -0.42 (0.38), residues: 184 loop : -0.77 (0.11), residues: 3082 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 835 time to evaluate : 5.359 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 outliers start: 18 outliers final: 9 residues processed: 842 average time/residue: 0.7153 time to fit residues: 1059.3816 Evaluate side-chains 816 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 807 time to evaluate : 5.231 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5950 time to fit residues: 16.5937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 1.9990 chunk 623 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 539 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 586 optimal weight: 0.0470 chunk 245 optimal weight: 0.9990 chunk 602 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Y 5 GLN ** Q 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 261 GLN ** b 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 72 HIS c 413 ASN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN ** 11 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 95 ASN 12 196 HIS 14 96 ASN ** 15 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 161 ASN ** 17 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076420 restraints weight = 206235.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078844 restraints weight = 179227.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078428 restraints weight = 107870.422| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 77742 Z= 0.206 Angle : 0.655 21.307 108698 Z= 0.290 Chirality : 0.043 0.299 10276 Planarity : 0.004 0.056 13979 Dihedral : 16.065 153.272 12846 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.10), residues: 6884 helix: 0.65 (0.09), residues: 3616 sheet: -0.54 (0.37), residues: 190 loop : -0.75 (0.11), residues: 3078 =============================================================================== Job complete usr+sys time: 18254.37 seconds wall clock time: 321 minutes 33.77 seconds (19293.77 seconds total)