Starting phenix.real_space_refine (version: dev) on Mon Feb 27 23:00:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/02_2023/6j3y_9775_updated.pdb" } resolution = 3.3 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= 0.001 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 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 70136 Number of models: 1 Model: "" Number of chains: 90 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: "31" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "32" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "33" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "34" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "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: 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: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1150 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 2, 'LMG': 1, 'OEX': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 485 Unusual residues: {'CLA': 4, 'LMG': 1, 'PHO': 1, 'PL9': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'LHG': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 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: 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: "W" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 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: 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: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1099 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 2, 'OEX': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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: 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: 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: "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: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 841 Unusual residues: {'A86': 5, 'CLA': 10, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 866 Unusual residues: {'A86': 7, 'CLA': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "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: "31" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 818 Unusual residues: {'A86': 6, 'CLA': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "32" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 889 Unusual residues: {'A86': 6, 'CLA': 10, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "33" Number of atoms: 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: "34" 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 Time building chain proxies: 29.81, per 1000 atoms: 0.43 Number of scatterers: 70136 At special positions: 0 Unit cell: (216.16, 287.84, 124.32, 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 158 11.99 O 11528 8.00 N 9818 7.00 C 48386 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 Number of custom bonds: simple=148, symmetry=0 Number of additional bonds: simple=148, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.81 Conformation dependent library (CDL) restraints added in 6.9 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: 12808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 290 helices and 20 sheets defined 51.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.893A pdb=" N TRP A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 Proline residue: A 39 - end of helix removed outlier: 3.831A pdb=" N ILE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 removed outlier: 3.741A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.738A pdb=" N GLY A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.533A 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: 4.220A 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: 3.579A 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: 3.712A 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: 3.975A 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: 3.503A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.612A 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: 3.684A pdb=" N LEU C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER C 120 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.741A 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: 4.051A 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: 3.946A pdb=" N LEU C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 211 removed outlier: 4.096A 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: 3.510A pdb=" N ARG C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.505A 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: 3.505A pdb=" N SER C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 304 through 320 removed outlier: 3.688A 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: 3.793A pdb=" N PHE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 32 through 52 removed outlier: 3.638A pdb=" N LEU D 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 5.161A 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: 3.972A 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: 3.913A 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: 3.754A pdb=" N GLY D 202 " --> pdb=" O MET D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.772A pdb=" N GLN D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 289 removed outlier: 3.578A 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: 3.697A 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: 3.545A pdb=" N VAL D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.573A pdb=" N ARG D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 327 removed outlier: 3.664A 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: 3.509A 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: 3.976A 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: 4.164A 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: 3.526A 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: 3.692A 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: 3.574A pdb=" N PHE M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 8 No H-bonds generated for 'chain 'O' and resid 5 through 8' Processing helix chain 'O' and resid 11 through 14 No H-bonds generated for 'chain 'O' and resid 11 through 14' Processing helix chain 'O' and resid 183 through 188 removed outlier: 3.510A pdb=" N PHE O 186 " --> pdb=" O ALA O 183 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY O 187 " --> pdb=" O GLU O 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 22 removed outlier: 3.700A 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: 3.752A 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: 3.582A 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: 3.525A 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: 3.654A pdb=" N THR Z 19 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) Proline residue: Z 21 - end of helix Processing helix chain 'Z' and resid 29 through 32 No H-bonds generated for 'chain 'Z' and resid 29 through 32' Processing helix chain 'Z' and resid 35 through 57 removed outlier: 3.756A 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: 3.503A pdb=" N VAL Q 130 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 144 removed outlier: 3.794A 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: 4.539A pdb=" N THR Q 143 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 156 removed outlier: 4.201A 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: 3.722A pdb=" N LEU Q 156 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 180 removed outlier: 3.581A 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: 3.534A pdb=" N ALA W 36 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE W 39 " --> pdb=" O ALA W 36 " (cutoff:3.500A) removed outlier: 3.655A 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: 3.553A 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: 3.641A pdb=" N LEU W 50 " --> pdb=" O SER W 47 " (cutoff:3.500A) Processing helix chain '0' and resid 10 through 24 removed outlier: 3.921A 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: 3.534A 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: 3.724A 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: 3.533A 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: 4.219A pdb=" N ALA a 276 " --> pdb=" O HIS a 272 " (cutoff:3.500A) Proline residue: a 279 - end of helix removed outlier: 3.917A pdb=" N THR a 292 " --> pdb=" O MET a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 329 Processing helix chain 'b' and resid 5 through 10 removed outlier: 3.990A pdb=" N VAL b 8 " --> pdb=" O TRP b 5 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS b 9 " --> pdb=" O TYR b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 44 removed outlier: 3.580A 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: 3.529A 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: 3.718A 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: 3.644A pdb=" N SER b 240 " --> pdb=" O THR b 236 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER b 243 " --> pdb=" O SER b 239 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE b 247 " --> pdb=" O SER b 243 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA b 248 " --> pdb=" O ALA b 244 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 251 " --> pdb=" O PHE b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 273 through 276 No H-bonds generated for 'chain 'b' and resid 273 through 276' Processing helix chain 'b' and resid 281 through 293 removed outlier: 3.935A pdb=" N SER b 291 " --> pdb=" O GLN b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 304 removed outlier: 3.712A pdb=" N ARG b 304 " --> pdb=" O GLN b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 312 Processing helix chain 'b' and resid 315 through 317 No H-bonds generated for 'chain 'b' and resid 315 through 317' Processing helix chain 'b' and resid 319 through 321 No H-bonds generated for 'chain 'b' and resid 319 through 321' Processing helix chain 'b' and resid 330 through 334 removed outlier: 3.976A pdb=" N ASP b 334 " --> pdb=" O ASN b 331 " (cutoff:3.500A) Processing helix chain 'b' and resid 392 through 395 No H-bonds generated for 'chain 'b' and resid 392 through 395' Processing helix chain 'b' and resid 404 through 406 No H-bonds generated for 'chain 'b' and resid 404 through 406' Processing helix chain 'b' and resid 414 through 422 removed outlier: 3.757A pdb=" N LYS b 419 " --> pdb=" O PRO b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 447 through 474 removed outlier: 3.821A pdb=" N ALA b 459 " --> pdb=" O HIS b 455 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU b 460 " --> pdb=" O ALA b 456 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE b 464 " --> pdb=" O LEU b 460 " (cutoff:3.500A) Processing helix chain 'b' and resid 476 through 478 No H-bonds generated for 'chain 'b' and resid 476 through 478' Processing helix chain 'c' and resid 37 through 40 Processing helix chain 'c' and resid 45 through 71 removed outlier: 3.503A pdb=" N VAL c 66 " --> pdb=" O ALA c 62 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 93 removed outlier: 3.612A pdb=" N ALA c 91 " --> pdb=" O ILE c 87 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR c 92 " --> pdb=" O GLN c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 129 removed outlier: 3.683A pdb=" N LEU c 117 " --> pdb=" O GLY c 113 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER c 120 " --> pdb=" O HIS c 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA c 121 " --> pdb=" O LEU c 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE c 122 " --> pdb=" O ILE c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 138 through 141 No H-bonds generated for 'chain 'c' and resid 138 through 141' Processing helix chain 'c' and resid 153 through 178 removed outlier: 3.529A pdb=" N LEU c 165 " --> pdb=" O ILE c 161 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER c 170 " --> pdb=" O LEU c 166 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU c 173 " --> pdb=" O GLY c 169 " (cutoff:3.500A) removed outlier: 3.607A 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: 3.846A 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: 3.505A pdb=" N ALA c 261 " --> pdb=" O TRP c 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 256 through 261' Processing helix chain 'c' and resid 266 through 290 removed outlier: 3.751A pdb=" N LEU c 270 " --> pdb=" O GLY c 266 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA c 275 " --> pdb=" O SER c 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER c 278 " --> pdb=" O LEU c 274 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP c 289 " --> pdb=" O ALA c 285 " (cutoff:3.500A) Processing helix chain 'c' and resid 297 through 300 No H-bonds generated for 'chain 'c' and resid 297 through 300' Processing helix chain 'c' and resid 304 through 320 removed outlier: 3.688A 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: 3.870A 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: 3.594A 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: 3.652A pdb=" N LEU c 436 " --> pdb=" O ALA c 432 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 21 Processing helix chain 'd' and resid 32 through 52 removed outlier: 3.638A pdb=" N LEU d 36 " --> pdb=" O GLY d 33 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE d 37 " --> pdb=" O LEU d 34 " (cutoff:3.500A) Proline residue: d 38 - end of helix removed outlier: 3.764A pdb=" N TYR d 41 " --> pdb=" O PRO d 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU d 42 " --> pdb=" O THR d 39 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA d 44 " --> pdb=" O TYR d 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY d 45 " --> pdb=" O LEU d 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY d 46 " --> pdb=" O ALA d 43 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.655A 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: 3.520A 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: 3.545A pdb=" N VAL d 286 " --> pdb=" O SER d 282 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 306 removed outlier: 3.573A pdb=" N ARG d 303 " --> pdb=" O SER d 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 327 removed outlier: 3.664A 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: 4.280A 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: 3.976A 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: 4.164A 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: 3.604A pdb=" N TYR l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR l 35 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 37 Proline residue: m 18 - end of helix removed outlier: 3.547A pdb=" N ASN m 24 " --> pdb=" O LEU m 20 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE m 26 " --> pdb=" O LEU m 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 8 No H-bonds generated for 'chain 'o' and resid 5 through 8' Processing helix chain 'o' and resid 11 through 14 No H-bonds generated for 'chain 'o' and resid 11 through 14' Processing helix chain 'o' and resid 183 through 188 removed outlier: 3.510A pdb=" N PHE o 186 " --> pdb=" O ALA o 183 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY o 187 " --> pdb=" O GLU o 184 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 22 removed outlier: 3.700A 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: 3.752A 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: 3.503A 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: 3.632A pdb=" N VAL x 19 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE x 22 " --> pdb=" O VAL x 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER x 32 " --> pdb=" O VAL x 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 25 removed outlier: 3.688A 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: 3.654A pdb=" N THR z 19 " --> pdb=" O GLY z 15 " (cutoff:3.500A) Proline residue: z 21 - end of helix Processing helix chain 'z' and resid 29 through 32 No H-bonds generated for 'chain 'z' and resid 29 through 32' Processing helix chain 'z' and resid 35 through 57 removed outlier: 3.756A pdb=" N ARG z 39 " --> pdb=" O GLY z 35 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE z 40 " --> pdb=" O LYS z 36 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.670A pdb=" N LEU q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS q 120 " --> pdb=" O LEU q 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN q 121 " --> pdb=" O ALA q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 126 through 131 removed outlier: 3.503A pdb=" N VAL q 130 " --> pdb=" O ILE q 126 " (cutoff:3.500A) Processing helix chain 'q' and resid 136 through 144 removed outlier: 3.792A 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: 4.201A 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: 4.512A 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: 3.989A 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: 3.533A pdb=" N ALA w 36 " --> pdb=" O ARG w 33 " (cutoff:3.500A) removed outlier: 4.183A 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: 3.779A 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: 4.242A pdb=" N SER w 47 " --> pdb=" O ALA w 44 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU w 50 " --> pdb=" O SER w 47 " (cutoff:3.500A) Processing helix chain '5' and resid 10 through 24 removed outlier: 3.946A pdb=" N UNK 5 15 " --> pdb=" O UNK 5 11 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK 5 16 " --> pdb=" O UNK 5 12 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 27 removed outlier: 3.722A pdb=" N UNK 6 11 " --> pdb=" O UNK 6 7 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK 6 12 " --> pdb=" O UNK 6 8 " (cutoff:3.500A) removed outlier: 3.507A 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: 4.297A pdb=" N VAL11 80 " --> pdb=" O GLY11 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS11 81 " --> pdb=" O THR11 78 " (cutoff:3.500A) Processing helix chain '11' and resid 106 through 111 removed outlier: 4.098A pdb=" N ILE11 109 " --> pdb=" O VAL11 106 " (cutoff:3.500A) removed outlier: 3.807A 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: 3.703A 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: 4.629A pdb=" N ARG12 65 " --> pdb=" O ALA12 62 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS12 67 " --> pdb=" O GLU12 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL12 70 " --> pdb=" O HIS12 67 " (cutoff:3.500A) removed outlier: 3.840A 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: 4.588A 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: 3.703A 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: 4.368A pdb=" N ARG13 61 " --> pdb=" O GLU13 58 " (cutoff:3.500A) removed outlier: 4.630A 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: 4.588A pdb=" N VAL13 76 " --> pdb=" O ALA13 73 " (cutoff:3.500A) removed outlier: 4.296A 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: 3.807A 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: 4.214A 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: 3.841A pdb=" N MET14 72 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL14 75 " --> pdb=" O MET14 72 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL14 76 " --> pdb=" O ALA14 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL14 80 " --> pdb=" O GLY14 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS14 81 " --> pdb=" O THR14 78 " (cutoff:3.500A) Processing helix chain '14' and resid 106 through 111 removed outlier: 4.099A pdb=" N ILE14 109 " --> pdb=" O VAL14 106 " (cutoff:3.500A) removed outlier: 3.806A 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: 4.190A pdb=" N ASN14 161 " --> pdb=" O ALA14 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA14 180 " --> pdb=" O GLY14 176 " (cutoff:3.500A) Processing helix chain '14' and resid 188 through 194 Processing helix chain '31' and resid 33 through 35 No H-bonds generated for 'chain '31' and resid 33 through 35' Processing helix chain '31' and resid 49 through 52 No H-bonds generated for 'chain '31' and resid 49 through 52' Processing helix chain '31' and resid 56 through 82 removed outlier: 4.367A pdb=" N ARG31 61 " --> pdb=" O GLU31 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG31 65 " --> pdb=" O ALA31 62 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS31 67 " --> pdb=" O GLU31 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL31 70 " --> pdb=" O HIS31 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET31 72 " --> pdb=" O ARG31 69 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL31 75 " --> pdb=" O MET31 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL31 76 " --> pdb=" O ALA31 73 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL31 80 " --> pdb=" O GLY31 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS31 81 " --> pdb=" O THR31 78 " (cutoff:3.500A) Processing helix chain '31' and resid 106 through 111 removed outlier: 4.099A pdb=" N ILE31 109 " --> pdb=" O VAL31 106 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG31 110 " --> pdb=" O ASP31 107 " (cutoff:3.500A) Processing helix chain '31' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU31 126 " --> pdb=" O ALA31 122 " (cutoff:3.500A) Processing helix chain '31' and resid 145 through 147 No H-bonds generated for 'chain '31' and resid 145 through 147' Processing helix chain '31' and resid 153 through 180 removed outlier: 4.190A pdb=" N ASN31 161 " --> pdb=" O ALA31 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA31 180 " --> pdb=" O GLY31 176 " (cutoff:3.500A) Processing helix chain '31' and resid 188 through 194 Processing helix chain '32' and resid 33 through 35 No H-bonds generated for 'chain '32' and resid 33 through 35' Processing helix chain '32' and resid 49 through 52 No H-bonds generated for 'chain '32' and resid 49 through 52' Processing helix chain '32' and resid 56 through 82 removed outlier: 4.368A pdb=" N ARG32 61 " --> pdb=" O GLU32 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG32 65 " --> pdb=" O ALA32 62 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS32 67 " --> pdb=" O GLU32 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL32 70 " --> pdb=" O HIS32 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET32 72 " --> pdb=" O ARG32 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL32 75 " --> pdb=" O MET32 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL32 76 " --> pdb=" O ALA32 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL32 80 " --> pdb=" O GLY32 77 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS32 81 " --> pdb=" O THR32 78 " (cutoff:3.500A) Processing helix chain '32' and resid 106 through 111 removed outlier: 4.099A pdb=" N ILE32 109 " --> pdb=" O VAL32 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG32 110 " --> pdb=" O ASP32 107 " (cutoff:3.500A) Processing helix chain '32' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU32 126 " --> pdb=" O ALA32 122 " (cutoff:3.500A) Processing helix chain '32' and resid 145 through 147 No H-bonds generated for 'chain '32' and resid 145 through 147' Processing helix chain '32' and resid 153 through 180 removed outlier: 4.189A pdb=" N ASN32 161 " --> pdb=" O ALA32 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA32 180 " --> pdb=" O GLY32 176 " (cutoff:3.500A) Processing helix chain '32' and resid 188 through 194 Processing helix chain '33' and resid 33 through 35 No H-bonds generated for 'chain '33' and resid 33 through 35' Processing helix chain '33' and resid 49 through 52 No H-bonds generated for 'chain '33' and resid 49 through 52' Processing helix chain '33' and resid 56 through 82 removed outlier: 4.368A pdb=" N ARG33 61 " --> pdb=" O GLU33 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG33 65 " --> pdb=" O ALA33 62 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS33 67 " --> pdb=" O GLU33 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL33 70 " --> pdb=" O HIS33 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET33 72 " --> pdb=" O ARG33 69 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL33 75 " --> pdb=" O MET33 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL33 76 " --> pdb=" O ALA33 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL33 80 " --> pdb=" O GLY33 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS33 81 " --> pdb=" O THR33 78 " (cutoff:3.500A) Processing helix chain '33' and resid 106 through 111 removed outlier: 4.099A pdb=" N ILE33 109 " --> pdb=" O VAL33 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG33 110 " --> pdb=" O ASP33 107 " (cutoff:3.500A) Processing helix chain '33' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU33 126 " --> pdb=" O ALA33 122 " (cutoff:3.500A) Processing helix chain '33' and resid 145 through 147 No H-bonds generated for 'chain '33' and resid 145 through 147' Processing helix chain '33' and resid 153 through 180 removed outlier: 4.189A pdb=" N ASN33 161 " --> pdb=" O ALA33 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA33 180 " --> pdb=" O GLY33 176 " (cutoff:3.500A) Processing helix chain '33' and resid 188 through 194 Processing helix chain '34' and resid 33 through 35 No H-bonds generated for 'chain '34' and resid 33 through 35' Processing helix chain '34' and resid 49 through 52 No H-bonds generated for 'chain '34' and resid 49 through 52' Processing helix chain '34' and resid 56 through 82 removed outlier: 4.368A pdb=" N ARG34 61 " --> pdb=" O GLU34 58 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG34 65 " --> pdb=" O ALA34 62 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS34 67 " --> pdb=" O GLU34 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL34 70 " --> pdb=" O HIS34 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET34 72 " --> pdb=" O ARG34 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL34 75 " --> pdb=" O MET34 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL34 76 " --> pdb=" O ALA34 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL34 80 " --> pdb=" O GLY34 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS34 81 " --> pdb=" O THR34 78 " (cutoff:3.500A) Processing helix chain '34' and resid 106 through 111 removed outlier: 4.100A pdb=" N ILE34 109 " --> pdb=" O VAL34 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG34 110 " --> pdb=" O ASP34 107 " (cutoff:3.500A) Processing helix chain '34' and resid 114 through 129 removed outlier: 3.723A pdb=" N LEU34 126 " --> pdb=" O ALA34 122 " (cutoff:3.500A) Processing helix chain '34' and resid 145 through 147 No H-bonds generated for 'chain '34' and resid 145 through 147' Processing helix chain '34' and resid 153 through 180 removed outlier: 4.190A pdb=" N ASN34 161 " --> pdb=" O ALA34 157 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA34 180 " --> pdb=" O GLY34 176 " (cutoff:3.500A) Processing helix chain '34' and resid 188 through 194 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: 4.777A pdb=" N TRP O 50 " --> pdb=" O LEU O 237 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU O 237 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.803A 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: 6.425A 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: 4.862A pdb=" N ILE O 200 " --> pdb=" O THR O 221 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU O 223 " --> pdb=" O GLY O 198 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY O 198 " --> pdb=" O LEU O 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 92 through 96 Processing sheet with id= I, first strand: chain 'O' and resid 103 through 109 Processing sheet with id= J, first strand: chain 'V' and resid 9 through 11 Processing sheet with id= K, first strand: chain 'b' and resid 166 through 169 Processing sheet with id= L, first strand: chain 'b' and resid 345 through 347 Processing sheet with id= M, first strand: chain 'b' and resid 336 through 340 removed outlier: 6.809A pdb=" N GLU b 431 " --> pdb=" O GLU b 338 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'b' and resid 369 through 371 Processing sheet with id= O, first strand: chain 'c' and resid 183 through 185 Processing sheet with id= P, first strand: chain 'c' and resid 339 through 341 Processing sheet with id= Q, first strand: chain 'o' and resid 64 through 68 removed outlier: 6.793A pdb=" N LYS o 239 " --> pdb=" O LYS o 48 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP o 50 " --> pdb=" O LEU o 237 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU o 237 " --> pdb=" O TRP o 50 " (cutoff:3.500A) removed outlier: 4.803A 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: 3.759A 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: 6.424A pdb=" N VAL o 219 " --> pdb=" O MET o 202 " (cutoff:3.500A) removed outlier: 4.977A 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: 7.661A 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 2076 hydrogen bonds defined for protein. 5532 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: 20.47 Time building geometry restraints manager: 25.08 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: 71942 1.68 - 2.19: 1070 2.19 - 2.71: 12 2.71 - 3.22: 0 3.22 - 3.73: 8 Bond restraints: 73032 Sorted by residual: bond pdb=" C4 A8632 304 " pdb=" C5 A8632 304 " ideal model delta sigma weight residual 1.431 1.663 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C4 A8633 302 " pdb=" C5 A8633 302 " ideal model delta sigma weight residual 1.431 1.662 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C4 A8611 316 " pdb=" C5 A8611 316 " ideal model delta sigma weight residual 1.431 1.662 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C4 A8613 317 " pdb=" C5 A8613 317 " ideal model delta sigma weight residual 1.431 1.662 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C4 A8612 304 " pdb=" C5 A8612 304 " ideal model delta sigma weight residual 1.431 1.662 -0.231 2.00e-02 2.50e+03 1.33e+02 ... (remaining 73027 not shown) Histogram of bond angle deviations from ideal: 59.40 - 83.44: 150 83.44 - 107.47: 6932 107.47 - 131.50: 93226 131.50 - 155.54: 1018 155.54 - 179.57: 376 Bond angle restraints: 101702 Sorted by residual: angle pdb=" C19 A8633 312 " pdb=" C20 A8633 312 " pdb=" O1 A8633 312 " ideal model delta sigma weight residual 115.66 154.72 -39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C19 A8634 313 " pdb=" C20 A8634 313 " pdb=" O1 A8634 313 " ideal model delta sigma weight residual 115.66 154.72 -39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C19 A8612 314 " pdb=" C20 A8612 314 " pdb=" O1 A8612 314 " ideal model delta sigma weight residual 115.66 154.72 -39.06 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C19 A8614 312 " pdb=" C20 A8614 312 " pdb=" O1 A8614 312 " ideal model delta sigma weight residual 115.66 154.71 -39.05 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C19 A8613 312 " pdb=" C20 A8613 312 " pdb=" O1 A8613 312 " ideal model delta sigma weight residual 115.66 154.70 -39.04 3.00e+00 1.11e-01 1.69e+02 ... (remaining 101697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.57: 34945 30.57 - 61.14: 1649 61.14 - 91.71: 252 91.71 - 122.28: 59 122.28 - 152.84: 33 Dihedral angle restraints: 36938 sinusoidal: 16804 harmonic: 20134 Sorted by residual: 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 93.00 167.27 -74.27 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 93.00 167.25 -74.25 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CA ARG a 140 " pdb=" C ARG a 140 " pdb=" N PRO a 141 " pdb=" CA PRO a 141 " ideal model delta harmonic sigma weight residual -180.00 -147.71 -32.29 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 36935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 9482 0.335 - 0.669: 58 0.669 - 1.004: 0 1.004 - 1.339: 0 1.339 - 1.673: 48 Chirality restraints: 9588 Sorted by residual: chirality pdb=" C20 A8614 312 " pdb=" C15 A8614 312 " pdb=" C19 A8614 312 " pdb=" C21 A8614 312 " both_signs ideal model delta sigma weight residual True 1.08 2.75 -1.67 2.00e-01 2.50e+01 7.00e+01 chirality pdb=" C20 A8613 312 " pdb=" C15 A8613 312 " pdb=" C19 A8613 312 " pdb=" C21 A8613 312 " both_signs ideal model delta sigma weight residual True 1.08 2.75 -1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" C20 A8631 310 " pdb=" C15 A8631 310 " pdb=" C19 A8631 310 " pdb=" C21 A8631 310 " 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 9585 not shown) Planarity restraints: 12968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR b 623 " 0.012 2.00e-02 2.50e+03 2.64e-01 6.98e+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 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR B 623 " -0.038 2.00e-02 2.50e+03 2.63e-01 6.94e+02 pdb=" C11 BCR B 623 " 0.272 2.00e-02 2.50e+03 pdb=" C12 BCR B 623 " -0.413 2.00e-02 2.50e+03 pdb=" C13 BCR B 623 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 BCR a 405 " -0.252 2.00e-02 2.50e+03 2.23e-01 6.23e+02 pdb=" C17 BCR a 405 " 0.413 2.00e-02 2.50e+03 pdb=" C18 BCR a 405 " -0.034 2.00e-02 2.50e+03 pdb=" C19 BCR a 405 " -0.119 2.00e-02 2.50e+03 pdb=" C36 BCR a 405 " -0.007 2.00e-02 2.50e+03 ... (remaining 12965 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 19 2.08 - 2.78: 16591 2.78 - 3.49: 86270 3.49 - 4.19: 183399 4.19 - 4.90: 310871 Nonbonded interactions: 597150 Sorted by model distance: nonbonded pdb=" OE2 GLU c 352 " pdb=" O3 OEX c 501 " model vdw 1.372 3.040 nonbonded pdb=" OE2 GLU C 352 " pdb=" O3 OEX C 501 " model vdw 1.433 3.040 nonbonded pdb=" O PHE11 146 " pdb=" O5 A8611 316 " model vdw 1.620 3.040 nonbonded pdb=" O PHE33 146 " pdb=" O5 A8633 302 " model vdw 1.667 3.040 nonbonded pdb=" O PHE31 146 " pdb=" O5 A8631 316 " model vdw 1.709 3.040 ... (remaining 597145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 31) selection = chain '1' selection = (chain '5' and resid 2 through 31) selection = chain '6' } ncs_group { reference = (chain '11' and (resid 31 through 206 or (resid 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '12' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '13' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '14' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '31' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '32' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '33' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) selection = (chain '34' and (resid 31 through 206 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 n \ ame CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1A or name O1D or nam \ e O2A or name O2D or name OBD or name MG )) or resid 314 or resid 316)) } ncs_group { reference = chain '2' selection = chain '7' } ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 21 through 471 or resid 501 through 518)) selection = (chain 'c' and (resid 21 through 471 or resid 501 through 518)) } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and resid 9 through 83) selection = chain 'e' } ncs_group { reference = chain 'F' selection = (chain 'f' and (resid 16 through 43 or resid 101)) } 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' and resid 2 through 43) selection = (chain 'm' and resid 2 through 43) } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'Q' selection = (chain 'q' and resid 70 through 206) } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = chain 'U' selection = chain 'u' } ncs_group { reference = chain 'V' selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'w' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 158 5.21 5 S 222 5.16 5 C 48386 2.51 5 N 9818 2.21 5 O 11528 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.770 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: 30.850 Check model and map are aligned: 0.830 Process input model: 136.150 Find NCS groups from input model: 4.100 Set up NCS constraints: 0.990 Set refine NCS operators: 0.000 Set scattering table: 0.530 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 0.250 73032 Z= 1.003 Angle : 1.721 39.064 101702 Z= 0.698 Chirality : 0.138 1.673 9588 Planarity : 0.014 0.264 12968 Dihedral : 17.957 152.845 24124 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.07), residues: 6884 helix: -4.12 (0.04), residues: 3574 sheet: -1.77 (0.33), residues: 236 loop : -2.37 (0.10), residues: 3074 *********************** 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 1365 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1347 time to evaluate : 5.362 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 outliers start: 18 outliers final: 1 residues processed: 1363 average time/residue: 0.7272 time to fit residues: 1659.2621 Evaluate side-chains 810 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 809 time to evaluate : 5.259 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5265 time to fit residues: 7.4852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 580 optimal weight: 0.8980 chunk 521 optimal weight: 0.9980 chunk 289 optimal weight: 0.1980 chunk 178 optimal weight: 0.0970 chunk 351 optimal weight: 0.5980 chunk 278 optimal weight: 0.7980 chunk 539 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 327 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 624 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 87 ASN B 179 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 311 GLN C 325 ASN C 383 GLN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 193 ASN ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN O 13 GLN O 222 GLN V 34 ASN V 49 ASN V 78 ASN Q 124 GLN Q 192 ASN ** a 303 ASN ** 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 311 GLN c 325 ASN c 383 GLN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 ASN d 193 ASN ** d 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 229 ASN ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 349 ASN ** h 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 7 ASN o 222 GLN v 34 ASN v 49 ASN v 78 ASN y 33 ASN q 192 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 13 83 ASN 13 161 ASN 13 177 ASN 14 177 ASN 31 83 ASN ** 31 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31 161 ASN 31 177 ASN 32 83 ASN 32 161 ASN 33 83 ASN 33 161 ASN 33 177 ASN 33 186 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 73032 Z= 0.183 Angle : 0.713 9.271 101702 Z= 0.314 Chirality : 0.044 0.289 9588 Planarity : 0.005 0.067 12968 Dihedral : 19.755 173.874 12078 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.12 % 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: -2.92 (0.09), residues: 6884 helix: -2.01 (0.07), residues: 3648 sheet: -1.47 (0.34), residues: 230 loop : -1.69 (0.10), residues: 3006 *********************** 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 1001 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 938 time to evaluate : 6.657 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: 63 outliers final: 32 residues processed: 964 average time/residue: 0.7229 time to fit residues: 1206.4790 Evaluate side-chains 797 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 765 time to evaluate : 5.320 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5672 time to fit residues: 41.6506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 0.3980 chunk 193 optimal weight: 10.0000 chunk 519 optimal weight: 3.9990 chunk 425 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 625 optimal weight: 2.9990 chunk 676 optimal weight: 0.9980 chunk 557 optimal weight: 0.9980 chunk 620 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 502 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 219 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN Q 192 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 GLN ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 82 GLN c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 ASN d 219 ASN ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN l 14 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN 13 177 ASN 14 186 GLN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 82 ASN 33 177 ASN 33 186 GLN 33 196 HIS ** 34 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 73032 Z= 0.265 Angle : 0.693 9.893 101702 Z= 0.305 Chirality : 0.045 0.341 9588 Planarity : 0.005 0.067 12968 Dihedral : 18.141 170.993 12078 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.49 % 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: -1.59 (0.09), residues: 6884 helix: -0.76 (0.08), residues: 3618 sheet: -0.88 (0.37), residues: 206 loop : -1.30 (0.11), residues: 3060 *********************** 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 885 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 801 time to evaluate : 5.412 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: 84 outliers final: 35 residues processed: 852 average time/residue: 0.6870 time to fit residues: 1018.5114 Evaluate side-chains 753 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 718 time to evaluate : 5.415 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5156 time to fit residues: 41.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 0.8980 chunk 470 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 420 optimal weight: 1.9990 chunk 628 optimal weight: 0.0170 chunk 665 optimal weight: 0.3980 chunk 328 optimal weight: 0.7980 chunk 595 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN Y 5 GLN a 303 ASN c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN l 14 ASN o 109 GLN u 15 ASN v 49 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN 13 82 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 73032 Z= 0.194 Angle : 0.618 10.098 101702 Z= 0.273 Chirality : 0.043 0.308 9588 Planarity : 0.004 0.059 12968 Dihedral : 17.559 170.677 12078 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 1.46 % 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: -0.95 (0.10), residues: 6884 helix: -0.20 (0.08), residues: 3652 sheet: -0.66 (0.37), residues: 208 loop : -1.05 (0.11), residues: 3024 *********************** 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 860 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 778 time to evaluate : 5.432 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 outliers start: 82 outliers final: 30 residues processed: 817 average time/residue: 0.6782 time to fit residues: 965.1443 Evaluate side-chains 739 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 709 time to evaluate : 5.382 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5412 time to fit residues: 37.1890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 553 optimal weight: 1.9990 chunk 377 optimal weight: 0.0370 chunk 9 optimal weight: 3.9990 chunk 495 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 567 optimal weight: 0.0980 chunk 459 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 596 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 ASN c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN o 139 GLN v 17 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 96 ASN 33 196 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 73032 Z= 0.190 Angle : 0.601 9.353 101702 Z= 0.266 Chirality : 0.042 0.313 9588 Planarity : 0.004 0.058 12968 Dihedral : 17.089 168.199 12078 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.91 % 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: -0.53 (0.10), residues: 6884 helix: 0.18 (0.08), residues: 3648 sheet: -0.68 (0.36), residues: 228 loop : -0.88 (0.11), residues: 3008 *********************** 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 797 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 746 time to evaluate : 5.537 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: 51 outliers final: 17 residues processed: 768 average time/residue: 0.6883 time to fit residues: 922.4928 Evaluate side-chains 722 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 705 time to evaluate : 5.331 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5544 time to fit residues: 24.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 223 optimal weight: 6.9990 chunk 598 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 665 optimal weight: 4.9990 chunk 552 optimal weight: 0.3980 chunk 308 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 349 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 GLN Q 192 ASN W 57 ASN ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN o 139 GLN o 222 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 82 ASN 14 186 GLN 33 82 ASN 33 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 73032 Z= 0.374 Angle : 0.712 12.574 101702 Z= 0.314 Chirality : 0.047 0.366 9588 Planarity : 0.005 0.058 12968 Dihedral : 17.445 165.813 12078 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.88 % 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: -0.53 (0.10), residues: 6884 helix: 0.13 (0.08), residues: 3660 sheet: -0.53 (0.37), residues: 214 loop : -0.83 (0.12), residues: 3010 *********************** 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 834 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 728 time to evaluate : 5.516 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 outliers start: 106 outliers final: 54 residues processed: 784 average time/residue: 0.6823 time to fit residues: 938.8881 Evaluate side-chains 735 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 681 time to evaluate : 5.338 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5405 time to fit residues: 62.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 641 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 chunk 486 optimal weight: 3.9990 chunk 376 optimal weight: 2.9990 chunk 560 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 663 optimal weight: 1.9990 chunk 414 optimal weight: 0.5980 chunk 404 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 GLN c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN o 139 GLN o 197 GLN v 17 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 73032 Z= 0.170 Angle : 0.598 10.865 101702 Z= 0.265 Chirality : 0.042 0.314 9588 Planarity : 0.004 0.058 12968 Dihedral : 16.843 162.842 12078 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.84 % 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: -0.19 (0.10), residues: 6884 helix: 0.45 (0.09), residues: 3660 sheet: -0.52 (0.36), residues: 224 loop : -0.73 (0.12), residues: 3000 *********************** 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 804 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 757 time to evaluate : 5.347 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: 47 outliers final: 11 residues processed: 786 average time/residue: 0.6922 time to fit residues: 962.3719 Evaluate side-chains 714 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 703 time to evaluate : 5.433 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5753 time to fit residues: 18.5582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 410 optimal weight: 1.9990 chunk 264 optimal weight: 0.0980 chunk 396 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 421 optimal weight: 1.9990 chunk 451 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 521 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 17 ASN ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN ** m 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN ** 13 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 73032 Z= 0.244 Angle : 0.627 10.035 101702 Z= 0.279 Chirality : 0.044 0.321 9588 Planarity : 0.004 0.057 12968 Dihedral : 16.794 158.359 12078 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.94 % 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: -0.13 (0.10), residues: 6884 helix: 0.51 (0.09), residues: 3664 sheet: -0.49 (0.36), residues: 224 loop : -0.71 (0.12), residues: 2996 *********************** 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 772 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 719 time to evaluate : 5.383 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: 53 outliers final: 27 residues processed: 743 average time/residue: 0.6874 time to fit residues: 892.9861 Evaluate side-chains 714 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 687 time to evaluate : 5.373 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5546 time to fit residues: 35.4249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 603 optimal weight: 0.9990 chunk 635 optimal weight: 0.3980 chunk 579 optimal weight: 3.9990 chunk 617 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 485 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 558 optimal weight: 0.8980 chunk 584 optimal weight: 0.5980 chunk 615 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN M 28 GLN ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 17 ASN ** c 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN ** m 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN o 197 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN ** 13 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 73032 Z= 0.189 Angle : 0.597 9.706 101702 Z= 0.266 Chirality : 0.043 0.301 9588 Planarity : 0.004 0.056 12968 Dihedral : 16.494 155.184 12078 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.59 % 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: -0.00 (0.10), residues: 6884 helix: 0.62 (0.09), residues: 3672 sheet: -0.49 (0.36), residues: 224 loop : -0.66 (0.12), residues: 2988 *********************** 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 761 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 728 time to evaluate : 5.433 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 outliers start: 33 outliers final: 13 residues processed: 747 average time/residue: 0.6975 time to fit residues: 909.0381 Evaluate side-chains 705 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 692 time to evaluate : 5.635 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.5548 time to fit residues: 20.1802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 405 optimal weight: 2.9990 chunk 653 optimal weight: 2.9990 chunk 398 optimal weight: 0.6980 chunk 309 optimal weight: 0.6980 chunk 454 optimal weight: 0.9990 chunk 685 optimal weight: 0.9980 chunk 630 optimal weight: 2.9990 chunk 545 optimal weight: 7.9990 chunk 56 optimal weight: 0.0870 chunk 421 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN M 28 GLN ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN ** m 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN ** 13 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 73032 Z= 0.181 Angle : 0.591 10.739 101702 Z= 0.264 Chirality : 0.042 0.287 9588 Planarity : 0.004 0.055 12968 Dihedral : 16.216 149.957 12078 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 0.72 (0.09), residues: 3668 sheet: -0.56 (0.35), residues: 232 loop : -0.62 (0.12), residues: 2984 ********************** 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 759 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 741 time to evaluate : 5.740 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 outliers start: 18 outliers final: 8 residues processed: 750 average time/residue: 0.6800 time to fit residues: 889.7510 Evaluate side-chains 713 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 705 time to evaluate : 5.382 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6139 time to fit residues: 15.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 433 optimal weight: 0.9990 chunk 581 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 503 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 546 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 561 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 GLN ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 14 ASN m 28 GLN o 139 GLN o 197 GLN 11 177 ASN ** 13 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083331 restraints weight = 144501.160| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.02 r_work: 0.2937 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 73032 Z= 0.239 Angle : 0.623 11.502 101702 Z= 0.277 Chirality : 0.044 0.319 9588 Planarity : 0.004 0.055 12968 Dihedral : 16.248 146.196 12078 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.44 % 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: 0.67 (0.09), residues: 3670 sheet: -0.56 (0.36), residues: 228 loop : -0.63 (0.12), residues: 2986 =============================================================================== Job complete usr+sys time: 16446.15 seconds wall clock time: 289 minutes 47.98 seconds (17387.98 seconds total)