Starting phenix.real_space_refine on Fri Mar 15 18:33:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/03_2024/6j3y_9775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/03_2024/6j3y_9775.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/03_2024/6j3y_9775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/03_2024/6j3y_9775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/03_2024/6j3y_9775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/03_2024/6j3y_9775_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Ca 2 9.91 5 Mn 8 7.51 5 Fe 6 7.16 5 P 8 5.49 5 Mg 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. Process input model Symmetric amino acids flipped Residue "A ARG 136": "NH1" <-> "NH2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "I TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "Q ARG 122": "NH1" <-> "NH2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 154": "NH1" <-> "NH2" Residue "a ARG 136": "NH1" <-> "NH2" Residue "b PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 272": "NH1" <-> "NH2" Residue "b PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 378": "NH1" <-> "NH2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b ARG 385": "NH1" <-> "NH2" Residue "b PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 447": "NH1" <-> "NH2" Residue "c PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 459": "NH1" <-> "NH2" Residue "c ARG 468": "NH1" <-> "NH2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 179": "NH1" <-> "NH2" Residue "d ARG 250": "NH1" <-> "NH2" Residue "d ARG 264": "NH1" <-> "NH2" Residue "d ARG 293": "NH1" <-> "NH2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "i TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "l ARG 15": "NH1" <-> "NH2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "o TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 150": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "q ARG 122": "NH1" <-> "NH2" Residue "q ARG 144": "NH1" <-> "NH2" Residue "q ARG 154": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 26.36, per 1000 atoms: 0.38 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: 22.34 Conformation dependent library (CDL) restraints added in 7.0 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: 8.04 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: 19.23 Time building geometry restraints manager: 24.37 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 - 26.68: 36325 26.68 - 53.36: 2258 53.36 - 80.04: 521 80.04 - 106.72: 210 106.72 - 133.40: 72 Dihedral angle restraints: 39386 sinusoidal: 19252 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 39383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 9502 0.335 - 0.669: 58 0.669 - 1.004: 0 1.004 - 1.339: 0 1.339 - 1.673: 48 Chirality restraints: 9608 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 9605 not shown) Planarity restraints: 12984 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 12981 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 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: 5.700 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: 26.850 Check model and map are aligned: 0.750 Set scattering table: 0.480 Process input model: 130.900 Find NCS groups from input model: 3.480 Set up NCS constraints: 1.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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= 1.017 Angle : 1.774 39.064 101702 Z= 0.712 Chirality : 0.139 1.673 9608 Planarity : 0.015 0.264 12984 Dihedral : 19.440 133.404 26572 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.32 % Allowed : 2.88 % Favored : 96.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 142 HIS 0.017 0.004 HIS f 22 PHE 0.040 0.004 PHE C 282 TYR 0.042 0.003 TYR h 49 ARG 0.015 0.001 ARG C 213 *********************** 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 : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8122 (tt0) cc_final: 0.7912 (tt0) REVERT: B 407 ASN cc_start: 0.8863 (t0) cc_final: 0.8551 (t0) REVERT: B 437 LEU cc_start: 0.8321 (mt) cc_final: 0.8087 (mp) REVERT: D 22 LYS cc_start: 0.8901 (mttt) cc_final: 0.8661 (mttm) REVERT: F 38 MET cc_start: 0.8266 (mtm) cc_final: 0.7978 (mtm) REVERT: J 31 SER cc_start: 0.9211 (m) cc_final: 0.8812 (t) REVERT: J 35 LEU cc_start: 0.8318 (mt) cc_final: 0.8035 (tp) REVERT: K 17 SER cc_start: 0.9003 (p) cc_final: 0.8516 (p) REVERT: L 25 ILE cc_start: 0.9146 (mt) cc_final: 0.8930 (mp) REVERT: M 5 PHE cc_start: 0.7630 (m-80) cc_final: 0.7184 (p90) REVERT: M 13 LEU cc_start: 0.9197 (mt) cc_final: 0.8966 (mp) REVERT: O 11 TYR cc_start: 0.8885 (t80) cc_final: 0.8612 (t80) REVERT: O 139 GLN cc_start: 0.8264 (tt0) cc_final: 0.7818 (pp30) REVERT: O 202 MET cc_start: 0.8224 (mtm) cc_final: 0.7693 (mtm) REVERT: U 76 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8203 (mtmm) REVERT: U 86 THR cc_start: 0.8326 (m) cc_final: 0.8091 (p) REVERT: V 134 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8598 (pttm) REVERT: Y 7 ILE cc_start: 0.8988 (mt) cc_final: 0.8450 (pt) REVERT: X 5 LEU cc_start: 0.9260 (tp) cc_final: 0.8989 (tp) REVERT: b 98 LEU cc_start: 0.9269 (tp) cc_final: 0.8919 (mt) REVERT: b 407 ASN cc_start: 0.8835 (t0) cc_final: 0.8544 (t0) REVERT: b 437 LEU cc_start: 0.8301 (mt) cc_final: 0.8052 (mp) REVERT: d 22 LYS cc_start: 0.8921 (mttt) cc_final: 0.8676 (mttm) REVERT: d 281 SER cc_start: 0.9177 (p) cc_final: 0.8953 (p) REVERT: k 17 SER cc_start: 0.8939 (p) cc_final: 0.8478 (p) REVERT: m 5 PHE cc_start: 0.7677 (m-80) cc_final: 0.7165 (p90) REVERT: m 13 LEU cc_start: 0.9239 (mt) cc_final: 0.8945 (mp) REVERT: m 20 LEU cc_start: 0.9038 (mt) cc_final: 0.8835 (mt) REVERT: o 7 ASN cc_start: 0.9122 (m-40) cc_final: 0.8894 (m110) REVERT: o 96 ASN cc_start: 0.8115 (m-40) cc_final: 0.7869 (p0) REVERT: u 76 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8103 (mtmm) REVERT: v 134 LYS cc_start: 0.9007 (ptpt) cc_final: 0.8623 (pttm) REVERT: y 7 ILE cc_start: 0.9073 (mt) cc_final: 0.8418 (pt) REVERT: 12 37 VAL cc_start: 0.9029 (t) cc_final: 0.8811 (m) REVERT: 13 96 ASN cc_start: 0.8139 (m-40) cc_final: 0.7938 (t0) REVERT: 13 124 PHE cc_start: 0.8435 (m-80) cc_final: 0.8119 (m-80) REVERT: 13 137 TYR cc_start: 0.8055 (m-80) cc_final: 0.7695 (m-80) REVERT: 13 189 TYR cc_start: 0.8342 (t80) cc_final: 0.8044 (t80) REVERT: 32 91 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7708 (tt) REVERT: 32 136 LYS cc_start: 0.9014 (tttt) cc_final: 0.8678 (tttt) REVERT: 32 145 TYR cc_start: 0.7762 (t80) cc_final: 0.7490 (t80) REVERT: 33 137 TYR cc_start: 0.7972 (m-80) cc_final: 0.7732 (m-10) outliers start: 18 outliers final: 1 residues processed: 1363 average time/residue: 0.7415 time to fit residues: 1692.5564 Evaluate side-chains 824 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 822 time to evaluate : 4.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain 32 residue 91 LEU 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 ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN O 13 GLN O 222 GLN V 34 ASN V 49 ASN V 78 ASN Q 124 GLN Q 192 ASN 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 ** l 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 0.8199 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 73032 Z= 0.183 Angle : 0.711 9.702 101702 Z= 0.313 Chirality : 0.044 0.284 9608 Planarity : 0.005 0.067 12984 Dihedral : 20.016 166.513 14530 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.12 % Allowed : 8.46 % Favored : 90.42 % 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: -2.87 (0.09), residues: 6884 helix: -1.96 (0.07), residues: 3648 sheet: -1.51 (0.33), residues: 242 loop : -1.69 (0.10), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 131 HIS 0.008 0.002 HIS C 116 PHE 0.025 0.002 PHE13 123 TYR 0.019 0.001 TYR33 189 ARG 0.012 0.001 ARG w 71 *********************** 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 1016 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 953 time to evaluate : 6.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7682 (mmm) cc_final: 0.7313 (mmm) REVERT: B 98 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8802 (mt) REVERT: D 22 LYS cc_start: 0.8761 (mttt) cc_final: 0.8518 (mttp) REVERT: F 38 MET cc_start: 0.8234 (mtm) cc_final: 0.7837 (mtm) REVERT: H 52 SER cc_start: 0.9144 (p) cc_final: 0.8938 (t) REVERT: J 23 MET cc_start: 0.7969 (tpp) cc_final: 0.7733 (tpp) REVERT: J 31 SER cc_start: 0.9253 (m) cc_final: 0.8881 (t) REVERT: J 35 LEU cc_start: 0.8379 (mt) cc_final: 0.8075 (tp) REVERT: M 5 PHE cc_start: 0.7577 (m-80) cc_final: 0.7193 (p90) REVERT: O 11 TYR cc_start: 0.8847 (t80) cc_final: 0.8594 (t80) REVERT: O 103 TYR cc_start: 0.8384 (p90) cc_final: 0.8100 (p90) REVERT: U 23 SER cc_start: 0.8269 (m) cc_final: 0.7969 (p) REVERT: V 134 LYS cc_start: 0.9015 (ptpt) cc_final: 0.8602 (pttm) REVERT: X 33 ASP cc_start: 0.4175 (OUTLIER) cc_final: 0.3973 (t0) REVERT: Q 146 MET cc_start: 0.8223 (mtt) cc_final: 0.8007 (mtm) REVERT: a 288 MET cc_start: 0.7715 (mmm) cc_final: 0.7072 (mmm) REVERT: b 25 MET cc_start: 0.8256 (tpp) cc_final: 0.8042 (tpt) REVERT: b 453 TYR cc_start: 0.8947 (t80) cc_final: 0.8733 (t80) REVERT: d 22 LYS cc_start: 0.8860 (mttt) cc_final: 0.8574 (mttp) REVERT: d 281 SER cc_start: 0.9099 (p) cc_final: 0.8887 (p) REVERT: d 328 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7469 (ttp) REVERT: k 41 ILE cc_start: 0.8797 (tp) cc_final: 0.8554 (tt) REVERT: m 5 PHE cc_start: 0.7593 (m-80) cc_final: 0.7130 (p90) REVERT: o 7 ASN cc_start: 0.9065 (m-40) cc_final: 0.8752 (m110) REVERT: o 103 TYR cc_start: 0.8470 (p90) cc_final: 0.8022 (p90) REVERT: u 23 SER cc_start: 0.8253 (m) cc_final: 0.7980 (p) REVERT: v 25 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8209 (mm110) REVERT: v 134 LYS cc_start: 0.9050 (ptpt) cc_final: 0.8629 (pttm) REVERT: y 7 ILE cc_start: 0.8759 (mt) cc_final: 0.8498 (pt) REVERT: x 33 ASP cc_start: 0.3306 (OUTLIER) cc_final: 0.2962 (t0) REVERT: q 122 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7986 (mmt180) REVERT: q 146 MET cc_start: 0.8346 (mtt) cc_final: 0.7994 (mtm) REVERT: w 40 LEU cc_start: 0.9204 (mt) cc_final: 0.8981 (mt) REVERT: w 53 TYR cc_start: 0.8301 (m-80) cc_final: 0.7863 (m-80) REVERT: 12 37 VAL cc_start: 0.8988 (t) cc_final: 0.8742 (m) REVERT: 13 189 TYR cc_start: 0.8348 (t80) cc_final: 0.8099 (t80) REVERT: 31 34 GLU cc_start: 0.8277 (mp0) cc_final: 0.8010 (mp0) outliers start: 63 outliers final: 33 residues processed: 980 average time/residue: 0.6937 time to fit residues: 1172.5893 Evaluate side-chains 807 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 769 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain d residue 328 MET Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain u residue 32 VAL Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 25 GLN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain x residue 33 ASP Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 32 residue 78 THR Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 33 residue 188 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 0.4980 chunk 193 optimal weight: 0.0170 chunk 519 optimal weight: 3.9990 chunk 425 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 625 optimal weight: 3.9990 chunk 676 optimal weight: 0.7980 chunk 557 optimal weight: 0.5980 chunk 620 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 502 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** D 219 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** M 4 GLN O 109 GLN Q 192 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 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** l 14 ASN m 4 GLN ** o 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN ** 13 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 186 GLN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 82 ASN ** 33 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 73032 Z= 0.168 Angle : 0.632 9.681 101702 Z= 0.278 Chirality : 0.043 0.321 9608 Planarity : 0.004 0.060 12984 Dihedral : 18.343 166.045 14528 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.49 % Allowed : 10.48 % Favored : 88.02 % 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: -1.67 (0.09), residues: 6884 helix: -0.83 (0.08), residues: 3664 sheet: -1.03 (0.34), residues: 232 loop : -1.33 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP11 131 HIS 0.009 0.001 HIS W 42 PHE 0.019 0.001 PHE b 246 TYR 0.019 0.001 TYR14 189 ARG 0.005 0.000 ARG12 59 *********************** 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 919 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 835 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.8584 (ptp) cc_final: 0.8321 (ptm) REVERT: D 22 LYS cc_start: 0.8692 (mttt) cc_final: 0.8463 (mttm) REVERT: D 281 SER cc_start: 0.9108 (p) cc_final: 0.8897 (p) REVERT: D 300 GLN cc_start: 0.8821 (mt0) cc_final: 0.8504 (mt0) REVERT: E 43 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8698 (tt) REVERT: F 38 MET cc_start: 0.8298 (mtm) cc_final: 0.7925 (mtm) REVERT: J 31 SER cc_start: 0.9282 (m) cc_final: 0.8824 (t) REVERT: L 25 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8943 (mp) REVERT: M 5 PHE cc_start: 0.7650 (m-80) cc_final: 0.7253 (p90) REVERT: O 11 TYR cc_start: 0.8822 (t80) cc_final: 0.8574 (t80) REVERT: O 103 TYR cc_start: 0.8572 (p90) cc_final: 0.8295 (p90) REVERT: U 79 GLU cc_start: 0.8383 (pm20) cc_final: 0.8149 (pm20) REVERT: V 28 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7336 (ptm160) REVERT: V 128 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7463 (mm-30) REVERT: V 134 LYS cc_start: 0.9055 (ptpt) cc_final: 0.8580 (pttm) REVERT: Q 81 GLN cc_start: 0.6679 (mt0) cc_final: 0.6450 (mt0) REVERT: b 256 MET cc_start: 0.9073 (tpp) cc_final: 0.8477 (tpt) REVERT: d 22 LYS cc_start: 0.8835 (mttt) cc_final: 0.8588 (mttp) REVERT: d 281 SER cc_start: 0.9095 (p) cc_final: 0.8889 (p) REVERT: e 43 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8728 (tt) REVERT: f 38 MET cc_start: 0.8264 (mtm) cc_final: 0.7878 (mtm) REVERT: k 41 ILE cc_start: 0.8804 (tp) cc_final: 0.8584 (tt) REVERT: l 25 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8945 (mp) REVERT: m 5 PHE cc_start: 0.7586 (m-80) cc_final: 0.7203 (p90) REVERT: o 103 TYR cc_start: 0.8560 (p90) cc_final: 0.8104 (p90) REVERT: o 130 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7032 (p0) REVERT: u 76 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8207 (mtmm) REVERT: u 79 GLU cc_start: 0.8399 (pm20) cc_final: 0.8125 (pm20) REVERT: v 134 LYS cc_start: 0.9072 (ptpt) cc_final: 0.8654 (pttm) REVERT: q 122 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7701 (mmt180) REVERT: w 40 LEU cc_start: 0.9191 (mt) cc_final: 0.8983 (mt) REVERT: 12 37 VAL cc_start: 0.8941 (t) cc_final: 0.8675 (m) REVERT: 12 78 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8386 (p) REVERT: 12 110 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8326 (mtm-85) REVERT: 13 189 TYR cc_start: 0.8377 (t80) cc_final: 0.8136 (t80) REVERT: 14 188 MET cc_start: 0.7721 (tpp) cc_final: 0.7403 (tpp) REVERT: 14 192 TYR cc_start: 0.7677 (m-10) cc_final: 0.7344 (m-80) REVERT: 31 34 GLU cc_start: 0.8434 (mp0) cc_final: 0.8220 (mp0) REVERT: 31 172 MET cc_start: 0.8623 (mmm) cc_final: 0.8366 (mmp) REVERT: 32 172 MET cc_start: 0.8774 (mmt) cc_final: 0.8463 (mmm) outliers start: 84 outliers final: 34 residues processed: 882 average time/residue: 0.6523 time to fit residues: 994.4089 Evaluate side-chains 784 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 744 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 139 GLN Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 66 ILE Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 161 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 0.0170 chunk 470 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 420 optimal weight: 2.9990 chunk 628 optimal weight: 4.9990 chunk 665 optimal weight: 0.1980 chunk 328 optimal weight: 0.9980 chunk 595 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- 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 219 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN Q 192 ASN c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN 13 82 ASN 13 177 ASN 13 196 HIS ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 82 ASN 33 177 ASN 33 186 GLN 33 196 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2978 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= 0.224 Angle : 0.634 10.464 101702 Z= 0.279 Chirality : 0.044 0.309 9608 Planarity : 0.004 0.057 12984 Dihedral : 17.498 167.837 14528 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.11 % Allowed : 10.87 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.10), residues: 6884 helix: -0.15 (0.08), residues: 3612 sheet: -0.70 (0.37), residues: 212 loop : -1.09 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP31 131 HIS 0.010 0.002 HIS w 42 PHE 0.031 0.002 PHE o 138 TYR 0.018 0.001 TYR33 189 ARG 0.006 0.000 ARG b 220 *********************** 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 888 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 769 time to evaluate : 5.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7654 (mmm) cc_final: 0.7047 (mmm) REVERT: B 256 MET cc_start: 0.9087 (tpp) cc_final: 0.8463 (tpt) REVERT: C 286 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9063 (mm) REVERT: D 22 LYS cc_start: 0.8833 (mttt) cc_final: 0.8583 (mttm) REVERT: D 200 VAL cc_start: 0.9102 (t) cc_final: 0.8887 (m) REVERT: E 43 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8739 (tt) REVERT: F 38 MET cc_start: 0.8357 (mtm) cc_final: 0.7974 (mtm) REVERT: H 9 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7512 (mm-30) REVERT: J 25 SER cc_start: 0.9287 (p) cc_final: 0.9031 (p) REVERT: J 31 SER cc_start: 0.9305 (m) cc_final: 0.8842 (t) REVERT: L 25 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8902 (mp) REVERT: M 5 PHE cc_start: 0.7668 (m-80) cc_final: 0.7219 (p90) REVERT: M 28 GLN cc_start: 0.8780 (pp30) cc_final: 0.8482 (pp30) REVERT: O 103 TYR cc_start: 0.8637 (p90) cc_final: 0.8360 (p90) REVERT: U 79 GLU cc_start: 0.8393 (pm20) cc_final: 0.8125 (pm20) REVERT: V 28 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7357 (ptm160) REVERT: V 128 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7442 (mm-30) REVERT: V 134 LYS cc_start: 0.9085 (ptpt) cc_final: 0.8711 (pttp) REVERT: Q 81 GLN cc_start: 0.6541 (mt0) cc_final: 0.6336 (mt0) REVERT: Q 192 ASN cc_start: 0.7699 (t0) cc_final: 0.7463 (t0) REVERT: b 256 MET cc_start: 0.9079 (tpp) cc_final: 0.8461 (tpt) REVERT: c 286 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9048 (mm) REVERT: d 22 LYS cc_start: 0.8868 (mttt) cc_final: 0.8589 (mttp) REVERT: e 43 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8700 (tt) REVERT: f 38 MET cc_start: 0.8355 (mtm) cc_final: 0.7919 (mtm) REVERT: k 41 ILE cc_start: 0.8800 (tp) cc_final: 0.8538 (tt) REVERT: l 25 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8898 (mp) REVERT: m 5 PHE cc_start: 0.7688 (m-80) cc_final: 0.7179 (p90) REVERT: m 28 GLN cc_start: 0.8747 (pp30) cc_final: 0.8286 (pp30) REVERT: u 79 GLU cc_start: 0.8426 (pm20) cc_final: 0.8106 (pm20) REVERT: v 13 ASP cc_start: 0.7492 (p0) cc_final: 0.7157 (p0) REVERT: v 134 LYS cc_start: 0.9124 (ptpt) cc_final: 0.8741 (pttp) REVERT: w 40 LEU cc_start: 0.9178 (mt) cc_final: 0.8940 (mt) REVERT: 11 91 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8292 (tp) REVERT: 11 181 GLU cc_start: 0.8078 (tp30) cc_final: 0.7877 (tp30) REVERT: 12 37 VAL cc_start: 0.8989 (t) cc_final: 0.8708 (m) REVERT: 12 78 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8436 (p) REVERT: 12 110 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8420 (mtm-85) REVERT: 13 123 PHE cc_start: 0.8780 (t80) cc_final: 0.8580 (t80) REVERT: 13 189 TYR cc_start: 0.8375 (t80) cc_final: 0.8137 (t80) REVERT: 31 91 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8296 (tp) REVERT: 31 171 MET cc_start: 0.9029 (mtm) cc_final: 0.8802 (mtm) REVERT: 31 172 MET cc_start: 0.8655 (mmm) cc_final: 0.8442 (mmp) REVERT: 32 78 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8462 (p) REVERT: 32 172 MET cc_start: 0.8822 (mmt) cc_final: 0.8512 (mmm) REVERT: 34 196 HIS cc_start: 0.5838 (t70) cc_final: 0.5563 (t70) outliers start: 119 outliers final: 67 residues processed: 829 average time/residue: 0.6463 time to fit residues: 929.2373 Evaluate side-chains 793 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 716 time to evaluate : 4.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 286 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain t residue 2 GLU Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 12 VAL Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 24 ASN Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 11 residue 117 LEU Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 13 residue 174 ILE Chi-restraints excluded: chain 13 residue 177 ASN Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 95 ASN Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 31 residue 91 LEU Chi-restraints excluded: chain 31 residue 117 LEU Chi-restraints excluded: chain 31 residue 135 SER Chi-restraints excluded: chain 31 residue 138 ASP Chi-restraints excluded: chain 32 residue 72 MET Chi-restraints excluded: chain 32 residue 78 THR Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 33 residue 198 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 553 optimal weight: 0.7980 chunk 377 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 495 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 567 optimal weight: 4.9990 chunk 459 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 339 optimal weight: 0.9980 chunk 596 optimal weight: 0.0670 chunk 167 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN m 4 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 15 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 96 ASN 13 177 ASN 13 196 HIS 33 82 ASN 33 177 ASN 33 196 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 73032 Z= 0.169 Angle : 0.587 10.152 101702 Z= 0.259 Chirality : 0.042 0.292 9608 Planarity : 0.004 0.057 12984 Dihedral : 16.758 169.405 14528 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.83 % Allowed : 11.96 % Favored : 86.21 % 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: -0.51 (0.10), residues: 6884 helix: 0.20 (0.08), residues: 3664 sheet: -0.75 (0.35), residues: 232 loop : -0.89 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP31 131 HIS 0.014 0.001 HIS c 116 PHE 0.021 0.001 PHE34 123 TYR 0.019 0.001 TYR34 189 ARG 0.004 0.000 ARG12 59 *********************** 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 870 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 767 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 MET cc_start: 0.9093 (tpp) cc_final: 0.8395 (tpt) REVERT: C 286 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8960 (mm) REVERT: D 22 LYS cc_start: 0.8746 (mttt) cc_final: 0.8522 (mttm) REVERT: D 200 VAL cc_start: 0.9083 (t) cc_final: 0.8858 (m) REVERT: E 43 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8773 (tt) REVERT: F 38 MET cc_start: 0.8423 (mtm) cc_final: 0.8072 (mtm) REVERT: H 9 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7425 (mm-30) REVERT: J 25 SER cc_start: 0.9268 (p) cc_final: 0.8995 (p) REVERT: J 31 SER cc_start: 0.9295 (m) cc_final: 0.8809 (t) REVERT: L 25 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8919 (mp) REVERT: M 5 PHE cc_start: 0.7652 (m-80) cc_final: 0.7228 (p90) REVERT: V 28 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7251 (ptm160) REVERT: V 128 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7436 (mm-30) REVERT: V 134 LYS cc_start: 0.9081 (ptpt) cc_final: 0.8657 (pttp) REVERT: Y 1 MET cc_start: 0.6691 (mmm) cc_final: 0.6175 (mtp) REVERT: Q 81 GLN cc_start: 0.6518 (mt0) cc_final: 0.6283 (mt0) REVERT: a 288 MET cc_start: 0.7127 (mmm) cc_final: 0.6804 (mmm) REVERT: b 256 MET cc_start: 0.9101 (tpp) cc_final: 0.8438 (tpt) REVERT: d 22 LYS cc_start: 0.8799 (mttt) cc_final: 0.8583 (mttm) REVERT: d 301 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7285 (mm-30) REVERT: e 20 TYR cc_start: 0.8688 (t80) cc_final: 0.8457 (t80) REVERT: e 43 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8748 (tt) REVERT: e 59 GLN cc_start: 0.7987 (mp10) cc_final: 0.7751 (mp10) REVERT: f 38 MET cc_start: 0.8354 (mtm) cc_final: 0.7963 (mtm) REVERT: h 9 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7372 (mm-30) REVERT: k 41 ILE cc_start: 0.8754 (tp) cc_final: 0.8462 (tt) REVERT: l 25 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8856 (mp) REVERT: m 5 PHE cc_start: 0.7674 (m-80) cc_final: 0.7186 (p90) REVERT: m 28 GLN cc_start: 0.8754 (pp30) cc_final: 0.8466 (pp30) REVERT: o 168 MET cc_start: 0.8772 (pmm) cc_final: 0.8541 (pmm) REVERT: v 13 ASP cc_start: 0.7511 (p0) cc_final: 0.7176 (p0) REVERT: v 134 LYS cc_start: 0.9124 (ptpt) cc_final: 0.8692 (pttp) REVERT: q 162 GLN cc_start: 0.8498 (mm110) cc_final: 0.8221 (mp10) REVERT: w 40 LEU cc_start: 0.9179 (mt) cc_final: 0.8917 (mt) REVERT: 12 35 LEU cc_start: 0.8766 (mt) cc_final: 0.8419 (mt) REVERT: 12 37 VAL cc_start: 0.8816 (t) cc_final: 0.8593 (m) REVERT: 12 78 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8490 (p) REVERT: 12 110 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8402 (mtm-85) REVERT: 13 123 PHE cc_start: 0.8830 (t80) cc_final: 0.8599 (t80) REVERT: 13 177 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8032 (t0) REVERT: 13 189 TYR cc_start: 0.8373 (t80) cc_final: 0.8126 (t80) REVERT: 14 192 TYR cc_start: 0.7621 (m-10) cc_final: 0.7331 (m-80) REVERT: 31 171 MET cc_start: 0.8984 (mtm) cc_final: 0.8686 (mtm) REVERT: 32 78 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8501 (p) REVERT: 32 91 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8226 (tp) REVERT: 32 172 MET cc_start: 0.8869 (mmt) cc_final: 0.8570 (mmm) REVERT: 34 196 HIS cc_start: 0.5750 (t70) cc_final: 0.5248 (t70) outliers start: 103 outliers final: 59 residues processed: 823 average time/residue: 0.7046 time to fit residues: 1008.2384 Evaluate side-chains 785 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 717 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 12 VAL Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 174 ILE Chi-restraints excluded: chain 13 residue 177 ASN Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 31 residue 117 LEU Chi-restraints excluded: chain 32 residue 72 MET Chi-restraints excluded: chain 32 residue 78 THR Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 186 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 223 optimal weight: 7.9990 chunk 598 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 390 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 665 optimal weight: 4.9990 chunk 552 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 55 optimal weight: 0.0000 chunk 220 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- 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** O 197 GLN O 222 GLN Q 192 ASN ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN m 4 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 222 GLN v 49 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 177 ASN 13 177 ASN 13 191 GLN 33 82 ASN 33 177 ASN 33 196 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 73032 Z= 0.385 Angle : 0.722 12.715 101702 Z= 0.318 Chirality : 0.048 0.382 9608 Planarity : 0.005 0.057 12984 Dihedral : 17.102 168.145 14528 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.67 % Allowed : 11.98 % Favored : 85.36 % 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: -0.54 (0.10), residues: 6884 helix: 0.17 (0.08), residues: 3630 sheet: -0.48 (0.39), residues: 196 loop : -0.90 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP31 131 HIS 0.016 0.002 HIS c 116 PHE 0.024 0.002 PHE B 211 TYR 0.020 0.002 TYR H 49 ARG 0.006 0.001 ARG31 168 *********************** 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 879 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 729 time to evaluate : 5.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7682 (mmm) cc_final: 0.6929 (mmm) REVERT: B 256 MET cc_start: 0.9119 (tpp) cc_final: 0.8536 (tpt) REVERT: C 286 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9175 (mm) REVERT: D 22 LYS cc_start: 0.8994 (mttt) cc_final: 0.8702 (mttp) REVERT: D 301 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7284 (mm-30) REVERT: E 43 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8814 (tt) REVERT: H 9 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7685 (mm-30) REVERT: J 25 SER cc_start: 0.9335 (p) cc_final: 0.9053 (p) REVERT: L 25 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8910 (mp) REVERT: M 5 PHE cc_start: 0.7725 (m-80) cc_final: 0.7227 (p90) REVERT: M 28 GLN cc_start: 0.8965 (pp30) cc_final: 0.8664 (pp30) REVERT: V 13 ASP cc_start: 0.7464 (p0) cc_final: 0.7142 (p0) REVERT: Y 1 MET cc_start: 0.6797 (mmm) cc_final: 0.6482 (mtp) REVERT: Q 192 ASN cc_start: 0.7804 (t0) cc_final: 0.7599 (t0) REVERT: a 288 MET cc_start: 0.7182 (mmm) cc_final: 0.6946 (mmm) REVERT: b 256 MET cc_start: 0.9126 (tpp) cc_final: 0.8540 (tpt) REVERT: c 286 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9159 (mm) REVERT: d 22 LYS cc_start: 0.8931 (mttt) cc_final: 0.8670 (mttp) REVERT: d 301 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7211 (mm-30) REVERT: e 43 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8825 (tt) REVERT: j 25 SER cc_start: 0.9318 (p) cc_final: 0.9099 (p) REVERT: l 25 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8781 (mp) REVERT: m 5 PHE cc_start: 0.7760 (m-80) cc_final: 0.7220 (p90) REVERT: m 28 GLN cc_start: 0.9056 (pp30) cc_final: 0.8740 (pp30) REVERT: u 79 GLU cc_start: 0.8448 (pm20) cc_final: 0.8140 (pm20) REVERT: v 13 ASP cc_start: 0.7583 (p0) cc_final: 0.7271 (p0) REVERT: v 134 LYS cc_start: 0.9127 (ptpt) cc_final: 0.8680 (ptpp) REVERT: y 1 MET cc_start: 0.6758 (mmm) cc_final: 0.6422 (mtp) REVERT: w 40 LEU cc_start: 0.9196 (mt) cc_final: 0.8983 (mt) REVERT: 12 37 VAL cc_start: 0.8849 (t) cc_final: 0.8622 (m) REVERT: 12 78 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (p) REVERT: 13 123 PHE cc_start: 0.8892 (t80) cc_final: 0.8659 (t80) REVERT: 13 177 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7940 (t0) REVERT: 13 189 TYR cc_start: 0.8424 (t80) cc_final: 0.8149 (t80) REVERT: 14 196 HIS cc_start: 0.6401 (t-90) cc_final: 0.6129 (t70) REVERT: 32 78 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8639 (p) REVERT: 32 90 TYR cc_start: 0.7653 (t80) cc_final: 0.7092 (t80) REVERT: 32 91 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8579 (tp) REVERT: 32 172 MET cc_start: 0.8867 (mmt) cc_final: 0.8573 (mmm) REVERT: 34 90 TYR cc_start: 0.5411 (t80) cc_final: 0.5167 (t80) REVERT: 34 196 HIS cc_start: 0.6479 (t70) cc_final: 0.5850 (t70) outliers start: 150 outliers final: 91 residues processed: 813 average time/residue: 0.6839 time to fit residues: 972.6611 Evaluate side-chains 780 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 679 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 334 ASP Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 286 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain t residue 2 GLU Chi-restraints excluded: chain u residue 16 ILE Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 12 VAL Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 24 ASN Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 11 residue 117 LEU Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 148 THR Chi-restraints excluded: chain 13 residue 174 ILE Chi-restraints excluded: chain 13 residue 177 ASN Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 31 residue 117 LEU Chi-restraints excluded: chain 31 residue 135 SER Chi-restraints excluded: chain 31 residue 138 ASP Chi-restraints excluded: chain 32 residue 78 THR Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 150 ILE Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 186 GLN 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: 0.5980 chunk 379 optimal weight: 2.9990 chunk 486 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 560 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 663 optimal weight: 0.8980 chunk 414 optimal weight: 0.0970 chunk 404 optimal weight: 0.6980 chunk 306 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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** O 197 GLN V 118 HIS ** Q 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 303 ASN b 179 GLN c 413 ASN ** c 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN m 4 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 197 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 177 ASN 13 191 GLN 33 177 ASN 33 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3538 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= 0.155 Angle : 0.586 10.775 101702 Z= 0.261 Chirality : 0.042 0.313 9608 Planarity : 0.004 0.057 12984 Dihedral : 16.493 170.719 14528 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.83 % Allowed : 13.20 % Favored : 84.97 % 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: -0.18 (0.10), residues: 6884 helix: 0.47 (0.09), residues: 3668 sheet: -0.69 (0.36), residues: 220 loop : -0.73 (0.12), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP11 131 HIS 0.016 0.001 HIS C 116 PHE 0.015 0.001 PHE33 123 TYR 0.013 0.001 TYR14 90 ARG 0.011 0.000 ARG34 168 *********************** 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 864 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 761 time to evaluate : 4.900 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: A 288 MET cc_start: 0.7540 (mmm) cc_final: 0.7255 (mmm) REVERT: B 256 MET cc_start: 0.9108 (tpp) cc_final: 0.8441 (tpt) REVERT: B 479 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: D 22 LYS cc_start: 0.8788 (mttt) cc_final: 0.8529 (mttp) REVERT: D 301 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7210 (mm-30) REVERT: E 43 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (tt) REVERT: H 9 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7559 (mm-30) REVERT: I 35 LYS cc_start: 0.6848 (mttp) cc_final: 0.6605 (mtpt) REVERT: J 25 SER cc_start: 0.9325 (p) cc_final: 0.9059 (p) REVERT: L 25 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8756 (mp) REVERT: M 5 PHE cc_start: 0.7686 (m-80) cc_final: 0.7229 (p90) REVERT: M 28 GLN cc_start: 0.8803 (pp30) cc_final: 0.8511 (pp30) REVERT: V 13 ASP cc_start: 0.7468 (p0) cc_final: 0.7096 (p0) REVERT: Q 192 ASN cc_start: 0.7775 (t0) cc_final: 0.7564 (t0) REVERT: W 63 PHE cc_start: 0.8165 (t80) cc_final: 0.7927 (t80) REVERT: a 91 MET cc_start: 0.8710 (mmm) cc_final: 0.8152 (tpp) REVERT: a 288 MET cc_start: 0.7240 (mmm) cc_final: 0.7002 (mmm) REVERT: b 256 MET cc_start: 0.9114 (tpp) cc_final: 0.8441 (tpt) REVERT: b 479 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: c 286 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8977 (mm) REVERT: c 468 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7193 (ttp80) REVERT: d 22 LYS cc_start: 0.8862 (mttt) cc_final: 0.8600 (mttp) REVERT: d 198 MET cc_start: 0.8277 (mtt) cc_final: 0.7925 (mtt) REVERT: d 301 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7213 (mm-30) REVERT: e 43 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8783 (tt) REVERT: j 25 SER cc_start: 0.9296 (p) cc_final: 0.9079 (p) REVERT: l 25 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8727 (mp) REVERT: m 5 PHE cc_start: 0.7753 (m-80) cc_final: 0.7242 (p90) REVERT: m 28 GLN cc_start: 0.8939 (pp30) cc_final: 0.8625 (pp30) REVERT: v 13 ASP cc_start: 0.7598 (p0) cc_final: 0.7277 (p0) REVERT: v 134 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8561 (ptpp) REVERT: w 63 PHE cc_start: 0.8323 (t80) cc_final: 0.8095 (t80) REVERT: 11 154 GLU cc_start: 0.7218 (pp20) cc_final: 0.6996 (pp20) REVERT: 12 35 LEU cc_start: 0.8838 (mt) cc_final: 0.8490 (mt) REVERT: 13 123 PHE cc_start: 0.8854 (t80) cc_final: 0.8645 (t80) REVERT: 13 189 TYR cc_start: 0.8354 (t80) cc_final: 0.8117 (t80) REVERT: 14 196 HIS cc_start: 0.6538 (t-90) cc_final: 0.6237 (t70) REVERT: 31 152 ASP cc_start: 0.7442 (t0) cc_final: 0.7187 (t0) REVERT: 32 78 THR cc_start: 0.8839 (m) cc_final: 0.8584 (p) REVERT: 32 90 TYR cc_start: 0.7718 (t80) cc_final: 0.7178 (t80) REVERT: 32 91 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8193 (tp) REVERT: 32 172 MET cc_start: 0.8862 (mmt) cc_final: 0.8560 (mmm) REVERT: 34 196 HIS cc_start: 0.6452 (t70) cc_final: 0.5786 (t70) outliers start: 103 outliers final: 58 residues processed: 816 average time/residue: 0.6650 time to fit residues: 937.6648 Evaluate side-chains 780 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 714 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 286 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain u residue 16 ILE Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 90 TYR Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 175 MET Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 34 residue 114 THR Chi-restraints excluded: chain 34 residue 186 GLN 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: 4.9990 chunk 396 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 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: 0.5980 chunk 61 optimal weight: 3.9990 chunk 521 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** ** Q 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 303 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** h 47 GLN m 4 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 191 GLN 33 177 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 73032 Z= 0.253 Angle : 0.628 10.101 101702 Z= 0.278 Chirality : 0.044 0.327 9608 Planarity : 0.004 0.056 12984 Dihedral : 16.460 170.274 14528 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.04 % Allowed : 13.18 % Favored : 84.77 % 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: -0.12 (0.10), residues: 6884 helix: 0.52 (0.09), residues: 3656 sheet: -0.60 (0.37), residues: 216 loop : -0.69 (0.12), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP11 131 HIS 0.020 0.002 HIS c 116 PHE 0.017 0.002 PHE b 211 TYR 0.016 0.001 TYR v 136 ARG 0.008 0.000 ARG34 168 *********************** 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 845 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 730 time to evaluate : 4.942 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: B 256 MET cc_start: 0.9116 (tpp) cc_final: 0.8463 (tpt) REVERT: B 479 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: C 286 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9074 (mm) REVERT: D 22 LYS cc_start: 0.8813 (mttt) cc_final: 0.8541 (mttp) REVERT: D 301 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7126 (mm-30) REVERT: E 43 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8740 (tt) REVERT: H 9 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7630 (mm-30) REVERT: J 25 SER cc_start: 0.9271 (p) cc_final: 0.9014 (p) REVERT: L 25 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8889 (mp) REVERT: M 5 PHE cc_start: 0.7703 (m-80) cc_final: 0.7242 (p90) REVERT: M 28 GLN cc_start: 0.8900 (pp30) cc_final: 0.8586 (pp30) REVERT: V 13 ASP cc_start: 0.7438 (p0) cc_final: 0.7105 (p0) REVERT: V 134 LYS cc_start: 0.9141 (ptpp) cc_final: 0.8827 (ptpp) REVERT: b 256 MET cc_start: 0.9124 (tpp) cc_final: 0.8469 (tpt) REVERT: b 479 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: c 286 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9022 (mm) REVERT: d 22 LYS cc_start: 0.8814 (mttt) cc_final: 0.8567 (mttm) REVERT: d 301 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7254 (mm-30) REVERT: e 43 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8742 (tt) REVERT: j 25 SER cc_start: 0.9272 (p) cc_final: 0.9046 (p) REVERT: k 41 ILE cc_start: 0.8774 (tp) cc_final: 0.8554 (tt) REVERT: l 25 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8751 (mp) REVERT: m 5 PHE cc_start: 0.7763 (m-80) cc_final: 0.7195 (p90) REVERT: m 28 GLN cc_start: 0.9058 (pp30) cc_final: 0.8747 (pp30) REVERT: v 13 ASP cc_start: 0.7639 (p0) cc_final: 0.7330 (p0) REVERT: v 134 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8544 (ptpp) REVERT: 11 154 GLU cc_start: 0.7169 (pp20) cc_final: 0.6954 (pp20) REVERT: 12 35 LEU cc_start: 0.8860 (mt) cc_final: 0.8499 (mt) REVERT: 12 37 VAL cc_start: 0.8847 (t) cc_final: 0.8508 (p) REVERT: 12 78 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8596 (p) REVERT: 13 123 PHE cc_start: 0.8894 (t80) cc_final: 0.8689 (t80) REVERT: 13 175 MET cc_start: 0.8395 (mmp) cc_final: 0.8079 (mmp) REVERT: 13 189 TYR cc_start: 0.8376 (t80) cc_final: 0.8121 (t80) REVERT: 14 196 HIS cc_start: 0.6737 (t-90) cc_final: 0.6342 (t70) REVERT: 32 78 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8580 (p) REVERT: 32 90 TYR cc_start: 0.7764 (t80) cc_final: 0.7302 (t80) REVERT: 32 91 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8320 (tp) REVERT: 32 172 MET cc_start: 0.8864 (mmt) cc_final: 0.8559 (mmm) REVERT: 34 196 HIS cc_start: 0.6532 (t70) cc_final: 0.5846 (t70) outliers start: 115 outliers final: 80 residues processed: 793 average time/residue: 0.6506 time to fit residues: 893.5941 Evaluate side-chains 789 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 698 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain a residue 303 ASN Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 334 ASP Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 286 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 106 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain t residue 2 GLU Chi-restraints excluded: chain u residue 16 ILE Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 23 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 12 residue 90 TYR Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 31 residue 135 SER Chi-restraints excluded: chain 31 residue 138 ASP Chi-restraints excluded: chain 32 residue 72 MET Chi-restraints excluded: chain 32 residue 78 THR Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 150 ILE Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 114 THR Chi-restraints excluded: chain 34 residue 186 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 603 optimal weight: 0.0060 chunk 635 optimal weight: 0.6980 chunk 579 optimal weight: 3.9990 chunk 617 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 485 optimal weight: 7.9990 chunk 189 optimal weight: 0.2980 chunk 558 optimal weight: 3.9990 chunk 584 optimal weight: 0.9990 chunk 615 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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** ** Q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 303 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** ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN o 7 ASN o 197 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 191 GLN 33 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3715 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= 0.191 Angle : 0.594 9.529 101702 Z= 0.265 Chirality : 0.042 0.305 9608 Planarity : 0.004 0.055 12984 Dihedral : 16.203 169.979 14528 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.87 % Allowed : 13.43 % Favored : 84.70 % 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: 0.01 (0.10), residues: 6884 helix: 0.64 (0.09), residues: 3672 sheet: -0.60 (0.37), residues: 216 loop : -0.65 (0.12), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP11 131 HIS 0.017 0.001 HIS c 116 PHE 0.020 0.001 PHE a 302 TYR 0.019 0.001 TYR v 136 ARG 0.007 0.000 ARG34 168 *********************** 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 838 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 733 time to evaluate : 4.957 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: B 256 MET cc_start: 0.9123 (tpp) cc_final: 0.8439 (tpt) REVERT: B 479 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: C 286 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8973 (mm) REVERT: D 22 LYS cc_start: 0.8817 (mttt) cc_final: 0.8563 (mttm) REVERT: D 301 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7208 (mm-30) REVERT: E 43 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8713 (tt) REVERT: H 9 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7590 (mm-30) REVERT: J 25 SER cc_start: 0.9209 (p) cc_final: 0.8974 (p) REVERT: L 25 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8854 (mp) REVERT: M 5 PHE cc_start: 0.7714 (m-80) cc_final: 0.7266 (p90) REVERT: M 28 GLN cc_start: 0.8835 (pp30) cc_final: 0.8543 (pp30) REVERT: O 199 ARG cc_start: 0.8220 (tpp-160) cc_final: 0.7800 (tpt170) REVERT: V 5 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7568 (mm-30) REVERT: V 13 ASP cc_start: 0.7363 (p0) cc_final: 0.7085 (p0) REVERT: V 134 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8853 (ptpp) REVERT: b 256 MET cc_start: 0.9128 (tpp) cc_final: 0.8445 (tpt) REVERT: b 479 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: c 286 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8963 (mm) REVERT: d 22 LYS cc_start: 0.8870 (mttt) cc_final: 0.8629 (mttm) REVERT: d 198 MET cc_start: 0.8265 (mtt) cc_final: 0.7958 (mtt) REVERT: d 301 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7270 (mm-30) REVERT: e 43 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8791 (tt) REVERT: j 25 SER cc_start: 0.9245 (p) cc_final: 0.9034 (p) REVERT: k 41 ILE cc_start: 0.8787 (tp) cc_final: 0.8529 (tt) REVERT: l 25 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8711 (mp) REVERT: m 5 PHE cc_start: 0.7773 (m-80) cc_final: 0.7217 (p90) REVERT: m 28 GLN cc_start: 0.9047 (pp30) cc_final: 0.8727 (pp30) REVERT: v 13 ASP cc_start: 0.7659 (p0) cc_final: 0.7334 (p0) REVERT: v 134 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8646 (ptpp) REVERT: 11 140 ASP cc_start: 0.7509 (p0) cc_final: 0.7306 (p0) REVERT: 12 35 LEU cc_start: 0.8814 (mt) cc_final: 0.8463 (mt) REVERT: 12 78 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8616 (p) REVERT: 13 123 PHE cc_start: 0.8883 (t80) cc_final: 0.8680 (t80) REVERT: 13 189 TYR cc_start: 0.8346 (t80) cc_final: 0.8106 (t80) REVERT: 14 196 HIS cc_start: 0.6682 (t-90) cc_final: 0.6401 (t70) REVERT: 32 72 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8444 (mtp) REVERT: 32 78 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8607 (p) REVERT: 32 90 TYR cc_start: 0.7780 (t80) cc_final: 0.7388 (t80) REVERT: 32 172 MET cc_start: 0.8863 (mmt) cc_final: 0.8578 (mmm) REVERT: 34 196 HIS cc_start: 0.6610 (t70) cc_final: 0.5928 (t70) outliers start: 105 outliers final: 73 residues processed: 791 average time/residue: 0.6550 time to fit residues: 893.8077 Evaluate side-chains 788 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 704 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 286 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 281 SER Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 106 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain t residue 26 THR Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 12 VAL Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 23 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain z residue 11 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 24 ASN Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 12 residue 90 TYR Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 32 residue 72 MET Chi-restraints excluded: chain 32 residue 78 THR Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 114 THR Chi-restraints excluded: chain 34 residue 186 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 405 optimal weight: 0.0060 chunk 653 optimal weight: 5.9990 chunk 398 optimal weight: 0.0570 chunk 309 optimal weight: 0.5980 chunk 454 optimal weight: 4.9990 chunk 685 optimal weight: 0.8980 chunk 630 optimal weight: 0.9990 chunk 545 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 421 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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** ** 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** m 4 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 191 GLN ** 33 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 73032 Z= 0.159 Angle : 0.576 10.661 101702 Z= 0.257 Chirality : 0.041 0.282 9608 Planarity : 0.004 0.055 12984 Dihedral : 15.864 168.878 14528 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.56 % Allowed : 13.84 % Favored : 84.59 % 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: 0.15 (0.10), residues: 6884 helix: 0.78 (0.09), residues: 3668 sheet: -0.64 (0.36), residues: 220 loop : -0.62 (0.12), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP31 131 HIS 0.015 0.001 HIS c 116 PHE 0.019 0.001 PHE C 433 TYR 0.019 0.001 TYR v 136 ARG 0.006 0.000 ARG34 168 ********************** 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 826 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 738 time to evaluate : 5.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7587 (mmp) cc_final: 0.7355 (mmm) REVERT: B 256 MET cc_start: 0.9134 (tpp) cc_final: 0.8426 (tpt) REVERT: B 479 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: C 286 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8857 (mm) REVERT: D 22 LYS cc_start: 0.8754 (mttt) cc_final: 0.8492 (mttp) REVERT: D 293 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7593 (ptt90) REVERT: D 301 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7160 (mm-30) REVERT: E 43 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8711 (tt) REVERT: H 9 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7627 (mm-30) REVERT: J 25 SER cc_start: 0.9201 (p) cc_final: 0.8980 (p) REVERT: L 25 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8888 (mp) REVERT: M 5 PHE cc_start: 0.7722 (m-80) cc_final: 0.7223 (p90) REVERT: M 28 GLN cc_start: 0.8782 (pp30) cc_final: 0.8471 (pp30) REVERT: O 199 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7768 (tpt170) REVERT: V 5 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7527 (mm-30) REVERT: V 13 ASP cc_start: 0.7361 (p0) cc_final: 0.7114 (p0) REVERT: V 134 LYS cc_start: 0.9077 (ptpp) cc_final: 0.8690 (ptpp) REVERT: b 256 MET cc_start: 0.9141 (tpp) cc_final: 0.8434 (tpt) REVERT: b 479 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: c 286 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8861 (mm) REVERT: d 22 LYS cc_start: 0.8746 (mttt) cc_final: 0.8517 (mttm) REVERT: d 293 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7641 (ptt90) REVERT: d 301 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7080 (mm-30) REVERT: e 43 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8756 (tt) REVERT: l 25 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8742 (mp) REVERT: m 5 PHE cc_start: 0.7754 (m-80) cc_final: 0.7220 (p90) REVERT: m 28 GLN cc_start: 0.9008 (pp30) cc_final: 0.8679 (pp30) REVERT: v 5 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7458 (mm-30) REVERT: v 13 ASP cc_start: 0.7624 (p0) cc_final: 0.7293 (p0) REVERT: v 134 LYS cc_start: 0.8941 (ptpt) cc_final: 0.8688 (ptpp) REVERT: y 17 MET cc_start: 0.6906 (ttp) cc_final: 0.6651 (ttp) REVERT: w 63 PHE cc_start: 0.8219 (t80) cc_final: 0.7982 (t80) REVERT: 12 35 LEU cc_start: 0.8771 (mt) cc_final: 0.8466 (mt) REVERT: 12 78 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8536 (p) REVERT: 13 189 TYR cc_start: 0.8334 (t80) cc_final: 0.8123 (t80) REVERT: 14 196 HIS cc_start: 0.6669 (t-90) cc_final: 0.6412 (t70) REVERT: 32 72 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8457 (mtp) REVERT: 32 90 TYR cc_start: 0.7786 (t80) cc_final: 0.7403 (t80) REVERT: 32 172 MET cc_start: 0.8876 (mmt) cc_final: 0.8603 (mmm) REVERT: 33 72 MET cc_start: 0.8455 (mtm) cc_final: 0.8083 (mtm) REVERT: 34 196 HIS cc_start: 0.6693 (t70) cc_final: 0.6026 (t70) outliers start: 88 outliers final: 68 residues processed: 784 average time/residue: 0.6441 time to fit residues: 872.3485 Evaluate side-chains 791 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 711 time to evaluate : 5.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 26 THR Chi-restraints excluded: chain U residue 14 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 286 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 281 SER Chi-restraints excluded: chain d residue 293 ARG Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 106 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain u residue 28 ASN Chi-restraints excluded: chain u residue 90 ASP Chi-restraints excluded: chain v residue 12 VAL Chi-restraints excluded: chain v residue 17 ASN Chi-restraints excluded: chain v residue 55 ASP Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 23 VAL Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 161 THR Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 59 ASP Chi-restraints excluded: chain w residue 67 ASP Chi-restraints excluded: chain 11 residue 101 ASP Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 78 THR Chi-restraints excluded: chain 12 residue 90 TYR Chi-restraints excluded: chain 12 residue 95 ASN Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 31 residue 101 ASP Chi-restraints excluded: chain 32 residue 72 MET Chi-restraints excluded: chain 32 residue 138 ASP Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 114 THR Chi-restraints excluded: chain 34 residue 186 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 433 optimal weight: 0.8980 chunk 581 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 503 optimal weight: 0.0010 chunk 80 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 546 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 561 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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** O 197 GLN ** Q 192 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** ** h 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN o 197 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 191 GLN 33 96 ASN 33 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084662 restraints weight = 144214.608| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.10 r_work: 0.2976 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 73032 Z= 0.175 Angle : 0.580 10.657 101702 Z= 0.259 Chirality : 0.042 0.294 9608 Planarity : 0.004 0.053 12984 Dihedral : 15.732 166.467 14528 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.65 % Allowed : 13.98 % Favored : 84.36 % 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: 0.20 (0.10), residues: 6884 helix: 0.83 (0.09), residues: 3672 sheet: -0.52 (0.36), residues: 220 loop : -0.61 (0.12), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP31 131 HIS 0.016 0.001 HIS C 116 PHE 0.040 0.001 PHE13 123 TYR 0.020 0.001 TYR v 136 ARG 0.006 0.000 ARG34 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16735.00 seconds wall clock time: 294 minutes 44.42 seconds (17684.42 seconds total)