Starting phenix.real_space_refine on Sun Sep 29 06:38:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/09_2024/6j3y_9775.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/09_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_9775/09_2024/6j3y_9775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/09_2024/6j3y_9775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/09_2024/6j3y_9775.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3y_9775/09_2024/6j3y_9775.cif" } 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. Time to flip 68 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 31.51, per 1000 atoms: 0.45 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 - 3.00 Amino acid : True - 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: 13.93 Conformation dependent library (CDL) restraints added in 5.7 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... Secondary structure from input PDB file: 290 helices and 27 sheets defined 58.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.893A pdb=" N TRP A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.831A pdb=" N ILE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.581A pdb=" N ASN A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 4.512A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) 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 142 through 147 removed outlier: 3.780A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.552A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.636A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 222 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) removed outlier: 3.623A pdb=" N SER A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.597A pdb=" N TYR A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 267 through 291 removed outlier: 4.220A pdb=" N ALA A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 330 Processing helix chain 'B' and resid 4 through 13 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) removed outlier: 3.982A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 13 " --> pdb=" O THR B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 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 62 through 67 Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 157 removed outlier: 3.544A pdb=" N SER B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.618A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) 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 222 through 229 Processing helix chain 'B' and resid 234 through 258 removed outlier: 3.507A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) 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 272 through 277 removed outlier: 3.571A pdb=" N SER B 277 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.935A pdb=" N SER B 291 " --> pdb=" O GLN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.511A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Proline residue: B 319 - end of helix removed outlier: 3.949A pdb=" N GLY B 322 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.997A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 403 through 407 removed outlier: 4.031A pdb=" N LEU B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 413 through 423 removed outlier: 3.757A pdb=" N LYS B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 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 479 removed outlier: 3.851A pdb=" N PHE B 479 " --> pdb=" O ARG B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.636A pdb=" N ILE C 41 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 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 88 through 94 removed outlier: 3.500A pdb=" N THR C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 131 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) removed outlier: 3.664A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 179 removed outlier: 3.721A pdb=" N THR C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) 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 203 through 212 removed outlier: 4.096A pdb=" N VAL C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 252 removed outlier: 3.846A pdb=" N TRP C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 262 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) removed outlier: 3.815A pdb=" N PHE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 291 removed outlier: 3.716A pdb=" N TYR C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) 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 296 through 301 Processing helix chain 'C' and resid 303 through 321 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 351 through 355 removed outlier: 3.638A pdb=" N MET C 354 " --> pdb=" O GLY C 351 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 355 " --> pdb=" O GLU C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 355' Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 374 through 381 Processing helix chain 'C' and resid 383 through 396 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 419 through 425 Processing helix chain 'C' and resid 427 through 452 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 12 through 22 removed outlier: 3.519A pdb=" N LEU D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 53 Proline residue: D 38 - end of helix removed outlier: 3.610A pdb=" N TYR D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 42 " --> pdb=" O PRO D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 107 through 136 removed outlier: 4.128A pdb=" N THR D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.601A pdb=" N ILE D 143 " --> pdb=" O PRO D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 157 removed outlier: 3.592A pdb=" N SER D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 163 removed outlier: 3.724A pdb=" N GLY D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.744A pdb=" N PHE D 168 " --> pdb=" O SER D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 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 189 through 192 Processing helix chain 'D' and resid 193 through 218 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 244 through 256 removed outlier: 3.772A pdb=" N GLN D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 287 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 297 through 307 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 328 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) removed outlier: 3.677A pdb=" N MET D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.626A pdb=" N GLN D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.566A pdb=" N ILE E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 15 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 10 through 16' Processing helix chain 'E' and resid 17 through 41 removed outlier: 3.742A pdb=" N TRP E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) 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 43 through 48 removed outlier: 3.615A pdb=" N PHE E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'F' and resid 17 through 36 removed outlier: 3.722A pdb=" N HIS F 22 " --> pdb=" O TRP F 18 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 26 " --> pdb=" O HIS F 22 " (cutoff:3.500A) Proline residue: F 27 - end of helix Processing helix chain 'H' and resid 5 through 16 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 27 through 50 removed outlier: 3.591A pdb=" N ILE H 33 " --> pdb=" O PRO H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 removed outlier: 3.551A pdb=" N LEU I 7 " --> pdb=" O THR I 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 23 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'J' and resid 8 through 30 removed outlier: 3.508A pdb=" N VAL J 12 " --> pdb=" O PRO J 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.770A pdb=" N VAL K 14 " --> pdb=" O GLU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 23 removed outlier: 3.716A pdb=" N ASP K 21 " --> pdb=" O SER K 17 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL K 22 " --> pdb=" O PRO K 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 41 removed outlier: 3.579A pdb=" N PHE K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 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 6 through 38 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) removed outlier: 4.082A pdb=" N GLY M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 4.017A pdb=" N LEU O 9 " --> pdb=" O GLN O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 15 removed outlier: 3.659A pdb=" N VAL O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 189 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 2 through 23 removed outlier: 3.908A pdb=" N TYR T 6 " --> pdb=" O GLU T 2 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL T 16 " --> pdb=" O GLY T 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 38 removed outlier: 3.685A pdb=" N LYS U 37 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET U 38 " --> pdb=" O TYR U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 52 removed outlier: 3.512A pdb=" N ILE U 49 " --> pdb=" O VAL U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 removed outlier: 3.688A pdb=" N ILE U 64 " --> pdb=" O LEU U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 78 removed outlier: 3.569A pdb=" N VAL U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE U 75 " --> pdb=" O GLU U 71 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR U 78 " --> pdb=" O VAL U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 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 41 through 45 removed outlier: 3.728A pdb=" N GLY V 44 " --> pdb=" O HIS V 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE V 45 " --> pdb=" O VAL V 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 41 through 45' Processing helix chain 'V' and resid 55 through 61 Processing helix chain 'V' and resid 68 through 78 Processing helix chain 'V' and resid 101 through 105 removed outlier: 3.656A pdb=" N MET V 104 " --> pdb=" O TYR V 101 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG V 105 " --> pdb=" O PRO V 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 101 through 105' Processing helix chain 'V' and resid 108 through 126 Proline residue: V 123 - end of helix Processing helix chain 'Y' and resid 3 through 17 Processing helix chain 'Y' and resid 20 through 31 removed outlier: 3.756A pdb=" N ILE Y 24 " --> pdb=" O GLY Y 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 33 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 26 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 removed outlier: 3.554A pdb=" N THR Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 33 Processing helix chain 'Z' and resid 34 through 58 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 105 through 124 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 125 through 132 removed outlier: 3.941A pdb=" N TYR Q 129 " --> pdb=" O LYS Q 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Q 130 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 145 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) removed outlier: 4.067A pdb=" N TYR Q 145 " --> pdb=" O GLU Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 148 through 157 removed outlier: 3.651A pdb=" N ALA Q 152 " --> pdb=" O GLU Q 148 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER Q 155 " --> pdb=" O GLY Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 181 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 184 through 206 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 25 through 29 Processing helix chain 'W' and resid 32 through 50 removed outlier: 4.219A pdb=" N ALA W 36 " --> pdb=" O LEU W 32 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA W 44 " --> pdb=" O LEU W 40 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE W 45 " --> pdb=" O GLY W 41 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 25 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 6 through 28 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 14 through 22 removed outlier: 3.893A pdb=" N TRP a 20 " --> pdb=" O ARG a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 54 removed outlier: 3.832A pdb=" N ILE a 50 " --> pdb=" O SER a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 108 removed outlier: 3.581A pdb=" N ASN a 108 " --> pdb=" O GLU a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 137 removed outlier: 4.512A pdb=" N GLN a 113 " --> pdb=" O GLY a 109 " (cutoff:3.500A) 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 142 through 147 removed outlier: 3.780A pdb=" N ALA a 146 " --> pdb=" O TRP a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 159 removed outlier: 3.552A pdb=" N VAL a 157 " --> pdb=" O ALA a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 159 through 165 Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 176 through 191 removed outlier: 3.636A pdb=" N PHE a 180 " --> pdb=" O ILE a 176 " (cutoff:3.500A) Processing helix chain 'a' and resid 198 through 222 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) removed outlier: 3.623A pdb=" N SER a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 232 through 237 removed outlier: 3.598A pdb=" N TYR a 235 " --> pdb=" O SER a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 247 through 259 Processing helix chain 'a' and resid 267 through 291 removed outlier: 4.219A pdb=" N ALA a 276 " --> pdb=" O HIS a 272 " (cutoff:3.500A) Proline residue: a 279 - end of helix Processing helix chain 'a' and resid 316 through 330 Processing helix chain 'b' and resid 4 through 13 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) removed outlier: 3.982A pdb=" N VAL b 11 " --> pdb=" O VAL b 8 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL b 12 " --> pdb=" O HIS b 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU b 13 " --> pdb=" O THR b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 45 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 62 through 67 Processing helix chain 'b' and resid 92 through 117 Processing helix chain 'b' and resid 120 through 124 Processing helix chain 'b' and resid 134 through 157 removed outlier: 3.545A pdb=" N SER b 146 " --> pdb=" O HIS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 191 Processing helix chain 'b' and resid 195 through 219 removed outlier: 3.618A pdb=" N ALA b 199 " --> pdb=" O PRO b 195 " (cutoff:3.500A) 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 222 through 229 Processing helix chain 'b' and resid 234 through 258 removed outlier: 3.508A pdb=" N LEU b 238 " --> pdb=" O ILE b 234 " (cutoff:3.500A) 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 272 through 277 removed outlier: 3.572A pdb=" N SER b 277 " --> pdb=" O TYR b 273 " (cutoff:3.500A) Processing helix chain 'b' and resid 280 through 294 removed outlier: 3.935A pdb=" N SER b 291 " --> pdb=" O GLN b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 303 Processing helix chain 'b' and resid 306 through 313 removed outlier: 3.511A pdb=" N ALA b 310 " --> pdb=" O PRO b 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP b 313 " --> pdb=" O LEU b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 314 through 322 Proline residue: b 319 - end of helix removed outlier: 3.949A pdb=" N GLY b 322 " --> pdb=" O PRO b 319 " (cutoff:3.500A) Processing helix chain 'b' and resid 330 through 335 removed outlier: 3.996A pdb=" N ASP b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 391 through 396 Processing helix chain 'b' and resid 403 through 407 removed outlier: 4.031A pdb=" N LEU b 406 " --> pdb=" O GLY b 403 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN b 407 " --> pdb=" O GLY b 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 403 through 407' Processing helix chain 'b' and resid 413 through 423 removed outlier: 3.757A pdb=" N LYS b 419 " --> pdb=" O PRO b 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS b 423 " --> pdb=" O LYS b 419 " (cutoff:3.500A) Processing helix chain 'b' and resid 446 through 475 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 479 removed outlier: 3.851A pdb=" N PHE b 479 " --> pdb=" O ARG b 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 476 through 479' Processing helix chain 'c' and resid 36 through 41 removed outlier: 3.636A pdb=" N ILE c 41 " --> pdb=" O ALA c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 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 88 through 94 removed outlier: 3.501A pdb=" N THR c 92 " --> pdb=" O GLN c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 131 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) removed outlier: 3.663A pdb=" N SER c 131 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 152 through 179 removed outlier: 3.721A pdb=" N THR c 156 " --> pdb=" O LYS c 152 " (cutoff:3.500A) 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 203 through 212 removed outlier: 4.095A pdb=" N VAL c 211 " --> pdb=" O ILE c 207 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE c 212 " --> pdb=" O PHE c 208 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 252 removed outlier: 3.846A pdb=" N TRP c 237 " --> pdb=" O GLY c 233 " (cutoff:3.500A) Processing helix chain 'c' and resid 255 through 262 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) removed outlier: 3.814A pdb=" N PHE c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 265 through 291 removed outlier: 3.717A pdb=" N TYR c 269 " --> pdb=" O SER c 265 " (cutoff:3.500A) 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 296 through 301 Processing helix chain 'c' and resid 303 through 321 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 351 through 355 removed outlier: 3.638A pdb=" N MET c 354 " --> pdb=" O GLY c 351 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG c 355 " --> pdb=" O GLU c 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 351 through 355' Processing helix chain 'c' and resid 364 through 368 Processing helix chain 'c' and resid 374 through 381 Processing helix chain 'c' and resid 383 through 396 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 419 through 425 Processing helix chain 'c' and resid 427 through 452 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 12 through 22 removed outlier: 3.520A pdb=" N LEU d 16 " --> pdb=" O GLY d 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS d 22 " --> pdb=" O ASP d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 53 Proline residue: d 38 - end of helix removed outlier: 3.609A pdb=" N TYR d 41 " --> pdb=" O PHE d 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU d 42 " --> pdb=" O PRO d 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 107 Processing helix chain 'd' and resid 107 through 136 removed outlier: 4.128A pdb=" N THR d 111 " --> pdb=" O GLY d 107 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA d 132 " --> pdb=" O GLN d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 145 removed outlier: 3.600A pdb=" N ILE d 143 " --> pdb=" O PRO d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 157 removed outlier: 3.592A pdb=" N SER d 154 " --> pdb=" O ALA d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 163 removed outlier: 3.723A pdb=" N GLY d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 169 removed outlier: 3.743A pdb=" N PHE d 168 " --> pdb=" O SER d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 187 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 189 through 192 Processing helix chain 'd' and resid 193 through 218 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 244 through 256 removed outlier: 3.771A pdb=" N GLN d 254 " --> pdb=" O ARG d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 287 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 297 through 307 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 328 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) removed outlier: 3.678A pdb=" N MET d 328 " --> pdb=" O ILE d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 328 through 333 removed outlier: 3.627A pdb=" N GLN d 333 " --> pdb=" O ALA d 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 removed outlier: 3.566A pdb=" N ILE e 14 " --> pdb=" O PRO e 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE e 15 " --> pdb=" O PHE e 11 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR e 16 " --> pdb=" O SER e 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 10 through 16' Processing helix chain 'e' and resid 17 through 41 removed outlier: 3.742A pdb=" N TRP e 21 " --> pdb=" O SER e 17 " (cutoff:3.500A) 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 43 through 48 removed outlier: 3.614A pdb=" N PHE e 48 " --> pdb=" O ALA e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 81 Processing helix chain 'f' and resid 17 through 36 removed outlier: 3.722A pdb=" N HIS f 22 " --> pdb=" O TRP f 18 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY f 23 " --> pdb=" O LEU f 19 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE f 26 " --> pdb=" O HIS f 22 " (cutoff:3.500A) Proline residue: f 27 - end of helix Processing helix chain 'h' and resid 5 through 16 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 27 through 50 removed outlier: 3.591A pdb=" N ILE h 33 " --> pdb=" O PRO h 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 24 removed outlier: 3.551A pdb=" N LEU i 7 " --> pdb=" O THR i 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE i 23 " --> pdb=" O PHE i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 30 Processing helix chain 'j' and resid 8 through 30 removed outlier: 3.508A pdb=" N VAL j 12 " --> pdb=" O PRO j 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU j 26 " --> pdb=" O THR j 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 14 removed outlier: 3.770A pdb=" N VAL k 14 " --> pdb=" O GLU k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 23 removed outlier: 3.715A pdb=" N ASP k 21 " --> pdb=" O SER k 17 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL k 22 " --> pdb=" O PRO k 18 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU k 23 " --> pdb=" O ILE k 19 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 41 removed outlier: 3.580A pdb=" N PHE k 29 " --> pdb=" O ILE k 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU k 31 " --> pdb=" O PRO k 27 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE k 35 " --> pdb=" O LEU k 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 38 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 6 through 38 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) removed outlier: 4.082A pdb=" N GLY m 38 " --> pdb=" O ALA m 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 9 removed outlier: 4.018A pdb=" N LEU o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 15 removed outlier: 3.658A pdb=" N VAL o 14 " --> pdb=" O SER o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 182 through 189 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 2 through 23 removed outlier: 3.907A pdb=" N TYR t 6 " --> pdb=" O GLU t 2 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL t 16 " --> pdb=" O GLY t 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 38 removed outlier: 3.685A pdb=" N LYS u 37 " --> pdb=" O ALA u 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET u 38 " --> pdb=" O TYR u 35 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 52 removed outlier: 3.512A pdb=" N ILE u 49 " --> pdb=" O VAL u 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 64 removed outlier: 3.688A pdb=" N ILE u 64 " --> pdb=" O LEU u 61 " (cutoff:3.500A) Processing helix chain 'u' and resid 70 through 78 removed outlier: 3.569A pdb=" N VAL u 74 " --> pdb=" O ALA u 70 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE u 75 " --> pdb=" O GLU u 71 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR u 78 " --> pdb=" O VAL u 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 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 41 through 45 removed outlier: 3.728A pdb=" N GLY v 44 " --> pdb=" O HIS v 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE v 45 " --> pdb=" O VAL v 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 41 through 45' Processing helix chain 'v' and resid 55 through 61 Processing helix chain 'v' and resid 68 through 78 Processing helix chain 'v' and resid 101 through 105 removed outlier: 3.654A pdb=" N MET v 104 " --> pdb=" O TYR v 101 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG v 105 " --> pdb=" O PRO v 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 101 through 105' Processing helix chain 'v' and resid 108 through 126 Proline residue: v 123 - end of helix Processing helix chain 'y' and resid 3 through 17 Processing helix chain 'y' and resid 20 through 31 removed outlier: 3.756A pdb=" N ILE y 24 " --> pdb=" O GLY y 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 33 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 26 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 removed outlier: 3.554A pdb=" N THR z 26 " --> pdb=" O VAL z 22 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 33 Processing helix chain 'z' and resid 34 through 58 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 105 through 124 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 125 through 132 removed outlier: 3.941A pdb=" N TYR q 129 " --> pdb=" O LYS q 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL q 130 " --> pdb=" O ILE q 126 " (cutoff:3.500A) Processing helix chain 'q' and resid 135 through 145 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) removed outlier: 4.067A pdb=" N TYR q 145 " --> pdb=" O GLU q 141 " (cutoff:3.500A) Processing helix chain 'q' and resid 148 through 157 removed outlier: 3.651A pdb=" N ALA q 152 " --> pdb=" O GLU q 148 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER q 155 " --> pdb=" O GLY q 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 159 through 181 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 184 through 206 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 25 through 29 Processing helix chain 'w' and resid 32 through 50 removed outlier: 4.219A pdb=" N ALA w 36 " --> pdb=" O LEU w 32 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL w 37 " --> pdb=" O ARG w 33 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA w 44 " --> pdb=" O LEU w 40 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE w 45 " --> pdb=" O GLY w 41 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU w 48 " --> pdb=" O ALA w 44 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 25 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 6 through 28 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 32 through 36 removed outlier: 3.524A pdb=" N LEU11 35 " --> pdb=" O GLU11 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY11 36 " --> pdb=" O ILE11 33 " (cutoff:3.500A) No H-bonds generated for 'chain '11' and resid 32 through 36' Processing helix chain '11' and resid 48 through 53 Processing helix chain '11' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA11 62 " --> pdb=" O GLU11 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS11 66 " --> pdb=" O ALA11 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL11 76 " --> pdb=" O MET11 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY11 77 " --> pdb=" O ALA11 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS11 81 " --> pdb=" O GLY11 77 " (cutoff:3.500A) Processing helix chain '11' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY11 108 " --> pdb=" O GLY11 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU11 126 " --> pdb=" O ALA11 122 " (cutoff:3.500A) Processing helix chain '11' and resid 144 through 148 removed outlier: 3.680A pdb=" N THR11 148 " --> pdb=" O TYR11 145 " (cutoff:3.500A) Processing helix chain '11' and resid 152 through 181 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 187 through 195 Processing helix chain '12' and resid 32 through 36 removed outlier: 3.523A pdb=" N LEU12 35 " --> pdb=" O GLU12 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY12 36 " --> pdb=" O ILE12 33 " (cutoff:3.500A) No H-bonds generated for 'chain '12' and resid 32 through 36' Processing helix chain '12' and resid 48 through 53 Processing helix chain '12' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA12 62 " --> pdb=" O GLU12 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS12 66 " --> pdb=" O ALA12 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL12 76 " --> pdb=" O MET12 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY12 77 " --> pdb=" O ALA12 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS12 81 " --> pdb=" O GLY12 77 " (cutoff:3.500A) Processing helix chain '12' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY12 108 " --> pdb=" O GLY12 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU12 126 " --> pdb=" O ALA12 122 " (cutoff:3.500A) Processing helix chain '12' and resid 144 through 148 removed outlier: 3.681A pdb=" N THR12 148 " --> pdb=" O TYR12 145 " (cutoff:3.500A) Processing helix chain '12' and resid 152 through 181 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 187 through 195 Processing helix chain '13' and resid 32 through 36 removed outlier: 3.524A pdb=" N LEU13 35 " --> pdb=" O GLU13 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY13 36 " --> pdb=" O ILE13 33 " (cutoff:3.500A) No H-bonds generated for 'chain '13' and resid 32 through 36' Processing helix chain '13' and resid 48 through 53 Processing helix chain '13' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA13 62 " --> pdb=" O GLU13 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS13 66 " --> pdb=" O ALA13 62 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL13 76 " --> pdb=" O MET13 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY13 77 " --> pdb=" O ALA13 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS13 81 " --> pdb=" O GLY13 77 " (cutoff:3.500A) Processing helix chain '13' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY13 108 " --> pdb=" O GLY13 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU13 126 " --> pdb=" O ALA13 122 " (cutoff:3.500A) Processing helix chain '13' and resid 144 through 148 removed outlier: 3.681A pdb=" N THR13 148 " --> pdb=" O TYR13 145 " (cutoff:3.500A) Processing helix chain '13' and resid 152 through 181 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 187 through 195 Processing helix chain '14' and resid 32 through 36 removed outlier: 3.524A pdb=" N LEU14 35 " --> pdb=" O GLU14 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY14 36 " --> pdb=" O ILE14 33 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 32 through 36' Processing helix chain '14' and resid 48 through 53 Processing helix chain '14' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA14 62 " --> pdb=" O GLU14 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS14 66 " --> pdb=" O ALA14 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL14 76 " --> pdb=" O MET14 72 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY14 77 " --> pdb=" O ALA14 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS14 81 " --> pdb=" O GLY14 77 " (cutoff:3.500A) Processing helix chain '14' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY14 108 " --> pdb=" O GLY14 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.722A pdb=" N LEU14 126 " --> pdb=" O ALA14 122 " (cutoff:3.500A) Processing helix chain '14' and resid 144 through 148 removed outlier: 3.680A pdb=" N THR14 148 " --> pdb=" O TYR14 145 " (cutoff:3.500A) Processing helix chain '14' and resid 152 through 181 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 187 through 195 Processing helix chain '31' and resid 32 through 36 removed outlier: 3.524A pdb=" N LEU31 35 " --> pdb=" O GLU31 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY31 36 " --> pdb=" O ILE31 33 " (cutoff:3.500A) No H-bonds generated for 'chain '31' and resid 32 through 36' Processing helix chain '31' and resid 48 through 53 Processing helix chain '31' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA31 62 " --> pdb=" O GLU31 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS31 66 " --> pdb=" O ALA31 62 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL31 76 " --> pdb=" O MET31 72 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY31 77 " --> pdb=" O ALA31 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS31 81 " --> pdb=" O GLY31 77 " (cutoff:3.500A) Processing helix chain '31' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY31 108 " --> pdb=" O GLY31 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU31 126 " --> pdb=" O ALA31 122 " (cutoff:3.500A) Processing helix chain '31' and resid 144 through 148 removed outlier: 3.681A pdb=" N THR31 148 " --> pdb=" O TYR31 145 " (cutoff:3.500A) Processing helix chain '31' and resid 152 through 181 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 187 through 195 Processing helix chain '32' and resid 32 through 36 removed outlier: 3.524A pdb=" N LEU32 35 " --> pdb=" O GLU32 32 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY32 36 " --> pdb=" O ILE32 33 " (cutoff:3.500A) No H-bonds generated for 'chain '32' and resid 32 through 36' Processing helix chain '32' and resid 48 through 53 Processing helix chain '32' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA32 62 " --> pdb=" O GLU32 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS32 66 " --> pdb=" O ALA32 62 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL32 76 " --> pdb=" O MET32 72 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY32 77 " --> pdb=" O ALA32 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS32 81 " --> pdb=" O GLY32 77 " (cutoff:3.500A) Processing helix chain '32' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY32 108 " --> pdb=" O GLY32 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU32 126 " --> pdb=" O ALA32 122 " (cutoff:3.500A) Processing helix chain '32' and resid 144 through 148 removed outlier: 3.680A pdb=" N THR32 148 " --> pdb=" O TYR32 145 " (cutoff:3.500A) Processing helix chain '32' and resid 152 through 181 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 187 through 195 Processing helix chain '33' and resid 32 through 36 removed outlier: 3.523A pdb=" N LEU33 35 " --> pdb=" O GLU33 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY33 36 " --> pdb=" O ILE33 33 " (cutoff:3.500A) No H-bonds generated for 'chain '33' and resid 32 through 36' Processing helix chain '33' and resid 48 through 53 Processing helix chain '33' and resid 56 through 83 removed outlier: 3.722A pdb=" N ALA33 62 " --> pdb=" O GLU33 58 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS33 66 " --> pdb=" O ALA33 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL33 76 " --> pdb=" O MET33 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY33 77 " --> pdb=" O ALA33 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS33 81 " --> pdb=" O GLY33 77 " (cutoff:3.500A) Processing helix chain '33' and resid 105 through 112 removed outlier: 3.862A pdb=" N GLY33 108 " --> pdb=" O GLY33 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU33 126 " --> pdb=" O ALA33 122 " (cutoff:3.500A) Processing helix chain '33' and resid 144 through 148 removed outlier: 3.682A pdb=" N THR33 148 " --> pdb=" O TYR33 145 " (cutoff:3.500A) Processing helix chain '33' and resid 152 through 181 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 187 through 195 Processing helix chain '34' and resid 32 through 36 removed outlier: 3.523A pdb=" N LEU34 35 " --> pdb=" O GLU34 32 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY34 36 " --> pdb=" O ILE34 33 " (cutoff:3.500A) No H-bonds generated for 'chain '34' and resid 32 through 36' Processing helix chain '34' and resid 48 through 53 Processing helix chain '34' and resid 56 through 83 removed outlier: 3.721A pdb=" N ALA34 62 " --> pdb=" O GLU34 58 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS34 66 " --> pdb=" O ALA34 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL34 76 " --> pdb=" O MET34 72 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY34 77 " --> pdb=" O ALA34 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS34 81 " --> pdb=" O GLY34 77 " (cutoff:3.500A) Processing helix chain '34' and resid 105 through 112 removed outlier: 3.863A pdb=" N GLY34 108 " --> pdb=" O GLY34 105 " (cutoff:3.500A) 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 113 through 130 removed outlier: 3.723A pdb=" N LEU34 126 " --> pdb=" O ALA34 122 " (cutoff:3.500A) Processing helix chain '34' and resid 144 through 148 removed outlier: 3.682A pdb=" N THR34 148 " --> pdb=" O TYR34 145 " (cutoff:3.500A) Processing helix chain '34' and resid 152 through 181 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 187 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.835A pdb=" N GLY C 400 " --> pdb=" O ASN A 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 307 removed outlier: 4.392A pdb=" N VAL A 306 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'B' and resid 336 through 342 removed outlier: 6.807A pdb=" N GLU B 431 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 340 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL B 429 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.727A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 77 Processing sheet with id=AB2, first strand: chain 'O' and resid 64 through 68 removed outlier: 4.309A pdb=" N ASP O 42 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE O 82 " --> pdb=" O ASP O 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS O 44 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP O 80 " --> pdb=" O CYS O 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 64 through 68 removed outlier: 5.698A pdb=" N MET O 43 " --> pdb=" O LYS O 245 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS O 245 " --> pdb=" O MET O 43 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE O 45 " --> pdb=" O TYR O 243 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR O 243 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE O 241 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS O 235 " --> pdb=" O GLU O 53 " (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: 6.865A pdb=" N GLU O 213 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL O 207 " --> pdb=" O GLU O 213 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY O 215 " --> pdb=" O ASN O 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN O 205 " --> pdb=" O GLY O 215 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU O 223 " --> pdb=" O GLN O 197 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN O 197 " --> pdb=" O LEU O 223 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP O 143 " --> pdb=" O VAL O 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'V' and resid 9 through 11 Processing sheet with id=AB6, first strand: chain 'a' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'a' and resid 81 through 82 Processing sheet with id=AB8, first strand: chain 'a' and resid 306 through 307 removed outlier: 4.391A pdb=" N VAL a 306 " --> pdb=" O ILE a 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 166 through 169 Processing sheet with id=AC1, first strand: chain 'b' and resid 336 through 342 removed outlier: 6.809A pdb=" N GLU b 431 " --> pdb=" O GLU b 338 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TRP b 340 " --> pdb=" O VAL b 429 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL b 429 " --> pdb=" O TRP b 340 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 377 through 380 removed outlier: 3.726A pdb=" N PHE b 346 " --> pdb=" O LEU b 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 183 through 185 Processing sheet with id=AC4, first strand: chain 'c' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'd' and resid 76 through 77 Processing sheet with id=AC6, first strand: chain 'o' and resid 64 through 68 removed outlier: 4.310A pdb=" N ASP o 42 " --> pdb=" O ILE o 82 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE o 82 " --> pdb=" O ASP o 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS o 44 " --> pdb=" O ASP o 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP o 80 " --> pdb=" O CYS o 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'o' and resid 64 through 68 removed outlier: 5.698A pdb=" N MET o 43 " --> pdb=" O LYS o 245 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS o 245 " --> pdb=" O MET o 43 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE o 45 " --> pdb=" O TYR o 243 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR o 243 " --> pdb=" O ILE o 45 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE o 241 " --> pdb=" O PRO o 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS o 235 " --> pdb=" O GLU o 53 " (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: 6.864A pdb=" N GLU o 213 " --> pdb=" O VAL o 207 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL o 207 " --> pdb=" O GLU o 213 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY o 215 " --> pdb=" O ASN o 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN o 205 " --> pdb=" O GLY o 215 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU o 223 " --> pdb=" O GLN o 197 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLN o 197 " --> pdb=" O LEU o 223 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP o 143 " --> pdb=" O VAL o 126 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'o' and resid 70 through 71 Processing sheet with id=AC9, first strand: chain 'v' and resid 9 through 11 2546 hydrogen bonds defined for protein. 7302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.25 Time building geometry restraints manager: 16.37 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: 0.00 - 7.81: 100971 7.81 - 15.63: 677 15.63 - 23.44: 6 23.44 - 31.25: 0 31.25 - 39.06: 48 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: 36295 26.68 - 53.36: 2278 53.36 - 80.04: 515 80.04 - 106.72: 210 106.72 - 133.40: 88 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: 12972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 403 " -0.071 2.00e-02 2.50e+03 1.01e-01 8.18e+02 pdb=" ND PHO D 403 " -0.147 2.00e-02 2.50e+03 pdb=" C1A PHO D 403 " -0.020 2.00e-02 2.50e+03 pdb=" C1B PHO D 403 " -0.003 2.00e-02 2.50e+03 pdb=" C1C PHO D 403 " -0.034 2.00e-02 2.50e+03 pdb=" C1D PHO D 403 " -0.077 2.00e-02 2.50e+03 pdb=" C2A PHO D 403 " 0.086 2.00e-02 2.50e+03 pdb=" C2B PHO D 403 " -0.064 2.00e-02 2.50e+03 pdb=" C2C PHO D 403 " 0.066 2.00e-02 2.50e+03 pdb=" C2D PHO D 403 " -0.057 2.00e-02 2.50e+03 pdb=" C3A PHO D 403 " 0.299 2.00e-02 2.50e+03 pdb=" C3B PHO D 403 " -0.120 2.00e-02 2.50e+03 pdb=" C3C PHO D 403 " 0.101 2.00e-02 2.50e+03 pdb=" C3D PHO D 403 " -0.077 2.00e-02 2.50e+03 pdb=" C4A PHO D 403 " 0.119 2.00e-02 2.50e+03 pdb=" C4B PHO D 403 " -0.109 2.00e-02 2.50e+03 pdb=" C4C PHO D 403 " 0.008 2.00e-02 2.50e+03 pdb=" C4D PHO D 403 " -0.098 2.00e-02 2.50e+03 pdb=" CAB PHO D 403 " -0.112 2.00e-02 2.50e+03 pdb=" CAC PHO D 403 " 0.230 2.00e-02 2.50e+03 pdb=" CAD PHO D 403 " -0.028 2.00e-02 2.50e+03 pdb=" CBD PHO D 403 " -0.020 2.00e-02 2.50e+03 pdb=" CHA PHO D 403 " -0.061 2.00e-02 2.50e+03 pdb=" CHB PHO D 403 " 0.112 2.00e-02 2.50e+03 pdb=" CHC PHO D 403 " -0.077 2.00e-02 2.50e+03 pdb=" CHD PHO D 403 " 0.003 2.00e-02 2.50e+03 pdb=" CMB PHO D 403 " 0.020 2.00e-02 2.50e+03 pdb=" CMC PHO D 403 " 0.153 2.00e-02 2.50e+03 pdb=" CMD PHO D 403 " -0.007 2.00e-02 2.50e+03 pdb=" NA PHO D 403 " 0.017 2.00e-02 2.50e+03 pdb=" NC PHO D 403 " -0.063 2.00e-02 2.50e+03 pdb=" OBD PHO D 403 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO d 403 " 0.071 2.00e-02 2.50e+03 1.01e-01 8.16e+02 pdb=" ND PHO d 403 " 0.148 2.00e-02 2.50e+03 pdb=" C1A PHO d 403 " 0.021 2.00e-02 2.50e+03 pdb=" C1B PHO d 403 " 0.003 2.00e-02 2.50e+03 pdb=" C1C PHO d 403 " 0.033 2.00e-02 2.50e+03 pdb=" C1D PHO d 403 " 0.077 2.00e-02 2.50e+03 pdb=" C2A PHO d 403 " -0.086 2.00e-02 2.50e+03 pdb=" C2B PHO d 403 " 0.063 2.00e-02 2.50e+03 pdb=" C2C PHO d 403 " -0.066 2.00e-02 2.50e+03 pdb=" C2D PHO d 403 " 0.056 2.00e-02 2.50e+03 pdb=" C3A PHO d 403 " -0.299 2.00e-02 2.50e+03 pdb=" C3B PHO d 403 " 0.121 2.00e-02 2.50e+03 pdb=" C3C PHO d 403 " -0.101 2.00e-02 2.50e+03 pdb=" C3D PHO d 403 " 0.077 2.00e-02 2.50e+03 pdb=" C4A PHO d 403 " -0.119 2.00e-02 2.50e+03 pdb=" C4B PHO d 403 " 0.109 2.00e-02 2.50e+03 pdb=" C4C PHO d 403 " -0.008 2.00e-02 2.50e+03 pdb=" C4D PHO d 403 " 0.098 2.00e-02 2.50e+03 pdb=" CAB PHO d 403 " 0.112 2.00e-02 2.50e+03 pdb=" CAC PHO d 403 " -0.230 2.00e-02 2.50e+03 pdb=" CAD PHO d 403 " 0.028 2.00e-02 2.50e+03 pdb=" CBD PHO d 403 " 0.020 2.00e-02 2.50e+03 pdb=" CHA PHO d 403 " 0.061 2.00e-02 2.50e+03 pdb=" CHB PHO d 403 " -0.112 2.00e-02 2.50e+03 pdb=" CHC PHO d 403 " 0.077 2.00e-02 2.50e+03 pdb=" CHD PHO d 403 " -0.003 2.00e-02 2.50e+03 pdb=" CMB PHO d 403 " -0.020 2.00e-02 2.50e+03 pdb=" CMC PHO d 403 " -0.153 2.00e-02 2.50e+03 pdb=" CMD PHO d 403 " 0.007 2.00e-02 2.50e+03 pdb=" NA PHO d 403 " -0.018 2.00e-02 2.50e+03 pdb=" NC PHO d 403 " 0.063 2.00e-02 2.50e+03 pdb=" OBD PHO d 403 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO a 403 " -0.040 2.00e-02 2.50e+03 9.51e-02 7.23e+02 pdb=" ND PHO a 403 " -0.063 2.00e-02 2.50e+03 pdb=" C1A PHO a 403 " 0.031 2.00e-02 2.50e+03 pdb=" C1B PHO a 403 " -0.038 2.00e-02 2.50e+03 pdb=" C1C PHO a 403 " 0.002 2.00e-02 2.50e+03 pdb=" C1D PHO a 403 " -0.010 2.00e-02 2.50e+03 pdb=" C2A PHO a 403 " 0.019 2.00e-02 2.50e+03 pdb=" C2B PHO a 403 " 0.078 2.00e-02 2.50e+03 pdb=" C2C PHO a 403 " -0.042 2.00e-02 2.50e+03 pdb=" C2D PHO a 403 " 0.009 2.00e-02 2.50e+03 pdb=" C3A PHO a 403 " -0.304 2.00e-02 2.50e+03 pdb=" C3B PHO a 403 " 0.122 2.00e-02 2.50e+03 pdb=" C3C PHO a 403 " -0.047 2.00e-02 2.50e+03 pdb=" C3D PHO a 403 " 0.062 2.00e-02 2.50e+03 pdb=" C4A PHO a 403 " -0.148 2.00e-02 2.50e+03 pdb=" C4B PHO a 403 " 0.035 2.00e-02 2.50e+03 pdb=" C4C PHO a 403 " 0.002 2.00e-02 2.50e+03 pdb=" C4D PHO a 403 " 0.036 2.00e-02 2.50e+03 pdb=" CAB PHO a 403 " 0.190 2.00e-02 2.50e+03 pdb=" CAC PHO a 403 " -0.101 2.00e-02 2.50e+03 pdb=" CAD PHO a 403 " 0.075 2.00e-02 2.50e+03 pdb=" CBD PHO a 403 " 0.180 2.00e-02 2.50e+03 pdb=" CHA PHO a 403 " 0.088 2.00e-02 2.50e+03 pdb=" CHB PHO a 403 " -0.139 2.00e-02 2.50e+03 pdb=" CHC PHO a 403 " 0.013 2.00e-02 2.50e+03 pdb=" CHD PHO a 403 " 0.018 2.00e-02 2.50e+03 pdb=" CMB PHO a 403 " 0.096 2.00e-02 2.50e+03 pdb=" CMC PHO a 403 " -0.087 2.00e-02 2.50e+03 pdb=" CMD PHO a 403 " -0.002 2.00e-02 2.50e+03 pdb=" NA PHO a 403 " -0.072 2.00e-02 2.50e+03 pdb=" NC PHO a 403 " 0.027 2.00e-02 2.50e+03 pdb=" OBD PHO a 403 " 0.008 2.00e-02 2.50e+03 ... (remaining 12969 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 19 2.08 - 2.78: 16544 2.78 - 3.49: 85896 3.49 - 4.19: 182371 4.19 - 4.90: 310472 Nonbonded interactions: 595302 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 595297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 6.040 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: 0.060 Extract box with map and model: 2.030 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 113.010 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.740 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.660 ------------------------------------------------------------------------------- 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= 1.018 Angle : 1.769 39.064 101702 Z= 0.710 Chirality : 0.139 1.673 9608 Planarity : 0.015 0.264 12972 Dihedral : 19.658 133.404 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 : 6.303 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: 0.7684 time to fit residues: 1772.6932 Evaluate side-chains 824 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 822 time to evaluate : 5.053 ------------------------------------------------------------------------------- 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: 0.9990 chunk 521 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 351 optimal weight: 0.5980 chunk 278 optimal weight: 0.3980 chunk 539 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 401 optimal weight: 3.9990 chunk 624 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 87 ASN B 179 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 82 GLN C 311 GLN C 325 ASN C 383 GLN C 416 ASN D 141 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN D 219 ASN D 229 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN H 57 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN M 4 GLN O 222 GLN U 52 HIS V 34 ASN V 49 ASN V 78 ASN Q 124 GLN Q 192 ASN ** a 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 53 ASN b 87 ASN b 179 GLN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 457 ASN c 82 GLN c 311 GLN c 325 ASN c 383 GLN c 416 ASN d 141 ASN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 ASN d 219 ASN d 229 ASN ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 349 ASN h 57 ASN l 7 ASN m 4 GLN o 222 GLN u 52 HIS v 34 ASN v 78 ASN y 33 ASN q 192 ASN w 57 ASN 11 83 ASN 11 96 ASN 11 161 ASN 11 177 ASN 11 191 GLN 12 83 ASN 12 161 ASN 13 83 ASN 13 161 ASN 13 177 ASN 14 177 ASN 31 83 ASN 31 96 ASN 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: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 73032 Z= 0.218 Angle : 0.747 11.897 101702 Z= 0.334 Chirality : 0.046 0.304 9608 Planarity : 0.006 0.057 12972 Dihedral : 20.630 162.290 14530 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.17 % Allowed : 8.01 % Favored : 90.81 % 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: -2.55 (0.09), residues: 6884 helix: -1.61 (0.07), residues: 3650 sheet: -1.61 (0.34), residues: 234 loop : -1.64 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 131 HIS 0.008 0.001 HIS d 213 PHE 0.026 0.002 PHE b 246 TYR 0.021 0.001 TYR33 189 ARG 0.009 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 1034 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 968 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7625 (mmm) cc_final: 0.7241 (mmm) REVERT: B 98 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8772 (mt) REVERT: D 22 LYS cc_start: 0.8791 (mttt) cc_final: 0.8531 (mttm) REVERT: D 281 SER cc_start: 0.9115 (p) cc_final: 0.8887 (p) REVERT: E 43 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8638 (tt) REVERT: F 38 MET cc_start: 0.8214 (mtm) cc_final: 0.7874 (mtm) REVERT: J 23 MET cc_start: 0.7998 (tpp) cc_final: 0.7745 (tpp) REVERT: J 31 SER cc_start: 0.9264 (m) cc_final: 0.9036 (t) REVERT: J 35 LEU cc_start: 0.8160 (mt) cc_final: 0.7882 (tp) REVERT: K 33 LEU cc_start: 0.9065 (tp) cc_final: 0.8780 (tp) REVERT: M 5 PHE cc_start: 0.7621 (m-80) cc_final: 0.7230 (p90) REVERT: O 103 TYR cc_start: 0.8439 (p90) cc_final: 0.8193 (p90) REVERT: O 139 GLN cc_start: 0.8033 (tt0) cc_final: 0.7708 (pp30) REVERT: U 79 GLU cc_start: 0.8485 (pm20) cc_final: 0.8191 (pm20) REVERT: V 134 LYS cc_start: 0.9043 (ptpt) cc_final: 0.8629 (pttm) REVERT: X 33 ASP cc_start: 0.3805 (OUTLIER) cc_final: 0.3360 (t0) REVERT: W 40 LEU cc_start: 0.8987 (mt) cc_final: 0.8725 (mt) REVERT: a 288 MET cc_start: 0.7668 (mmm) cc_final: 0.6967 (mmm) REVERT: d 22 LYS cc_start: 0.8879 (mttt) cc_final: 0.8595 (mttp) REVERT: e 43 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8620 (tt) REVERT: k 41 ILE cc_start: 0.8892 (tp) cc_final: 0.8556 (tt) REVERT: m 5 PHE cc_start: 0.7645 (m-80) cc_final: 0.7208 (p90) REVERT: o 7 ASN cc_start: 0.9048 (m-40) cc_final: 0.8701 (m110) REVERT: o 96 ASN cc_start: 0.8174 (m-40) cc_final: 0.7912 (m110) REVERT: o 103 TYR cc_start: 0.8536 (p90) cc_final: 0.8138 (p90) REVERT: u 10 VAL cc_start: 0.8528 (t) cc_final: 0.8089 (m) REVERT: u 23 SER cc_start: 0.8327 (m) cc_final: 0.7998 (p) REVERT: u 79 GLU cc_start: 0.8492 (pm20) cc_final: 0.8185 (pm20) REVERT: v 134 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8637 (pttm) REVERT: y 7 ILE cc_start: 0.8707 (mt) cc_final: 0.8415 (pt) REVERT: x 33 ASP cc_start: 0.3340 (OUTLIER) cc_final: 0.2691 (t0) REVERT: q 162 GLN cc_start: 0.8333 (mm110) cc_final: 0.7919 (mm110) REVERT: w 40 LEU cc_start: 0.8985 (mt) cc_final: 0.8754 (mt) REVERT: w 53 TYR cc_start: 0.8524 (m-80) cc_final: 0.8112 (m-80) REVERT: 11 32 GLU cc_start: 0.7580 (tp30) cc_final: 0.7362 (tp30) REVERT: 12 37 VAL cc_start: 0.8995 (t) cc_final: 0.8745 (m) REVERT: 12 78 THR cc_start: 0.9116 (m) cc_final: 0.8903 (p) REVERT: 13 96 ASN cc_start: 0.8130 (m-40) cc_final: 0.7813 (t0) REVERT: 13 189 TYR cc_start: 0.8419 (t80) cc_final: 0.8214 (t80) REVERT: 31 152 ASP cc_start: 0.7660 (t0) cc_final: 0.7439 (t0) REVERT: 31 186 GLN cc_start: 0.9066 (mt0) cc_final: 0.8045 (mt0) REVERT: 31 191 GLN cc_start: 0.8403 (mt0) cc_final: 0.8158 (mt0) REVERT: 32 96 ASN cc_start: 0.7930 (m-40) cc_final: 0.7633 (t0) outliers start: 66 outliers final: 31 residues processed: 1001 average time/residue: 0.6905 time to fit residues: 1194.8194 Evaluate side-chains 793 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 757 time to evaluate : 4.526 ------------------------------------------------------------------------------- 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 E residue 43 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 100 LEU 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 32 LEU Chi-restraints excluded: chain a residue 59 ASP 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 e residue 54 ASN Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain u residue 32 VAL 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 24 ASN Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 31 residue 135 SER Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 33 residue 188 MET Chi-restraints excluded: chain 34 residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 519 optimal weight: 2.9990 chunk 425 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 625 optimal weight: 4.9990 chunk 676 optimal weight: 0.3980 chunk 557 optimal weight: 3.9990 chunk 620 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 502 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** 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 222 GLN a 303 ASN a 310 GLN ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN o 222 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN 12 82 ASN 12 177 ASN 13 177 ASN 14 186 GLN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 177 ASN 33 186 GLN 33 196 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 73032 Z= 0.319 Angle : 0.737 13.413 101702 Z= 0.326 Chirality : 0.048 0.376 9608 Planarity : 0.005 0.061 12972 Dihedral : 19.086 166.361 14528 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.92 % Allowed : 9.70 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.10), residues: 6884 helix: -0.41 (0.08), residues: 3702 sheet: -1.17 (0.35), residues: 232 loop : -1.29 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP11 131 HIS 0.008 0.002 HIS b 23 PHE 0.020 0.002 PHE D 195 TYR 0.024 0.002 TYR h 49 ARG 0.006 0.001 ARG32 158 *********************** 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 905 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 797 time to evaluate : 5.119 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: D 22 LYS cc_start: 0.8864 (mttt) cc_final: 0.8605 (mttp) REVERT: E 43 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8622 (tt) REVERT: J 23 MET cc_start: 0.7895 (tpp) cc_final: 0.7677 (tpp) REVERT: J 25 SER cc_start: 0.9278 (p) cc_final: 0.8954 (p) REVERT: J 31 SER cc_start: 0.9321 (m) cc_final: 0.9058 (t) REVERT: K 33 LEU cc_start: 0.9127 (tp) cc_final: 0.8924 (tp) REVERT: L 25 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9008 (mp) REVERT: M 5 PHE cc_start: 0.7660 (m-80) cc_final: 0.7191 (p90) REVERT: M 28 GLN cc_start: 0.8873 (pp30) cc_final: 0.8556 (pp30) REVERT: O 103 TYR cc_start: 0.8663 (p90) cc_final: 0.8387 (p90) REVERT: U 23 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7992 (p) REVERT: U 79 GLU cc_start: 0.8586 (pm20) cc_final: 0.8243 (pm20) REVERT: V 83 ASP cc_start: 0.7852 (p0) cc_final: 0.7633 (p0) REVERT: V 111 ASP cc_start: 0.7922 (m-30) cc_final: 0.7573 (m-30) REVERT: V 128 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7442 (mm-30) REVERT: V 134 LYS cc_start: 0.9067 (ptpt) cc_final: 0.8705 (pttp) REVERT: X 33 ASP cc_start: 0.3604 (OUTLIER) cc_final: 0.3330 (t0) REVERT: Q 200 ASP cc_start: 0.7726 (m-30) cc_final: 0.7514 (m-30) REVERT: b 256 MET cc_start: 0.9134 (tpp) cc_final: 0.8464 (tpt) REVERT: d 22 LYS cc_start: 0.8899 (mttt) cc_final: 0.8611 (mttp) REVERT: e 43 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8589 (tt) REVERT: l 25 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8983 (mp) REVERT: m 5 PHE cc_start: 0.7649 (m-80) cc_final: 0.7193 (p90) REVERT: m 28 GLN cc_start: 0.8848 (pp30) cc_final: 0.8571 (pp30) REVERT: o 103 TYR cc_start: 0.8762 (p90) cc_final: 0.8309 (p90) REVERT: o 130 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7427 (p0) REVERT: u 23 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7983 (p) REVERT: u 76 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8193 (mtmm) REVERT: u 79 GLU cc_start: 0.8606 (pm20) cc_final: 0.8215 (pm20) REVERT: v 57 GLU cc_start: 0.8232 (tt0) cc_final: 0.8029 (tt0) REVERT: v 83 ASP cc_start: 0.7766 (p0) cc_final: 0.7508 (p0) REVERT: v 134 LYS cc_start: 0.9120 (ptpt) cc_final: 0.8740 (pttp) REVERT: y 7 ILE cc_start: 0.8792 (mt) cc_final: 0.8337 (pt) REVERT: x 33 ASP cc_start: 0.3020 (OUTLIER) cc_final: 0.2579 (t0) REVERT: w 40 LEU cc_start: 0.9108 (mt) cc_final: 0.8862 (mt) REVERT: w 53 TYR cc_start: 0.8553 (m-80) cc_final: 0.8079 (m-80) REVERT: 11 91 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8391 (tp) REVERT: 11 138 ASP cc_start: 0.7177 (t70) cc_final: 0.5640 (t70) REVERT: 11 140 ASP cc_start: 0.7385 (p0) cc_final: 0.6611 (p0) REVERT: 11 186 GLN cc_start: 0.9063 (mt0) cc_final: 0.8727 (mt0) REVERT: 12 37 VAL cc_start: 0.8986 (t) cc_final: 0.8759 (m) REVERT: 13 72 MET cc_start: 0.8539 (mtm) cc_final: 0.8319 (mtm) REVERT: 13 189 TYR cc_start: 0.8456 (t80) cc_final: 0.8178 (t80) REVERT: 14 178 MET cc_start: 0.8252 (mmt) cc_final: 0.8038 (mmt) REVERT: 31 45 ASP cc_start: 0.8695 (p0) cc_final: 0.8313 (p0) REVERT: 31 91 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8401 (tp) REVERT: 31 186 GLN cc_start: 0.9046 (mt0) cc_final: 0.8689 (mt0) REVERT: 32 91 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8386 (tp) REVERT: 32 96 ASN cc_start: 0.7934 (m-40) cc_final: 0.7663 (t0) REVERT: 32 172 MET cc_start: 0.8789 (mmt) cc_final: 0.8508 (mmm) outliers start: 108 outliers final: 49 residues processed: 863 average time/residue: 0.6966 time to fit residues: 1057.8379 Evaluate side-chains 777 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 716 time to evaluate : 5.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 102 GLU 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 E residue 77 LEU Chi-restraints excluded: chain F residue 19 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 96 ASN Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 35 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 13 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 12 SER Chi-restraints excluded: chain e residue 43 LEU Chi-restraints excluded: chain e residue 77 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 130 ASN Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain v residue 12 VAL 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 35 ILE Chi-restraints excluded: chain x residue 36 LEU Chi-restraints excluded: chain q residue 142 LEU Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain w residue 24 ASN Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 11 residue 117 LEU Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 13 residue 177 ASN Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 79 ILE 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 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 33 residue 177 ASN Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 0.4980 chunk 470 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 420 optimal weight: 0.6980 chunk 628 optimal weight: 0.8980 chunk 665 optimal weight: 6.9990 chunk 328 optimal weight: 0.5980 chunk 595 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** 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 109 GLN U 15 ASN V 49 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 300 GLN h 47 GLN v 118 HIS q 162 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN 13 177 ASN 32 82 ASN 33 177 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3188 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= 0.186 Angle : 0.637 12.624 101702 Z= 0.280 Chirality : 0.044 0.351 9608 Planarity : 0.004 0.049 12972 Dihedral : 18.280 168.505 14528 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.94 % Allowed : 10.61 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.10), residues: 6884 helix: 0.29 (0.08), residues: 3698 sheet: -0.87 (0.39), residues: 196 loop : -1.09 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 33 HIS 0.005 0.001 HIS W 42 PHE 0.018 0.001 PHE34 123 TYR 0.016 0.001 TYR33 189 ARG 0.005 0.000 ARG q 154 *********************** 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 902 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 793 time to evaluate : 5.107 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: 0.7762 (mmm) cc_final: 0.7353 (mmm) REVERT: C 286 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9040 (mm) REVERT: D 22 LYS cc_start: 0.8808 (mttt) cc_final: 0.8538 (mttp) REVERT: D 293 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7691 (ptt180) REVERT: J 24 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8770 (mp) REVERT: J 31 SER cc_start: 0.9243 (m) cc_final: 0.9000 (t) REVERT: K 33 LEU cc_start: 0.9054 (tp) cc_final: 0.8784 (tp) REVERT: L 25 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8910 (mp) REVERT: M 5 PHE cc_start: 0.7634 (m-80) cc_final: 0.7180 (p90) REVERT: M 28 GLN cc_start: 0.8797 (pp30) cc_final: 0.8352 (pp30) REVERT: O 103 TYR cc_start: 0.8611 (p90) cc_final: 0.8397 (p90) REVERT: V 13 ASP cc_start: 0.7378 (p0) cc_final: 0.7142 (p0) REVERT: V 111 ASP cc_start: 0.7783 (m-30) cc_final: 0.7435 (m-30) REVERT: V 128 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7420 (mm-30) REVERT: V 134 LYS cc_start: 0.9048 (ptpt) cc_final: 0.8680 (pttp) REVERT: Y 1 MET cc_start: 0.6592 (mmm) cc_final: 0.6194 (mtp) REVERT: X 33 ASP cc_start: 0.3470 (OUTLIER) cc_final: 0.3268 (t0) REVERT: Z 47 LEU cc_start: 0.8950 (tp) cc_final: 0.8591 (tp) REVERT: Q 105 ASN cc_start: 0.7956 (m-40) cc_final: 0.7682 (m-40) REVERT: b 256 MET cc_start: 0.9145 (tpp) cc_final: 0.8551 (tpt) REVERT: c 286 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9027 (mm) REVERT: c 468 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7201 (ttp80) REVERT: d 22 LYS cc_start: 0.8881 (mttt) cc_final: 0.8622 (mttm) REVERT: e 20 TYR cc_start: 0.8703 (t80) cc_final: 0.8434 (t80) REVERT: j 31 SER cc_start: 0.9298 (m) cc_final: 0.9012 (t) REVERT: k 41 ILE cc_start: 0.8931 (tp) cc_final: 0.8676 (tt) REVERT: l 25 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8718 (mp) REVERT: m 5 PHE cc_start: 0.7681 (m-80) cc_final: 0.7167 (p90) REVERT: m 28 GLN cc_start: 0.8696 (pp30) cc_final: 0.8310 (pp30) REVERT: o 103 TYR cc_start: 0.8647 (p90) cc_final: 0.8304 (p90) REVERT: u 10 VAL cc_start: 0.8626 (t) cc_final: 0.8198 (m) REVERT: u 76 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8444 (mtmm) REVERT: v 13 ASP cc_start: 0.7391 (p0) cc_final: 0.6991 (p0) REVERT: v 83 ASP cc_start: 0.7792 (p0) cc_final: 0.7579 (p0) REVERT: v 111 ASP cc_start: 0.7864 (m-30) cc_final: 0.7551 (m-30) REVERT: v 134 LYS cc_start: 0.9048 (ptpt) cc_final: 0.8689 (pttp) REVERT: x 33 ASP cc_start: 0.3759 (OUTLIER) cc_final: 0.3412 (t0) REVERT: q 122 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7943 (mmt180) REVERT: q 162 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7856 (mm-40) REVERT: w 53 TYR cc_start: 0.8554 (m-80) cc_final: 0.8144 (m-80) REVERT: 11 78 THR cc_start: 0.8935 (m) cc_final: 0.8686 (p) REVERT: 11 91 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8352 (tp) REVERT: 11 101 ASP cc_start: 0.7872 (p0) cc_final: 0.7468 (p0) REVERT: 11 138 ASP cc_start: 0.7205 (t70) cc_final: 0.5852 (t70) REVERT: 11 140 ASP cc_start: 0.7274 (p0) cc_final: 0.6326 (p0) REVERT: 12 37 VAL cc_start: 0.8840 (t) cc_final: 0.8610 (m) REVERT: 12 72 MET cc_start: 0.8764 (mtp) cc_final: 0.8525 (mtm) REVERT: 13 177 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8360 (t0) REVERT: 13 189 TYR cc_start: 0.8380 (t80) cc_final: 0.8133 (t80) REVERT: 31 45 ASP cc_start: 0.8378 (p0) cc_final: 0.8128 (p0) REVERT: 31 91 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8296 (tp) REVERT: 31 101 ASP cc_start: 0.7960 (p0) cc_final: 0.7584 (p0) REVERT: 31 171 MET cc_start: 0.9261 (mtm) cc_final: 0.9052 (mtm) REVERT: 32 35 LEU cc_start: 0.8805 (mt) cc_final: 0.8598 (mt) REVERT: 32 91 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8323 (tp) REVERT: 32 96 ASN cc_start: 0.7838 (m-40) cc_final: 0.7558 (t0) REVERT: 32 172 MET cc_start: 0.8796 (mmt) cc_final: 0.8505 (mmm) REVERT: 33 177 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8088 (t0) outliers start: 109 outliers final: 37 residues processed: 860 average time/residue: 0.6755 time to fit residues: 1008.2405 Evaluate side-chains 769 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 719 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 24 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Y residue 13 THR Chi-restraints excluded: chain X residue 33 ASP 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 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 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 v residue 12 VAL 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 q residue 161 THR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain w residue 24 ASN Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 13 residue 177 ASN Chi-restraints excluded: chain 14 residue 114 THR Chi-restraints excluded: chain 31 residue 91 LEU Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 177 ASN Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 79 ILE Chi-restraints excluded: chain 34 residue 100 SER Chi-restraints excluded: chain 34 residue 114 THR 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: 2.9990 chunk 9 optimal weight: 2.9990 chunk 495 optimal weight: 0.9980 chunk 274 optimal weight: 8.9990 chunk 567 optimal weight: 3.9990 chunk 459 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 596 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 188 HIS ** 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 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 GLN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 192 ASN W 57 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 128 GLN d 141 ASN ** d 188 HIS ** 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 109 GLN o 139 GLN o 197 GLN u 15 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN 11 177 ASN 33 177 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 73032 Z= 0.265 Angle : 0.666 14.392 101702 Z= 0.293 Chirality : 0.046 0.335 9608 Planarity : 0.004 0.048 12972 Dihedral : 17.850 167.684 14528 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.47 % Allowed : 10.73 % Favored : 86.80 % 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: -0.21 (0.10), residues: 6884 helix: 0.58 (0.09), residues: 3712 sheet: -0.81 (0.38), residues: 206 loop : -0.95 (0.11), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP11 131 HIS 0.006 0.001 HIS w 42 PHE 0.021 0.002 PHE b 211 TYR 0.019 0.001 TYR14 90 ARG 0.005 0.000 ARG11 168 *********************** 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 880 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 741 time to evaluate : 5.083 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: 0.9125 (tpp) cc_final: 0.8562 (tpt) REVERT: C 286 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9073 (mm) REVERT: D 22 LYS cc_start: 0.8863 (mttt) cc_final: 0.8582 (mttm) REVERT: D 293 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8135 (ptt90) REVERT: J 25 SER cc_start: 0.9273 (p) cc_final: 0.8996 (p) REVERT: J 31 SER cc_start: 0.9246 (m) cc_final: 0.8990 (t) REVERT: L 25 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8908 (mp) REVERT: M 5 PHE cc_start: 0.7625 (m-80) cc_final: 0.7194 (p90) REVERT: M 28 GLN cc_start: 0.8934 (pp30) cc_final: 0.8680 (pp30) REVERT: V 13 ASP cc_start: 0.7439 (p0) cc_final: 0.7153 (p0) REVERT: V 111 ASP cc_start: 0.7888 (m-30) cc_final: 0.7469 (m-30) REVERT: V 128 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7444 (mm-30) REVERT: V 134 LYS cc_start: 0.9057 (ptpt) cc_final: 0.8634 (ptpp) REVERT: Y 1 MET cc_start: 0.6604 (mmm) cc_final: 0.6376 (mtp) REVERT: Z 47 LEU cc_start: 0.8928 (tp) cc_final: 0.8719 (tp) REVERT: b 256 MET cc_start: 0.9118 (tpp) cc_final: 0.8583 (tpt) REVERT: c 286 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9063 (mm) REVERT: c 468 ARG cc_start: 0.7490 (ttp80) cc_final: 0.7206 (ttp80) REVERT: d 22 LYS cc_start: 0.8880 (mttt) cc_final: 0.8629 (mttm) REVERT: e 20 TYR cc_start: 0.8680 (t80) cc_final: 0.8442 (t80) REVERT: j 31 SER cc_start: 0.9256 (m) cc_final: 0.8977 (t) REVERT: k 41 ILE cc_start: 0.8959 (tp) cc_final: 0.8637 (tt) REVERT: l 25 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8893 (mp) REVERT: m 5 PHE cc_start: 0.7692 (m-80) cc_final: 0.7189 (p90) REVERT: m 28 GLN cc_start: 0.8810 (pp30) cc_final: 0.8342 (pp30) REVERT: u 10 VAL cc_start: 0.8649 (t) cc_final: 0.8216 (m) REVERT: v 13 ASP cc_start: 0.7459 (p0) cc_final: 0.6140 (p0) REVERT: y 1 MET cc_start: 0.6445 (mmm) cc_final: 0.6092 (mtp) REVERT: x 33 ASP cc_start: 0.3569 (OUTLIER) cc_final: 0.3358 (t0) REVERT: z 47 LEU cc_start: 0.8901 (tp) cc_final: 0.8670 (tp) REVERT: q 122 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7854 (mmm160) REVERT: 11 38 THR cc_start: 0.7609 (m) cc_final: 0.7270 (m) REVERT: 11 91 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8290 (tp) REVERT: 11 101 ASP cc_start: 0.7932 (p0) cc_final: 0.7568 (p0) REVERT: 11 140 ASP cc_start: 0.7240 (p0) cc_final: 0.7028 (p0) REVERT: 12 35 LEU cc_start: 0.8794 (mt) cc_final: 0.8579 (mt) REVERT: 12 37 VAL cc_start: 0.8795 (t) cc_final: 0.8587 (m) REVERT: 12 72 MET cc_start: 0.8741 (mtp) cc_final: 0.8457 (mtm) REVERT: 13 158 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7610 (tmt90) REVERT: 13 189 TYR cc_start: 0.8407 (t80) cc_final: 0.8119 (t80) REVERT: 14 178 MET cc_start: 0.8211 (mmt) cc_final: 0.7975 (mmt) REVERT: 31 45 ASP cc_start: 0.8503 (p0) cc_final: 0.8241 (p0) REVERT: 31 91 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8270 (tp) REVERT: 31 101 ASP cc_start: 0.8024 (p0) cc_final: 0.7662 (p0) REVERT: 32 35 LEU cc_start: 0.8856 (mt) cc_final: 0.8642 (mt) REVERT: 32 91 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8410 (tp) REVERT: 32 96 ASN cc_start: 0.7916 (m-40) cc_final: 0.7633 (t0) REVERT: 32 172 MET cc_start: 0.8836 (mmt) cc_final: 0.8551 (mmm) REVERT: 33 177 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8073 (t0) REVERT: 34 196 HIS cc_start: 0.6477 (t70) cc_final: 0.5924 (t70) outliers start: 139 outliers final: 75 residues processed: 826 average time/residue: 0.6568 time to fit residues: 951.2485 Evaluate side-chains 786 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 700 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 222 VAL 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 15 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain K residue 23 LEU 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 O residue 175 LEU Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Y residue 13 THR 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 W residue 32 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 59 ASP Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain c residue 58 MET Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 222 VAL 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 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 28 LEU Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain o residue 130 ASN Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 100 LEU Chi-restraints excluded: chain v residue 12 VAL 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 q residue 161 THR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain w residue 24 ASN Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 65 GLU Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 11 residue 117 LEU Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 11 residue 177 ASN Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 158 ARG Chi-restraints excluded: chain 13 residue 188 MET Chi-restraints excluded: chain 14 residue 79 ILE 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 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 177 ASN Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 79 ILE Chi-restraints excluded: chain 34 residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 223 optimal weight: 0.0170 chunk 598 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 390 optimal weight: 4.9990 chunk 164 optimal weight: 0.1980 chunk 665 optimal weight: 0.8980 chunk 552 optimal weight: 0.0070 chunk 308 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 220 optimal weight: 0.8980 chunk 349 optimal weight: 3.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 118 HIS Q 81 GLN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 96 ASN 13 177 ASN 33 177 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 73032 Z= 0.145 Angle : 0.593 11.937 101702 Z= 0.264 Chirality : 0.043 0.310 9608 Planarity : 0.004 0.050 12972 Dihedral : 17.194 168.256 14528 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 12.01 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 6884 helix: 0.86 (0.09), residues: 3762 sheet: -0.85 (0.36), residues: 220 loop : -0.89 (0.12), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP31 131 HIS 0.009 0.001 HIS d 213 PHE 0.017 0.001 PHE d 183 TYR 0.014 0.001 TYR33 44 ARG 0.005 0.000 ARG q 154 *********************** 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 872 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 776 time to evaluate : 5.084 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: B 256 MET cc_start: 0.9169 (tpp) cc_final: 0.8538 (tpt) REVERT: C 286 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8819 (mm) REVERT: C 468 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7025 (ttp80) REVERT: D 22 LYS cc_start: 0.8801 (mttt) cc_final: 0.8533 (mttm) REVERT: H 9 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7549 (mm-30) REVERT: J 24 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8819 (mp) REVERT: J 31 SER cc_start: 0.9168 (m) cc_final: 0.8936 (t) REVERT: L 25 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8906 (mp) REVERT: M 5 PHE cc_start: 0.7599 (m-80) cc_final: 0.7205 (p90) REVERT: M 28 GLN cc_start: 0.8850 (pp30) cc_final: 0.8587 (pp30) REVERT: V 13 ASP cc_start: 0.7455 (p0) cc_final: 0.6202 (p0) REVERT: V 111 ASP cc_start: 0.7785 (m-30) cc_final: 0.7415 (m-30) REVERT: V 128 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7405 (mm-30) REVERT: V 134 LYS cc_start: 0.9039 (ptpt) cc_final: 0.8597 (ptpp) REVERT: b 256 MET cc_start: 0.9149 (tpp) cc_final: 0.8566 (tpt) REVERT: c 286 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8847 (mm) REVERT: c 468 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7127 (ttp80) REVERT: d 22 LYS cc_start: 0.8786 (mttt) cc_final: 0.8501 (mttp) REVERT: e 20 TYR cc_start: 0.8605 (t80) cc_final: 0.8394 (t80) REVERT: h 9 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7562 (mm-30) REVERT: j 31 SER cc_start: 0.9213 (m) cc_final: 0.8920 (t) REVERT: k 41 ILE cc_start: 0.8942 (tp) cc_final: 0.8615 (tt) REVERT: l 25 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8746 (mp) REVERT: m 5 PHE cc_start: 0.7633 (m-80) cc_final: 0.7172 (p90) REVERT: u 10 VAL cc_start: 0.8607 (t) cc_final: 0.8180 (m) REVERT: v 134 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8644 (ptpp) REVERT: y 1 MET cc_start: 0.6584 (mmm) cc_final: 0.6354 (mtp) REVERT: x 33 ASP cc_start: 0.3233 (OUTLIER) cc_final: 0.3012 (t0) REVERT: q 91 VAL cc_start: 0.9195 (m) cc_final: 0.8943 (p) REVERT: 11 38 THR cc_start: 0.7336 (m) cc_final: 0.7024 (m) REVERT: 11 91 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8304 (tp) REVERT: 11 98 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8740 (mtpp) REVERT: 11 101 ASP cc_start: 0.7913 (p0) cc_final: 0.7507 (p0) REVERT: 12 32 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6724 (mm-30) REVERT: 12 72 MET cc_start: 0.8723 (mtp) cc_final: 0.8431 (mtm) REVERT: 13 72 MET cc_start: 0.8625 (mtm) cc_final: 0.8394 (mtm) REVERT: 13 158 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7643 (tmt90) REVERT: 13 189 TYR cc_start: 0.8453 (t80) cc_final: 0.8187 (t80) REVERT: 31 45 ASP cc_start: 0.8447 (p0) cc_final: 0.8185 (p0) REVERT: 31 91 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8290 (tp) REVERT: 31 98 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8816 (mtpp) REVERT: 31 101 ASP cc_start: 0.7993 (p0) cc_final: 0.7602 (p0) REVERT: 31 175 MET cc_start: 0.8737 (mmm) cc_final: 0.8472 (tpp) REVERT: 32 35 LEU cc_start: 0.8790 (mt) cc_final: 0.8564 (mt) REVERT: 32 49 TRP cc_start: 0.6735 (m100) cc_final: 0.6501 (m100) REVERT: 32 91 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (tp) REVERT: 32 96 ASN cc_start: 0.7809 (m-40) cc_final: 0.7531 (t0) REVERT: 32 172 MET cc_start: 0.8840 (mmt) cc_final: 0.8569 (mmm) REVERT: 33 177 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8008 (t0) REVERT: 34 196 HIS cc_start: 0.6399 (t70) cc_final: 0.5708 (t70) outliers start: 96 outliers final: 45 residues processed: 838 average time/residue: 0.6734 time to fit residues: 979.1069 Evaluate side-chains 765 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 709 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 116 HIS 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 J residue 24 LEU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL 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 W residue 32 LEU Chi-restraints excluded: chain W residue 57 ASN Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain a residue 290 ILE Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain c residue 116 HIS 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 k residue 17 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain u residue 16 ILE Chi-restraints excluded: chain v residue 12 VAL 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 q residue 161 THR Chi-restraints excluded: chain q residue 176 THR Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 65 GLU Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 12 residue 128 GLU Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 158 ARG Chi-restraints excluded: chain 14 residue 79 ILE Chi-restraints excluded: chain 31 residue 91 LEU Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 128 GLU Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 177 ASN Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 641 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 379 optimal weight: 0.6980 chunk 486 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 560 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 663 optimal weight: 0.6980 chunk 414 optimal weight: 0.0570 chunk 404 optimal weight: 0.9990 chunk 306 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN W 57 ASN a 303 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN q 162 GLN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN 13 177 ASN 31 177 ASN 33 177 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 73032 Z= 0.168 Angle : 0.596 12.832 101702 Z= 0.266 Chirality : 0.043 0.293 9608 Planarity : 0.004 0.049 12972 Dihedral : 16.942 165.557 14528 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.74 % Allowed : 12.35 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 6884 helix: 0.96 (0.09), residues: 3810 sheet: -0.73 (0.36), residues: 220 loop : -0.85 (0.12), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP11 131 HIS 0.010 0.001 HIS d 213 PHE 0.024 0.001 PHE14 123 TYR 0.023 0.001 TYR14 90 ARG 0.004 0.000 ARG32 59 *********************** 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 837 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 739 time to evaluate : 4.975 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: B 256 MET cc_start: 0.9159 (tpp) cc_final: 0.8575 (tpt) REVERT: B 479 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: C 286 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8860 (mm) REVERT: C 468 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7151 (ttp80) REVERT: D 22 LYS cc_start: 0.8843 (mttt) cc_final: 0.8515 (mttp) REVERT: H 9 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7570 (mm-30) REVERT: J 31 SER cc_start: 0.9157 (m) cc_final: 0.8923 (t) REVERT: L 25 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8919 (mp) REVERT: M 5 PHE cc_start: 0.7589 (m-80) cc_final: 0.7213 (p90) REVERT: M 28 GLN cc_start: 0.8886 (pp30) cc_final: 0.8621 (pp30) REVERT: V 111 ASP cc_start: 0.7795 (m-30) cc_final: 0.7336 (m-30) REVERT: V 134 LYS cc_start: 0.9053 (ptpt) cc_final: 0.8585 (ptpp) REVERT: b 256 MET cc_start: 0.9153 (tpp) cc_final: 0.8560 (tpt) REVERT: b 479 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: c 286 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8836 (mm) REVERT: c 468 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7194 (ttp80) REVERT: d 22 LYS cc_start: 0.8837 (mttt) cc_final: 0.8587 (mttp) REVERT: h 9 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7509 (mm-30) REVERT: j 31 SER cc_start: 0.9205 (m) cc_final: 0.8916 (t) REVERT: k 41 ILE cc_start: 0.8935 (tp) cc_final: 0.8631 (tt) REVERT: l 25 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8893 (mp) REVERT: m 5 PHE cc_start: 0.7627 (m-80) cc_final: 0.7192 (p90) REVERT: m 30 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7837 (mm-30) REVERT: u 10 VAL cc_start: 0.8616 (t) cc_final: 0.8185 (m) REVERT: v 134 LYS cc_start: 0.9111 (ptpp) cc_final: 0.8605 (ptpp) REVERT: q 91 VAL cc_start: 0.9213 (m) cc_final: 0.8963 (p) REVERT: q 122 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7780 (mmt180) REVERT: q 141 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7999 (tm-30) REVERT: q 154 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7840 (mtp180) REVERT: 11 98 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8759 (mtpp) REVERT: 11 101 ASP cc_start: 0.7921 (p0) cc_final: 0.7535 (p0) REVERT: 12 72 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8447 (mtm) REVERT: 12 186 GLN cc_start: 0.7392 (mt0) cc_final: 0.7035 (mt0) REVERT: 13 123 PHE cc_start: 0.8868 (t80) cc_final: 0.8649 (t80) REVERT: 13 158 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7672 (tmt90) REVERT: 13 189 TYR cc_start: 0.8370 (t80) cc_final: 0.8093 (t80) REVERT: 31 98 LYS cc_start: 0.9173 (mtpp) cc_final: 0.8876 (mtpp) REVERT: 31 101 ASP cc_start: 0.7884 (p0) cc_final: 0.7513 (p0) REVERT: 31 175 MET cc_start: 0.8800 (mmm) cc_final: 0.8494 (tpp) REVERT: 32 35 LEU cc_start: 0.8800 (mt) cc_final: 0.8575 (mt) REVERT: 32 91 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8246 (tp) REVERT: 32 96 ASN cc_start: 0.7786 (m-40) cc_final: 0.7512 (t0) REVERT: 32 172 MET cc_start: 0.8860 (mmt) cc_final: 0.8592 (mmm) REVERT: 33 72 MET cc_start: 0.8601 (mtm) cc_final: 0.7902 (mtm) outliers start: 98 outliers final: 62 residues processed: 800 average time/residue: 0.6351 time to fit residues: 887.6520 Evaluate side-chains 775 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 704 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 116 HIS 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 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 87 THR Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL 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 a residue 21 ILE Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 116 HIS 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 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 1 MET Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 211 ASP Chi-restraints excluded: chain u residue 100 LEU Chi-restraints excluded: chain v residue 12 VAL 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 w residue 25 GLU Chi-restraints excluded: chain w residue 32 LEU Chi-restraints excluded: chain w residue 65 GLU Chi-restraints excluded: chain w residue 66 ILE Chi-restraints excluded: chain 11 residue 177 ASN Chi-restraints excluded: chain 12 residue 72 MET Chi-restraints excluded: chain 12 residue 128 GLU Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 158 ARG Chi-restraints excluded: chain 14 residue 83 ASN Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 128 GLU Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 410 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 421 optimal weight: 0.9980 chunk 451 optimal weight: 3.9990 chunk 327 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 521 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 GLN Q 192 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 5 GLN y 33 ASN ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN 13 177 ASN 31 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3759 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= 0.210 Angle : 0.618 13.570 101702 Z= 0.275 Chirality : 0.044 0.307 9608 Planarity : 0.004 0.049 12972 Dihedral : 16.799 162.356 14528 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.76 % Allowed : 12.85 % Favored : 85.39 % 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: 0.35 (0.10), residues: 6884 helix: 1.06 (0.09), residues: 3768 sheet: -0.66 (0.37), residues: 216 loop : -0.75 (0.12), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP31 131 HIS 0.006 0.001 HIS d 213 PHE 0.022 0.001 PHE w 39 TYR 0.017 0.001 TYR34 189 ARG 0.005 0.000 ARG11 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 831 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 732 time to evaluate : 4.978 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: B 256 MET cc_start: 0.9144 (tpp) cc_final: 0.8566 (tpt) REVERT: B 479 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: C 286 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8901 (mm) REVERT: C 468 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7188 (ttp80) REVERT: D 22 LYS cc_start: 0.8860 (mttt) cc_final: 0.8558 (mttm) REVERT: H 9 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7596 (mm-30) REVERT: J 25 SER cc_start: 0.9300 (p) cc_final: 0.9024 (p) REVERT: J 31 SER cc_start: 0.9165 (m) cc_final: 0.8924 (t) REVERT: L 25 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8928 (mp) REVERT: M 5 PHE cc_start: 0.7584 (m-80) cc_final: 0.7224 (p90) REVERT: M 28 GLN cc_start: 0.8946 (pp30) cc_final: 0.8676 (pp30) REVERT: O 199 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7531 (tpt90) REVERT: V 111 ASP cc_start: 0.7790 (m-30) cc_final: 0.7454 (m-30) REVERT: V 134 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8585 (ptpp) REVERT: b 256 MET cc_start: 0.9140 (tpp) cc_final: 0.8598 (tpt) REVERT: b 479 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: c 286 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8905 (mm) REVERT: c 468 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7246 (ttp80) REVERT: d 22 LYS cc_start: 0.8793 (mttt) cc_final: 0.8523 (mttm) REVERT: h 9 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7509 (mm-30) REVERT: j 31 SER cc_start: 0.9184 (m) cc_final: 0.8912 (t) REVERT: k 41 ILE cc_start: 0.8940 (tp) cc_final: 0.8628 (tt) REVERT: l 25 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (mp) REVERT: m 5 PHE cc_start: 0.7625 (m-80) cc_final: 0.7190 (p90) REVERT: o 29 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: u 79 GLU cc_start: 0.8493 (pm20) cc_final: 0.8188 (pm20) REVERT: v 134 LYS cc_start: 0.9084 (ptpp) cc_final: 0.8624 (ptpp) REVERT: y 31 LYS cc_start: 0.8499 (tptt) cc_final: 0.8279 (mmtm) REVERT: z 29 GLU cc_start: 0.7227 (tt0) cc_final: 0.7025 (tt0) REVERT: 11 38 THR cc_start: 0.7425 (m) cc_final: 0.7067 (m) REVERT: 11 91 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8391 (tp) REVERT: 11 98 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8814 (mtpp) REVERT: 11 101 ASP cc_start: 0.7950 (p0) cc_final: 0.7574 (p0) REVERT: 12 186 GLN cc_start: 0.7419 (mt0) cc_final: 0.7218 (mt0) REVERT: 13 123 PHE cc_start: 0.8876 (t80) cc_final: 0.8658 (t80) REVERT: 13 175 MET cc_start: 0.8412 (mmp) cc_final: 0.8141 (mmp) REVERT: 13 189 TYR cc_start: 0.8347 (t80) cc_final: 0.8062 (t80) REVERT: 31 91 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8410 (tp) REVERT: 31 98 LYS cc_start: 0.9206 (mtpp) cc_final: 0.8524 (mtpp) REVERT: 31 101 ASP cc_start: 0.7902 (p0) cc_final: 0.7523 (p0) REVERT: 32 35 LEU cc_start: 0.8832 (mt) cc_final: 0.8612 (mt) REVERT: 32 91 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8361 (tp) REVERT: 32 96 ASN cc_start: 0.7831 (m-40) cc_final: 0.7555 (t0) REVERT: 32 172 MET cc_start: 0.8860 (mmt) cc_final: 0.8582 (mmm) outliers start: 99 outliers final: 62 residues processed: 792 average time/residue: 0.6352 time to fit residues: 879.8334 Evaluate side-chains 775 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 703 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 116 HIS 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 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 1 MET Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL 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 W residue 32 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 116 HIS 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 i residue 2 LEU Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain l residue 1 MET 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 29 GLU Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 211 ASP Chi-restraints excluded: chain u residue 100 LEU Chi-restraints excluded: chain v residue 12 VAL 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 11 residue 91 LEU Chi-restraints excluded: chain 11 residue 177 ASN Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 158 ARG Chi-restraints excluded: chain 14 residue 83 ASN Chi-restraints excluded: chain 14 residue 186 GLN 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 32 residue 91 LEU Chi-restraints excluded: chain 32 residue 94 SER Chi-restraints excluded: chain 32 residue 128 GLU Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Chi-restraints excluded: chain 34 residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 603 optimal weight: 4.9990 chunk 635 optimal weight: 0.5980 chunk 579 optimal weight: 4.9990 chunk 617 optimal weight: 0.8980 chunk 371 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 485 optimal weight: 0.8980 chunk 189 optimal weight: 0.5980 chunk 558 optimal weight: 0.9980 chunk 584 optimal weight: 1.9990 chunk 615 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN 13 177 ASN 31 177 ASN 33 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 73032 Z= 0.189 Angle : 0.610 13.287 101702 Z= 0.273 Chirality : 0.043 0.298 9608 Planarity : 0.004 0.049 12972 Dihedral : 16.608 160.799 14528 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.53 % Allowed : 13.26 % Favored : 85.22 % 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: 0.43 (0.10), residues: 6884 helix: 1.13 (0.09), residues: 3766 sheet: -0.70 (0.36), residues: 220 loop : -0.71 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP11 131 HIS 0.005 0.001 HIS c 396 PHE 0.034 0.001 PHE34 123 TYR 0.025 0.001 TYR14 90 ARG 0.004 0.000 ARG o 199 *********************** 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 825 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 739 time to evaluate : 5.234 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: B 256 MET cc_start: 0.9144 (tpp) cc_final: 0.8568 (tpt) REVERT: B 479 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: C 286 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8902 (mm) REVERT: C 319 ASP cc_start: 0.7834 (m-30) cc_final: 0.7589 (m-30) REVERT: C 468 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7183 (ttp80) REVERT: D 22 LYS cc_start: 0.8849 (mttt) cc_final: 0.8518 (mttp) REVERT: D 290 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8865 (mt) REVERT: H 9 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7629 (mm-30) REVERT: J 31 SER cc_start: 0.9152 (m) cc_final: 0.8915 (t) REVERT: L 25 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8893 (mp) REVERT: M 5 PHE cc_start: 0.7576 (m-80) cc_final: 0.7232 (p90) REVERT: M 28 GLN cc_start: 0.8955 (pp30) cc_final: 0.8673 (pp30) REVERT: O 199 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7477 (tpt170) REVERT: U 94 ASP cc_start: 0.7982 (p0) cc_final: 0.7773 (p0) REVERT: V 134 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8555 (ptpp) REVERT: b 256 MET cc_start: 0.9139 (tpp) cc_final: 0.8600 (tpt) REVERT: b 479 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: c 286 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8892 (mm) REVERT: c 468 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7240 (ttp80) REVERT: d 22 LYS cc_start: 0.8862 (mttt) cc_final: 0.8583 (mttp) REVERT: h 9 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7491 (mm-30) REVERT: j 31 SER cc_start: 0.9162 (m) cc_final: 0.8897 (t) REVERT: k 41 ILE cc_start: 0.8947 (tp) cc_final: 0.8638 (tt) REVERT: l 25 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8900 (mp) REVERT: m 5 PHE cc_start: 0.7593 (m-80) cc_final: 0.7170 (p90) REVERT: o 199 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7718 (tpt90) REVERT: u 79 GLU cc_start: 0.8518 (pm20) cc_final: 0.8228 (pm20) REVERT: v 134 LYS cc_start: 0.9035 (ptpp) cc_final: 0.8608 (ptpp) REVERT: 11 38 THR cc_start: 0.7298 (m) cc_final: 0.6921 (m) REVERT: 11 91 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8372 (tp) REVERT: 11 98 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8773 (mtpp) REVERT: 11 101 ASP cc_start: 0.7939 (p0) cc_final: 0.7569 (p0) REVERT: 12 186 GLN cc_start: 0.7392 (mt0) cc_final: 0.7140 (mt0) REVERT: 13 123 PHE cc_start: 0.8879 (t80) cc_final: 0.8661 (t80) REVERT: 13 175 MET cc_start: 0.8393 (mmp) cc_final: 0.8126 (mmp) REVERT: 13 189 TYR cc_start: 0.8396 (t80) cc_final: 0.8151 (t80) REVERT: 31 91 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (tp) REVERT: 31 98 LYS cc_start: 0.9200 (mtpp) cc_final: 0.8568 (mtpp) REVERT: 31 101 ASP cc_start: 0.7849 (p0) cc_final: 0.7496 (p0) REVERT: 32 35 LEU cc_start: 0.8854 (mt) cc_final: 0.8639 (mt) REVERT: 32 96 ASN cc_start: 0.7762 (m-40) cc_final: 0.7464 (t0) REVERT: 32 172 MET cc_start: 0.8862 (mmt) cc_final: 0.8581 (mmm) outliers start: 86 outliers final: 57 residues processed: 794 average time/residue: 0.6543 time to fit residues: 909.2950 Evaluate side-chains 772 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 706 time to evaluate : 5.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 116 HIS 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 290 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL 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 W residue 32 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 116 HIS 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 54 ASN Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 211 ASP Chi-restraints excluded: chain u residue 100 LEU Chi-restraints excluded: chain v residue 12 VAL 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 w residue 25 GLU Chi-restraints excluded: chain w residue 65 GLU Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 158 ARG Chi-restraints excluded: chain 14 residue 83 ASN Chi-restraints excluded: chain 14 residue 186 GLN Chi-restraints excluded: chain 31 residue 91 LEU Chi-restraints excluded: chain 31 residue 135 SER Chi-restraints excluded: chain 31 residue 177 ASN Chi-restraints excluded: chain 32 residue 128 GLU Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 405 optimal weight: 4.9990 chunk 653 optimal weight: 0.0050 chunk 398 optimal weight: 2.9990 chunk 309 optimal weight: 0.4980 chunk 454 optimal weight: 3.9990 chunk 685 optimal weight: 1.9990 chunk 630 optimal weight: 0.0970 chunk 545 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 421 optimal weight: 1.9990 chunk 334 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN 13 177 ASN 31 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 73032 Z= 0.179 Angle : 0.607 13.317 101702 Z= 0.273 Chirality : 0.043 0.287 9608 Planarity : 0.004 0.067 12972 Dihedral : 16.419 158.728 14528 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.33 % Allowed : 13.56 % Favored : 85.11 % 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: 0.47 (0.10), residues: 6884 helix: 1.17 (0.09), residues: 3766 sheet: -0.71 (0.36), residues: 220 loop : -0.70 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP11 131 HIS 0.005 0.001 HIS c 396 PHE 0.017 0.001 PHE C 433 TYR 0.023 0.001 TYR V 136 ARG 0.009 0.000 ARG I 34 ********************** 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 804 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 729 time to evaluate : 5.022 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: B 256 MET cc_start: 0.9149 (tpp) cc_final: 0.8571 (tpt) REVERT: B 479 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: C 286 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8832 (mm) REVERT: C 319 ASP cc_start: 0.7784 (m-30) cc_final: 0.7562 (m-30) REVERT: C 468 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7183 (ttp80) REVERT: D 22 LYS cc_start: 0.8865 (mttt) cc_final: 0.8541 (mttm) REVERT: D 290 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8788 (mt) REVERT: H 9 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7626 (mm-30) REVERT: I 35 LYS cc_start: 0.6763 (mttp) cc_final: 0.6271 (mtpt) REVERT: J 31 SER cc_start: 0.9143 (m) cc_final: 0.8907 (t) REVERT: L 25 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8874 (mp) REVERT: M 5 PHE cc_start: 0.7556 (m-80) cc_final: 0.7239 (p90) REVERT: M 28 GLN cc_start: 0.8911 (pp30) cc_final: 0.8596 (pp30) REVERT: O 139 GLN cc_start: 0.8421 (tt0) cc_final: 0.8072 (tm-30) REVERT: O 199 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7741 (tpp-160) REVERT: V 134 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8567 (ptpp) REVERT: b 256 MET cc_start: 0.9145 (tpp) cc_final: 0.8557 (tpt) REVERT: b 479 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: c 286 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8864 (mm) REVERT: c 468 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7237 (ttp80) REVERT: d 22 LYS cc_start: 0.8837 (mttt) cc_final: 0.8533 (mttm) REVERT: h 9 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7465 (mm-30) REVERT: j 31 SER cc_start: 0.9153 (m) cc_final: 0.8892 (t) REVERT: k 41 ILE cc_start: 0.8949 (tp) cc_final: 0.8639 (tt) REVERT: l 25 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8761 (mp) REVERT: m 5 PHE cc_start: 0.7576 (m-80) cc_final: 0.7191 (p90) REVERT: o 199 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7692 (tpt90) REVERT: u 79 GLU cc_start: 0.8500 (pm20) cc_final: 0.8221 (pm20) REVERT: v 134 LYS cc_start: 0.9084 (ptpp) cc_final: 0.8714 (ptpp) REVERT: z 1 MET cc_start: 0.7179 (tpt) cc_final: 0.6966 (tpp) REVERT: 11 38 THR cc_start: 0.7279 (m) cc_final: 0.6899 (m) REVERT: 11 91 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8390 (tp) REVERT: 11 98 LYS cc_start: 0.9189 (mtpp) cc_final: 0.8725 (mtpp) REVERT: 11 101 ASP cc_start: 0.7971 (p0) cc_final: 0.7621 (p0) REVERT: 11 140 ASP cc_start: 0.7388 (p0) cc_final: 0.7153 (p0) REVERT: 12 35 LEU cc_start: 0.8760 (mt) cc_final: 0.8493 (mt) REVERT: 12 186 GLN cc_start: 0.7411 (mt0) cc_final: 0.7130 (mt0) REVERT: 13 123 PHE cc_start: 0.8843 (t80) cc_final: 0.8640 (t80) REVERT: 13 175 MET cc_start: 0.8374 (mmp) cc_final: 0.8107 (mmp) REVERT: 13 189 TYR cc_start: 0.8425 (t80) cc_final: 0.8185 (t80) REVERT: 14 196 HIS cc_start: 0.6438 (t70) cc_final: 0.5910 (t70) REVERT: 31 91 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8377 (tp) REVERT: 31 98 LYS cc_start: 0.9213 (mtpp) cc_final: 0.8702 (mtpp) REVERT: 31 101 ASP cc_start: 0.7837 (p0) cc_final: 0.7498 (p0) REVERT: 32 35 LEU cc_start: 0.8862 (mt) cc_final: 0.8647 (mt) REVERT: 32 90 TYR cc_start: 0.8135 (t80) cc_final: 0.7665 (t80) REVERT: 32 172 MET cc_start: 0.8861 (mmt) cc_final: 0.8592 (mmm) REVERT: 34 196 HIS cc_start: 0.6709 (t70) cc_final: 0.6073 (t70) outliers start: 75 outliers final: 58 residues processed: 776 average time/residue: 0.6657 time to fit residues: 907.3106 Evaluate side-chains 775 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 708 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 116 HIS 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 290 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 24 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 87 THR Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 211 ASP Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 2 GLU Chi-restraints excluded: chain V residue 55 ASP Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 13 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 479 PHE Chi-restraints excluded: chain c residue 116 HIS 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 429 PHE Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain l residue 1 MET 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 87 THR Chi-restraints excluded: chain o residue 175 LEU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 211 ASP Chi-restraints excluded: chain u residue 16 ILE Chi-restraints excluded: chain u residue 100 LEU 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 176 THR Chi-restraints excluded: chain w residue 25 GLU Chi-restraints excluded: chain w residue 65 GLU Chi-restraints excluded: chain w residue 66 ILE Chi-restraints excluded: chain 11 residue 91 LEU Chi-restraints excluded: chain 12 residue 138 ASP Chi-restraints excluded: chain 12 residue 175 MET Chi-restraints excluded: chain 13 residue 158 ARG Chi-restraints excluded: chain 14 residue 83 ASN Chi-restraints excluded: chain 31 residue 91 LEU Chi-restraints excluded: chain 31 residue 135 SER Chi-restraints excluded: chain 31 residue 177 ASN Chi-restraints excluded: chain 32 residue 128 GLU Chi-restraints excluded: chain 32 residue 175 MET Chi-restraints excluded: chain 33 residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 433 optimal weight: 0.5980 chunk 581 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 503 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 151 optimal weight: 0.6980 chunk 546 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 561 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN 12 196 HIS 13 177 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083477 restraints weight = 144546.941| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.04 r_work: 0.2906 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 73032 Z= 0.183 Angle : 0.609 13.669 101702 Z= 0.274 Chirality : 0.043 0.283 9608 Planarity : 0.004 0.050 12972 Dihedral : 16.274 156.627 14528 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.47 % Allowed : 13.59 % Favored : 84.93 % 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: 0.50 (0.10), residues: 6884 helix: 1.19 (0.09), residues: 3768 sheet: -0.75 (0.36), residues: 220 loop : -0.68 (0.12), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP11 131 HIS 0.005 0.001 HIS c 396 PHE 0.019 0.001 PHE C 433 TYR 0.023 0.001 TYR14 90 ARG 0.008 0.000 ARG I 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17463.69 seconds wall clock time: 302 minutes 10.92 seconds (18130.92 seconds total)