Starting phenix.real_space_refine on Mon Sep 30 07:32:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/09_2024/6j3z_9776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/09_2024/6j3z_9776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/09_2024/6j3z_9776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/09_2024/6j3z_9776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/09_2024/6j3z_9776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j3z_9776/09_2024/6j3z_9776.cif" } resolution = 3.6 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Ca 2 9.91 5 Mn 8 7.51 5 Fe 6 7.16 5 P 8 5.49 5 Mg 184 5.21 5 S 222 5.16 5 C 51517 2.51 5 N 10435 2.21 5 O 12237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74619 Number of models: 1 Model: "" Number of chains: 97 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3812 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 28, 'TRANS': 455} Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3504 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain: "D" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2697 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 228 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "H" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 513 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "I" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 287 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "J" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 254 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "K" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "M" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 316 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1845 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 250 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "U" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 713 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 86} Chain: "V" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1037 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "Y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "X" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 263 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 447 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "Q" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "W" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "0" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "1" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "2" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "b" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3812 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 28, 'TRANS': 455} Chain: "c" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3504 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain: "d" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2697 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "e" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "f" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 228 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "h" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 513 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "i" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 287 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "j" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 254 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "k" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "l" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "m" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 316 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1845 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "t" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 250 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "u" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 713 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 86} Chain: "v" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1037 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "x" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 263 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 447 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "q" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "w" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 422 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "5" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "6" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "7" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "11" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "12" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "13" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "14" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "15" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "16" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "17" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "18" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1343 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "19" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1075 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'TRANS': 214} Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 215 Planarities with less than four sites: {'UNK:plan-1': 215} Unresolved non-hydrogen planarities: 215 Chain: "20" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 715 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'TRANS': 142} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 143 Planarities with less than four sites: {'UNK:plan-1': 143} Unresolved non-hydrogen planarities: 143 Chain: "21" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 775 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'TRANS': 154} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 155 Planarities with less than four sites: {'UNK:plan-1': 155} Unresolved non-hydrogen planarities: 155 Chain: "A" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 379 Unusual residues: {'BCR': 2, 'BCT': 1, 'CLA': 2, 'FE2': 1, 'LHG': 1, 'PHO': 1, 'SQD': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 1420 Unusual residues: {'BCR': 4, 'CLA': 16, 'LHG': 1, 'LMG': 2, 'LMU': 1, 'SQD': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "C" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1189 Unusual residues: {'BCR': 2, 'CLA': 15, 'DGD': 2, 'OEX': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 485 Unusual residues: {'CLA': 4, 'LMG': 1, 'PHO': 1, 'PL9': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'BCR': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'LHG': 2, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CLA': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "V" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "a" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 315 Unusual residues: {'BCR': 2, 'BCT': 1, 'CLA': 2, 'FE2': 1, 'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "b" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1348 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 2, 'SQD': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "c" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1190 Unusual residues: {'BCR': 4, 'CLA': 13, 'DGD': 2, 'LMG': 1, 'OEX': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "d" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 598 Unusual residues: {'CLA': 4, 'LHG': 1, 'LMG': 1, 'PHO': 2, 'PL9': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'BCR': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCR': 1, 'CLA': 1, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "v" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "11" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 818 Unusual residues: {'A86': 6, 'CLA': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "12" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 954 Unusual residues: {'A86': 6, 'CLA': 11, 'LMG': 1, 'LMU': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "13" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 753 Unusual residues: {'A86': 6, 'CLA': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "14" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 818 Unusual residues: {'A86': 6, 'CLA': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "15" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 801 Unusual residues: {'A86': 7, 'CLA': 9} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "16" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 657 Unusual residues: {'A86': 4, 'CLA': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "17" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 821 Unusual residues: {'A86': 7, 'CLA': 9} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "18" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 787 Unusual residues: {'A86': 4, 'CLA': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "19" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 609 Unusual residues: {'A86': 3, 'CLA': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 30 Chain: "20" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 660 Unusual residues: {'A86': 5, 'CLA': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Chain: "21" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 725 Unusual residues: {'A86': 5, 'CLA': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 33.47, per 1000 atoms: 0.45 Number of scatterers: 74619 At special positions: 0 Unit cell: (224, 248.64, 129.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 6 26.01 Mn 8 24.99 Ca 2 19.99 S 222 16.00 P 8 15.00 Mg 184 11.99 O 12237 8.00 N 10435 7.00 C 51517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 44 " distance=2.04 Simple disulfide: pdb=" SG CYS o 23 " - pdb=" SG CYS o 44 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM70068 O1 A8615 310 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=164, symmetry=0 Number of additional bonds: simple=164, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.71 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: 13834 Finding SS restraints... Secondary structure from input PDB file: 301 helices and 28 sheets defined 61.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.892A pdb=" N TRP A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.830A pdb=" N ILE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.582A pdb=" N ASN A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 4.511A 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: 3.739A pdb=" N GLY A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) 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: 4.221A 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: 3.983A 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: 3.502A 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: 3.685A pdb=" N LEU C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER C 120 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) 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: 4.050A pdb=" N LEU C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 removed outlier: 4.097A 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: 3.506A 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: 3.715A 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: 3.790A pdb=" N ALA C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 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: 3.792A pdb=" N PHE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 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: 3.610A 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: 3.602A 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: 3.753A 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: 3.698A pdb=" N GLY D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 307 removed outlier: 3.574A pdb=" N ARG D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 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: 3.676A 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: 3.694A 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: 3.975A 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: 3.720A pdb=" N ILE H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Proline residue: H 13 - end of helix Processing helix chain 'H' and resid 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: 3.507A 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: 3.769A 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: 3.726A 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: 3.576A pdb=" N PHE M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 4.083A 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: 3.509A pdb=" N PHE O 186 " --> pdb=" O ALA O 183 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY O 187 " --> pdb=" O GLU O 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 removed outlier: 3.909A 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: 3.511A 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: 3.568A 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: 3.525A 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: 3.727A pdb=" N GLY V 44 " --> pdb=" O HIS V 41 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.925A 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: 3.581A pdb=" N SER X 32 " --> pdb=" O VAL X 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 26 removed outlier: 3.689A pdb=" N ALA Z 7 " --> pdb=" O THR Z 3 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU Z 11 " --> pdb=" O ALA Z 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Z 12 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Z 17 " --> pdb=" O SER Z 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL Z 18 " --> pdb=" O LEU Z 14 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR Z 19 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) Proline residue: Z 21 - end of helix removed outlier: 3.555A 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: 3.940A pdb=" N TYR Q 129 " --> pdb=" O LYS Q 125 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL Q 130 " --> pdb=" O ILE Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 145 removed outlier: 3.793A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU Q 142 " --> pdb=" O VAL Q 138 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR Q 143 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) 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: 3.652A pdb=" N ALA Q 152 " --> pdb=" O GLU Q 148 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER Q 155 " --> pdb=" O GLY Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 181 removed outlier: 3.582A pdb=" N GLU Q 164 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA Q 166 " --> pdb=" O GLN Q 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU Q 167 " --> pdb=" O LYS Q 163 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL Q 168 " --> pdb=" O GLU Q 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE Q 169 " --> pdb=" O LYS Q 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 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: 3.753A 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: 3.828A 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: 3.535A pdb=" N UNK 1 21 " --> pdb=" O UNK 1 17 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK 1 25 " --> pdb=" O UNK 1 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 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: 4.513A 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: 3.723A pdb=" N GLY a 128 " --> pdb=" O SER a 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER a 134 " --> pdb=" O GLU a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 147 removed outlier: 3.779A 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: 3.637A 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: 3.532A pdb=" N LEU a 218 " --> pdb=" O MET a 214 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR a 220 " --> pdb=" O GLY a 216 " (cutoff:3.500A) 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: 3.599A 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: 4.006A 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: 3.887A pdb=" N ALA b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL b 44 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 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: 3.617A 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: 3.719A 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: 3.645A pdb=" N SER b 240 " --> pdb=" O THR b 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER b 243 " --> pdb=" O SER b 239 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE b 247 " --> pdb=" O SER b 243 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA b 248 " --> pdb=" O ALA b 244 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 251 " --> pdb=" O PHE b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 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: 3.934A 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: 3.659A 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: 3.824A pdb=" N PHE b 464 " --> pdb=" O LEU b 460 " (cutoff:3.500A) Processing helix chain 'b' and resid 476 through 479 removed outlier: 3.850A 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: 3.502A 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: 3.683A pdb=" N LEU c 117 " --> pdb=" O GLY c 113 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER c 120 " --> pdb=" O HIS c 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA c 121 " --> pdb=" O LEU c 117 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE c 122 " --> pdb=" O ILE c 118 " (cutoff:3.500A) 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: 3.722A pdb=" N THR c 156 " --> pdb=" O LYS c 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU c 165 " --> pdb=" O ILE c 161 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER c 170 " --> pdb=" O LEU c 166 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU c 173 " --> pdb=" O GLY c 169 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL c 174 " --> pdb=" O SER c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 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: 3.847A pdb=" N TRP c 237 " --> pdb=" O GLY c 233 " (cutoff:3.500A) Processing helix chain 'c' and resid 255 through 262 removed outlier: 3.508A pdb=" N ARG c 260 " --> pdb=" O ALA c 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA c 261 " --> pdb=" O TRP c 257 " (cutoff:3.500A) 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: 3.718A 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: 3.506A pdb=" N SER c 278 " --> pdb=" O LEU c 274 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP c 289 " --> pdb=" O ALA c 285 " (cutoff:3.500A) Processing helix chain 'c' and resid 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: 3.871A 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: 3.518A pdb=" N GLU c 392 " --> pdb=" O ARG c 388 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR c 395 " --> pdb=" O ALA c 391 " (cutoff:3.500A) Processing helix chain 'c' and resid 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: 3.651A pdb=" N LEU c 436 " --> pdb=" O ALA c 432 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA c 451 " --> pdb=" O ARG c 447 " (cutoff:3.500A) Processing helix chain 'd' and resid 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: 3.609A 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: 4.127A 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: 3.600A 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: 3.742A 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: 3.521A pdb=" N SER d 281 " --> pdb=" O GLY d 277 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY d 284 " --> pdb=" O THR d 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE d 285 " --> pdb=" O SER d 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL d 286 " --> pdb=" O SER d 282 " (cutoff:3.500A) Processing helix chain 'd' and resid 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: 3.508A 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: 3.565A pdb=" N ILE e 14 " --> pdb=" O PRO e 10 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.743A 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: 3.975A 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: 3.721A 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: 3.551A 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: 3.509A 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: 3.771A 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: 3.779A 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: 3.603A pdb=" N TYR l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR l 35 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 38 Proline residue: m 18 - end of helix removed outlier: 3.546A pdb=" N ASN m 24 " --> pdb=" O LEU m 20 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE m 26 " --> pdb=" O LEU m 22 " (cutoff:3.500A) 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: 3.753A 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: 3.727A 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: 3.655A 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: 3.755A 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: 3.533A pdb=" N ILE x 22 " --> pdb=" O VAL x 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER x 32 " --> pdb=" O VAL x 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 26 removed outlier: 3.689A pdb=" N ALA z 7 " --> pdb=" O THR z 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU z 11 " --> pdb=" O ALA z 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE z 12 " --> pdb=" O LEU z 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL z 17 " --> pdb=" O SER z 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL z 18 " --> pdb=" O LEU z 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR z 19 " --> pdb=" O GLY z 15 " (cutoff:3.500A) Proline residue: z 21 - end of helix 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: 3.757A pdb=" N ARG z 39 " --> pdb=" O GLY z 35 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE z 40 " --> pdb=" O LYS z 36 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL z 48 " --> pdb=" O TRP z 44 " (cutoff:3.500A) Processing helix chain 'q' and resid 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: 3.851A 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: 3.502A 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: 4.066A pdb=" N TYR q 145 " --> pdb=" O GLU q 141 " (cutoff:3.500A) Processing helix chain 'q' and resid 148 through 157 removed outlier: 3.652A pdb=" N ALA q 152 " --> pdb=" O GLU q 148 " (cutoff:3.500A) removed outlier: 3.711A 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: 3.988A pdb=" N GLU q 167 " --> pdb=" O LYS q 163 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL q 168 " --> pdb=" O GLU q 164 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE q 169 " --> pdb=" O LYS q 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP q 175 " --> pdb=" O ARG q 171 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR q 176 " --> pdb=" O ALA q 172 " (cutoff:3.500A) Processing helix chain 'q' and resid 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: 3.945A pdb=" N UNK 5 15 " --> pdb=" O UNK 5 11 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N UNK 5 16 " --> pdb=" O UNK 5 12 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 28 removed outlier: 3.722A pdb=" N UNK 6 11 " --> pdb=" O UNK 6 7 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK 6 12 " --> pdb=" O UNK 6 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK 6 21 " --> pdb=" O UNK 6 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N UNK 6 25 " --> pdb=" O UNK 6 21 " (cutoff:3.500A) Processing helix chain '11' and resid 32 through 36 removed outlier: 3.523A 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: 3.697A 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: 3.580A pdb=" N HIS11 81 " --> pdb=" O GLY11 77 " (cutoff:3.500A) Processing helix chain '11' and resid 105 through 112 removed outlier: 3.864A 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: 3.808A 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: 3.681A 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: 3.704A 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: 3.524A pdb=" N LEU12 35 " --> pdb=" O GLU12 32 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.764A 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: 3.862A 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: 3.704A 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: 3.696A pdb=" N VAL13 76 " --> pdb=" O MET13 72 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY13 77 " --> pdb=" O ALA13 73 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.806A 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: 3.683A 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: 3.523A pdb=" N LEU14 35 " --> pdb=" O GLU14 32 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.723A 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: 3.697A 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: 3.862A 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: 3.807A 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: 4.189A pdb=" N ASN14 161 " --> pdb=" O ALA14 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA14 180 " --> pdb=" O GLY14 176 " (cutoff:3.500A) Processing helix chain '14' and resid 187 through 195 Processing helix chain '15' and resid 31 through 36 removed outlier: 3.535A pdb=" N LEU15 35 " --> pdb=" O GLU15 32 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY15 36 " --> pdb=" O ILE15 33 " (cutoff:3.500A) Processing helix chain '15' and resid 48 through 53 Processing helix chain '15' and resid 56 through 83 removed outlier: 3.868A pdb=" N LYS15 66 " --> pdb=" O ALA15 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA15 73 " --> pdb=" O ARG15 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL15 76 " --> pdb=" O MET15 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS15 81 " --> pdb=" O GLY15 77 " (cutoff:3.500A) Processing helix chain '15' and resid 108 through 112 Processing helix chain '15' and resid 113 through 129 removed outlier: 3.572A pdb=" N ALA15 122 " --> pdb=" O ALA15 118 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE15 123 " --> pdb=" O GLN15 119 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU15 126 " --> pdb=" O ALA15 122 " (cutoff:3.500A) Processing helix chain '15' and resid 152 through 183 removed outlier: 3.591A pdb=" N ASN15 161 " --> pdb=" O ALA15 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL15 162 " --> pdb=" O ARG15 158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU15 164 " --> pdb=" O LEU15 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL15 179 " --> pdb=" O MET15 175 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA15 180 " --> pdb=" O GLY15 176 " (cutoff:3.500A) Processing helix chain '15' and resid 187 through 194 removed outlier: 3.645A pdb=" N TYR15 192 " --> pdb=" O MET15 188 " (cutoff:3.500A) Processing helix chain '16' and resid 56 through 83 removed outlier: 3.544A pdb=" N VAL16 63 " --> pdb=" O ARG16 59 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA16 71 " --> pdb=" O HIS16 67 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA16 73 " --> pdb=" O ARG16 69 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL16 76 " --> pdb=" O MET16 72 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY16 77 " --> pdb=" O ALA16 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS16 81 " --> pdb=" O GLY16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 106 through 111 removed outlier: 4.476A pdb=" N ARG16 110 " --> pdb=" O VAL16 106 " (cutoff:3.500A) Processing helix chain '16' and resid 113 through 130 removed outlier: 4.088A pdb=" N GLN16 119 " --> pdb=" O ALA16 115 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE16 123 " --> pdb=" O GLN16 119 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU16 126 " --> pdb=" O ALA16 122 " (cutoff:3.500A) Processing helix chain '16' and resid 152 through 183 removed outlier: 3.585A pdb=" N LYS16 156 " --> pdb=" O ASP16 152 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA16 157 " --> pdb=" O PRO16 153 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG16 158 " --> pdb=" O GLU16 154 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN16 161 " --> pdb=" O ALA16 157 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL16 162 " --> pdb=" O ARG16 158 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU16 164 " --> pdb=" O LEU16 160 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA16 169 " --> pdb=" O ASN16 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET16 171 " --> pdb=" O GLY16 167 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET16 172 " --> pdb=" O ARG16 168 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY16 173 " --> pdb=" O ALA16 169 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA16 180 " --> pdb=" O GLY16 176 " (cutoff:3.500A) Processing helix chain '16' and resid 187 through 195 removed outlier: 3.581A pdb=" N TYR16 192 " --> pdb=" O MET16 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA16 193 " --> pdb=" O TYR16 189 " (cutoff:3.500A) Processing helix chain '17' and resid 32 through 36 removed outlier: 3.776A pdb=" N LEU17 35 " --> pdb=" O GLU17 32 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY17 36 " --> pdb=" O ILE17 33 " (cutoff:3.500A) No H-bonds generated for 'chain '17' and resid 32 through 36' Processing helix chain '17' and resid 48 through 53 Processing helix chain '17' and resid 56 through 83 removed outlier: 3.649A pdb=" N ALA17 62 " --> pdb=" O GLU17 58 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA17 73 " --> pdb=" O ARG17 69 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL17 76 " --> pdb=" O MET17 72 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY17 77 " --> pdb=" O ALA17 73 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS17 81 " --> pdb=" O GLY17 77 " (cutoff:3.500A) Processing helix chain '17' and resid 105 through 112 removed outlier: 3.848A pdb=" N GLY17 108 " --> pdb=" O GLY17 105 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE17 109 " --> pdb=" O VAL17 106 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG17 110 " --> pdb=" O ASP17 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA17 111 " --> pdb=" O GLY17 108 " (cutoff:3.500A) Processing helix chain '17' and resid 113 through 130 removed outlier: 3.693A pdb=" N LEU17 126 " --> pdb=" O ALA17 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU17 128 " --> pdb=" O PHE17 124 " (cutoff:3.500A) Processing helix chain '17' and resid 153 through 183 removed outlier: 4.729A pdb=" N ALA17 157 " --> pdb=" O PRO17 153 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG17 158 " --> pdb=" O GLU17 154 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA17 170 " --> pdb=" O ASN17 166 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET17 171 " --> pdb=" O GLY17 167 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET17 172 " --> pdb=" O ARG17 168 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY17 173 " --> pdb=" O ALA17 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET17 175 " --> pdb=" O MET17 171 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA17 180 " --> pdb=" O GLY17 176 " (cutoff:3.500A) Processing helix chain '17' and resid 187 through 195 Processing helix chain '18' and resid 48 through 53 removed outlier: 3.850A pdb=" N SER18 52 " --> pdb=" O GLY18 48 " (cutoff:3.500A) Processing helix chain '18' and resid 56 through 83 removed outlier: 3.725A pdb=" N VAL18 63 " --> pdb=" O ARG18 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL18 76 " --> pdb=" O MET18 72 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS18 81 " --> pdb=" O GLY18 77 " (cutoff:3.500A) Processing helix chain '18' and resid 105 through 112 removed outlier: 3.925A pdb=" N GLY18 108 " --> pdb=" O GLY18 105 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE18 109 " --> pdb=" O VAL18 106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG18 110 " --> pdb=" O ASP18 107 " (cutoff:3.500A) Processing helix chain '18' and resid 113 through 129 removed outlier: 3.577A pdb=" N LEU18 126 " --> pdb=" O ALA18 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU18 129 " --> pdb=" O ALA18 125 " (cutoff:3.500A) Processing helix chain '18' and resid 144 through 148 Processing helix chain '18' and resid 152 through 183 removed outlier: 3.875A pdb=" N VAL18 162 " --> pdb=" O ARG18 158 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU18 163 " --> pdb=" O LYS18 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET18 172 " --> pdb=" O ARG18 168 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA18 180 " --> pdb=" O GLY18 176 " (cutoff:3.500A) Processing helix chain '18' and resid 187 through 194 removed outlier: 3.548A pdb=" N TYR18 192 " --> pdb=" O MET18 188 " (cutoff:3.500A) Processing helix chain '19' and resid 19 through 23 removed outlier: 3.809A pdb=" N UNK19 22 " --> pdb=" O UNK19 19 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N UNK19 23 " --> pdb=" O UNK19 20 " (cutoff:3.500A) No H-bonds generated for 'chain '19' and resid 19 through 23' Processing helix chain '19' and resid 57 through 68 removed outlier: 3.577A pdb=" N UNK19 63 " --> pdb=" O UNK19 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N UNK19 64 " --> pdb=" O UNK19 60 " (cutoff:3.500A) Processing helix chain '19' and resid 68 through 73 removed outlier: 3.527A pdb=" N UNK19 73 " --> pdb=" O UNK19 69 " (cutoff:3.500A) Processing helix chain '19' and resid 76 through 81 Processing helix chain '19' and resid 105 through 110 Processing helix chain '19' and resid 111 through 135 removed outlier: 3.743A pdb=" N UNK19 115 " --> pdb=" O UNK19 111 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK19 116 " --> pdb=" O UNK19 112 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N UNK19 125 " --> pdb=" O UNK19 121 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N UNK19 128 " --> pdb=" O UNK19 124 " (cutoff:3.500A) Processing helix chain '19' and resid 156 through 188 removed outlier: 3.923A pdb=" N UNK19 161 " --> pdb=" O UNK19 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK19 162 " --> pdb=" O UNK19 158 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N UNK19 174 " --> pdb=" O UNK19 170 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK19 176 " --> pdb=" O UNK19 172 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNK19 177 " --> pdb=" O UNK19 173 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N UNK19 179 " --> pdb=" O UNK19 175 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N UNK19 180 " --> pdb=" O UNK19 176 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK19 183 " --> pdb=" O UNK19 179 " (cutoff:3.500A) Processing helix chain '19' and resid 190 through 195 Processing helix chain '20' and resid 58 through 83 removed outlier: 3.982A pdb=" N UNK20 76 " --> pdb=" O UNK20 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK20 77 " --> pdb=" O UNK20 73 " (cutoff:3.500A) Processing helix chain '20' and resid 113 through 130 removed outlier: 3.646A pdb=" N UNK20 117 " --> pdb=" O UNK20 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK20 127 " --> pdb=" O UNK20 123 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNK20 128 " --> pdb=" O UNK20 124 " (cutoff:3.500A) Processing helix chain '20' and resid 155 through 183 removed outlier: 3.835A pdb=" N UNK20 169 " --> pdb=" O UNK20 165 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N UNK20 170 " --> pdb=" O UNK20 166 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N UNK20 172 " --> pdb=" O UNK20 168 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N UNK20 173 " --> pdb=" O UNK20 169 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N UNK20 175 " --> pdb=" O UNK20 171 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK20 178 " --> pdb=" O UNK20 174 " (cutoff:3.500A) Processing helix chain '21' and resid 48 through 53 removed outlier: 3.708A pdb=" N UNK21 52 " --> pdb=" O UNK21 48 " (cutoff:3.500A) Processing helix chain '21' and resid 56 through 83 removed outlier: 3.831A pdb=" N UNK21 63 " --> pdb=" O UNK21 59 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N UNK21 71 " --> pdb=" O UNK21 67 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK21 73 " --> pdb=" O UNK21 69 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N UNK21 76 " --> pdb=" O UNK21 72 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK21 77 " --> pdb=" O UNK21 73 " (cutoff:3.500A) Processing helix chain '21' and resid 107 through 112 Processing helix chain '21' and resid 113 through 130 removed outlier: 3.501A pdb=" N UNK21 118 " --> pdb=" O UNK21 114 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK21 119 " --> pdb=" O UNK21 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N UNK21 122 " --> pdb=" O UNK21 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N UNK21 128 " --> pdb=" O UNK21 124 " (cutoff:3.500A) Processing helix chain '21' and resid 144 through 148 removed outlier: 3.623A pdb=" N UNK21 147 " --> pdb=" O UNK21 144 " (cutoff:3.500A) Processing helix chain '21' and resid 152 through 184 removed outlier: 3.601A pdb=" N UNK21 157 " --> pdb=" O UNK21 153 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N UNK21 166 " --> pdb=" O UNK21 162 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK21 167 " --> pdb=" O UNK21 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK21 169 " --> pdb=" O UNK21 165 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N UNK21 170 " --> pdb=" O UNK21 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK21 172 " --> pdb=" O UNK21 168 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK21 175 " --> pdb=" O UNK21 171 " (cutoff:3.500A) Processing sheet with id=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 306 through 307 removed outlier: 4.392A pdb=" N VAL A 306 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA5, 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: 5.176A pdb=" N TRP B 340 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 429 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AA8, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'D' and resid 76 through 77 Processing sheet with id=AB1, 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: 6.280A pdb=" N CYS O 44 " --> pdb=" O ASP O 80 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP O 80 " --> pdb=" O CYS O 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 64 through 68 removed outlier: 5.697A pdb=" N MET O 43 " --> pdb=" O LYS O 245 " (cutoff:3.500A) removed outlier: 7.256A 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: 4.427A 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: 4.039A pdb=" N ASP O 143 " --> pdb=" O VAL O 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 70 through 71 Processing sheet with id=AB4, first strand: chain 'V' and resid 9 through 11 Processing sheet with id=AB5, first strand: chain 'a' and resid 58 through 59 Processing sheet with id=AB6, first strand: chain 'a' and resid 81 through 82 Processing sheet with id=AB7, first strand: chain 'a' and resid 297 through 298 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: 5.175A 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=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 'f' and resid 41 through 42 removed outlier: 4.302A pdb=" N UNK 7 12 " --> pdb=" O GLN f 42 " (cutoff:3.500A) Processing sheet with id=AC7, 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: 6.280A 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=AC8, 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: 7.256A 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: 5.106A pdb=" N LYS o 235 " --> pdb=" O GLU o 53 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY o 240 " --> pdb=" O PHE o 218 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY o 216 " --> pdb=" O PHE o 242 " (cutoff:3.500A) removed outlier: 6.864A 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: 7.203A 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: 4.038A pdb=" N ASP o 143 " --> pdb=" O VAL o 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'o' and resid 70 through 71 Processing sheet with id=AD1, first strand: chain 'v' and resid 9 through 11 2672 hydrogen bonds defined for protein. 7689 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: 21.72 Time building geometry restraints manager: 17.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.68: 76547 1.68 - 2.19: 1175 2.19 - 2.71: 12 2.71 - 3.22: 0 3.22 - 3.73: 8 Bond restraints: 77742 Sorted by residual: bond pdb=" C4 A8620 201 " pdb=" C5 A8620 201 " ideal model delta sigma weight residual 1.431 1.669 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C4 A8620 212 " pdb=" C5 A8620 212 " ideal model delta sigma weight residual 1.431 1.665 -0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4 A8619 311 " pdb=" C5 A8619 311 " ideal model delta sigma weight residual 1.431 1.664 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4 A8620 210 " pdb=" C5 A8620 210 " ideal model delta sigma weight residual 1.431 1.663 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C4 A8617 315 " pdb=" C5 A8617 315 " ideal model delta sigma weight residual 1.431 1.663 -0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 77737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.86: 107884 7.86 - 15.72: 747 15.72 - 23.58: 8 23.58 - 31.43: 0 31.43 - 39.29: 59 Bond angle restraints: 108698 Sorted by residual: angle pdb=" C19 A8617 311 " pdb=" C20 A8617 311 " pdb=" O1 A8617 311 " ideal model delta sigma weight residual 115.66 154.95 -39.29 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C19 A8617 315 " pdb=" C20 A8617 315 " pdb=" O1 A8617 315 " ideal model delta sigma weight residual 115.66 154.94 -39.28 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C19 A8618 313 " pdb=" C20 A8618 313 " pdb=" O1 A8618 313 " ideal model delta sigma weight residual 115.66 154.75 -39.09 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C19 A8620 210 " pdb=" C20 A8620 210 " pdb=" O1 A8620 210 " ideal model delta sigma weight residual 115.66 154.74 -39.08 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C19 A8611 310 " pdb=" C20 A8611 310 " pdb=" O1 A8611 310 " ideal model delta sigma weight residual 115.66 154.72 -39.06 3.00e+00 1.11e-01 1.70e+02 ... (remaining 108693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 38769 31.11 - 62.22: 2183 62.22 - 93.34: 446 93.34 - 124.45: 165 124.45 - 155.56: 57 Dihedral angle restraints: 41620 sinusoidal: 19950 harmonic: 21670 Sorted by residual: dihedral pdb=" CA UNK20 146 " pdb=" C UNK20 146 " pdb=" N UNK20 147 " pdb=" CA UNK20 147 " ideal model delta harmonic sigma weight residual -180.00 -134.10 -45.90 0 5.00e+00 4.00e-02 8.43e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 44 " pdb=" CB CYS O 44 " ideal model delta sinusoidal sigma weight residual 93.00 167.29 -74.29 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS o 23 " pdb=" SG CYS o 23 " pdb=" SG CYS o 44 " pdb=" CB CYS o 44 " ideal model delta sinusoidal sigma weight residual 93.00 167.26 -74.26 1 1.00e+01 1.00e-02 7.00e+01 ... (remaining 41617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 10155 0.336 - 0.672: 57 0.672 - 1.008: 4 1.008 - 1.344: 1 1.344 - 1.679: 59 Chirality restraints: 10276 Sorted by residual: chirality pdb=" C20 A8620 201 " pdb=" C15 A8620 201 " pdb=" C19 A8620 201 " pdb=" C21 A8620 201 " both_signs ideal model delta sigma weight residual True 1.08 2.76 -1.68 2.00e-01 2.50e+01 7.05e+01 chirality pdb=" C20 A8618 313 " pdb=" C15 A8618 313 " pdb=" C19 A8618 313 " pdb=" C21 A8618 313 " both_signs ideal model delta sigma weight residual True 1.08 2.76 -1.68 2.00e-01 2.50e+01 7.04e+01 chirality pdb=" C20 A8613 311 " pdb=" C15 A8613 311 " pdb=" C19 A8613 311 " pdb=" C21 A8613 311 " both_signs ideal model delta sigma weight residual True 1.08 2.75 -1.67 2.00e-01 2.50e+01 6.99e+01 ... (remaining 10273 not shown) Planarity restraints: 13967 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 " -0.148 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 " -0.034 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 " -0.056 2.00e-02 2.50e+03 pdb=" C3A PHO D 403 " 0.299 2.00e-02 2.50e+03 pdb=" C3B PHO D 403 " -0.120 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 " -0.097 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 " -0.076 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 404 " 0.071 2.00e-02 2.50e+03 1.01e-01 8.15e+02 pdb=" ND PHO d 404 " 0.148 2.00e-02 2.50e+03 pdb=" C1A PHO d 404 " 0.020 2.00e-02 2.50e+03 pdb=" C1B PHO d 404 " 0.003 2.00e-02 2.50e+03 pdb=" C1C PHO d 404 " 0.034 2.00e-02 2.50e+03 pdb=" C1D PHO d 404 " 0.077 2.00e-02 2.50e+03 pdb=" C2A PHO d 404 " -0.086 2.00e-02 2.50e+03 pdb=" C2B PHO d 404 " 0.063 2.00e-02 2.50e+03 pdb=" C2C PHO d 404 " -0.066 2.00e-02 2.50e+03 pdb=" C2D PHO d 404 " 0.055 2.00e-02 2.50e+03 pdb=" C3A PHO d 404 " -0.298 2.00e-02 2.50e+03 pdb=" C3B PHO d 404 " 0.121 2.00e-02 2.50e+03 pdb=" C3C PHO d 404 " -0.101 2.00e-02 2.50e+03 pdb=" C3D PHO d 404 " 0.077 2.00e-02 2.50e+03 pdb=" C4A PHO d 404 " -0.119 2.00e-02 2.50e+03 pdb=" C4B PHO d 404 " 0.109 2.00e-02 2.50e+03 pdb=" C4C PHO d 404 " -0.008 2.00e-02 2.50e+03 pdb=" C4D PHO d 404 " 0.097 2.00e-02 2.50e+03 pdb=" CAB PHO d 404 " 0.111 2.00e-02 2.50e+03 pdb=" CAC PHO d 404 " -0.230 2.00e-02 2.50e+03 pdb=" CAD PHO d 404 " 0.028 2.00e-02 2.50e+03 pdb=" CBD PHO d 404 " 0.019 2.00e-02 2.50e+03 pdb=" CHA PHO d 404 " 0.061 2.00e-02 2.50e+03 pdb=" CHB PHO d 404 " -0.111 2.00e-02 2.50e+03 pdb=" CHC PHO d 404 " 0.078 2.00e-02 2.50e+03 pdb=" CHD PHO d 404 " -0.003 2.00e-02 2.50e+03 pdb=" CMB PHO d 404 " -0.021 2.00e-02 2.50e+03 pdb=" CMC PHO d 404 " -0.153 2.00e-02 2.50e+03 pdb=" CMD PHO d 404 " 0.007 2.00e-02 2.50e+03 pdb=" NA PHO d 404 " -0.017 2.00e-02 2.50e+03 pdb=" NC PHO d 404 " 0.063 2.00e-02 2.50e+03 pdb=" OBD PHO d 404 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO d 403 " 0.040 2.00e-02 2.50e+03 9.50e-02 7.23e+02 pdb=" ND PHO d 403 " 0.063 2.00e-02 2.50e+03 pdb=" C1A PHO d 403 " -0.031 2.00e-02 2.50e+03 pdb=" C1B PHO d 403 " 0.037 2.00e-02 2.50e+03 pdb=" C1C PHO d 403 " -0.003 2.00e-02 2.50e+03 pdb=" C1D PHO d 403 " 0.010 2.00e-02 2.50e+03 pdb=" C2A PHO d 403 " -0.019 2.00e-02 2.50e+03 pdb=" C2B PHO d 403 " -0.078 2.00e-02 2.50e+03 pdb=" C2C PHO d 403 " 0.042 2.00e-02 2.50e+03 pdb=" C2D PHO d 403 " -0.009 2.00e-02 2.50e+03 pdb=" C3A PHO d 403 " 0.305 2.00e-02 2.50e+03 pdb=" C3B PHO d 403 " -0.122 2.00e-02 2.50e+03 pdb=" C3C PHO d 403 " 0.047 2.00e-02 2.50e+03 pdb=" C3D PHO d 403 " -0.062 2.00e-02 2.50e+03 pdb=" C4A PHO d 403 " 0.148 2.00e-02 2.50e+03 pdb=" C4B PHO d 403 " -0.034 2.00e-02 2.50e+03 pdb=" C4C PHO d 403 " -0.002 2.00e-02 2.50e+03 pdb=" C4D PHO d 403 " -0.036 2.00e-02 2.50e+03 pdb=" CAB PHO d 403 " -0.190 2.00e-02 2.50e+03 pdb=" CAC PHO d 403 " 0.101 2.00e-02 2.50e+03 pdb=" CAD PHO d 403 " -0.075 2.00e-02 2.50e+03 pdb=" CBD PHO d 403 " -0.180 2.00e-02 2.50e+03 pdb=" CHA PHO d 403 " -0.089 2.00e-02 2.50e+03 pdb=" CHB PHO d 403 " 0.139 2.00e-02 2.50e+03 pdb=" CHC PHO d 403 " -0.013 2.00e-02 2.50e+03 pdb=" CHD PHO d 403 " -0.018 2.00e-02 2.50e+03 pdb=" CMB PHO d 403 " -0.095 2.00e-02 2.50e+03 pdb=" CMC PHO d 403 " 0.087 2.00e-02 2.50e+03 pdb=" CMD PHO d 403 " 0.001 2.00e-02 2.50e+03 pdb=" NA PHO d 403 " 0.072 2.00e-02 2.50e+03 pdb=" NC PHO d 403 " -0.027 2.00e-02 2.50e+03 pdb=" OBD PHO d 403 " -0.008 2.00e-02 2.50e+03 ... (remaining 13964 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 27 2.09 - 2.80: 18484 2.80 - 3.50: 92470 3.50 - 4.20: 190843 4.20 - 4.90: 322643 Nonbonded interactions: 624467 Sorted by model distance: nonbonded pdb=" OE2 GLU c 352 " pdb=" O3 OEX c 501 " model vdw 1.392 3.040 nonbonded pdb=" O PHE18 146 " pdb=" O5 A8618 302 " model vdw 1.590 3.040 nonbonded pdb=" O PHE11 146 " pdb=" O5 A8611 316 " model vdw 1.619 3.040 nonbonded pdb=" OE2 GLU C 352 " pdb=" O3 OEX C 501 " model vdw 1.622 3.040 nonbonded pdb=" O PHE13 146 " pdb=" O5 A8613 301 " model vdw 1.632 3.040 ... (remaining 624462 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 30) selection = (chain '1' and resid 2 through 30) selection = (chain '5' and resid 2 through 30) selection = (chain '6' and resid 1 through 29) } ncs_group { reference = (chain '11' and (resid 31 through 206 or (resid 303 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or \ name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A \ or name O2D or name OBD or name MG )))) selection = (chain '12' and (resid 31 through 206 or (resid 303 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or \ name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A \ or name O2D or name OBD or name MG )))) selection = (chain '13' and (resid 31 through 206 or resid 303 or (resid 305 through 309 and \ (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or \ name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CED \ or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or name \ CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A or na \ me O1D or name O2A or name O2D or name OBD or name MG )))) selection = (chain '14' and (resid 31 through 206 or (resid 303 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or \ name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A \ or name O2D or name OBD or name MG )))) selection = (chain '15' and (resid 31 through 206 or (resid 303 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or \ name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A \ or name O2D or name OBD or name MG )))) selection = (chain '16' and (resid 31 through 206 or resid 303 or resid 305 through 309)) selection = (chain '17' and (resid 31 through 206 or (resid 303 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or \ name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A \ or name O2D or name OBD or name MG )))) selection = (chain '18' and (resid 31 through 206 or (resid 303 and (name NB or name ND or n \ ame C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C \ or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name \ C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or n \ ame CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD \ or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name \ CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or nam \ e O2D or name OBD or name MG )) or (resid 305 through 309 and (name NB or name N \ D or name C1A or name C1B or name C1C or name C1D or name C2A or name C2B or nam \ e C2C or name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or \ name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CA \ D or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or nam \ e CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or \ name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A \ or name O2D or name OBD or name MG )))) } ncs_group { reference = chain '2' selection = chain '7' } ncs_group { reference = (chain '20' and (resid 42 through 183 or resid 202 through 203 or (resid 204 thr \ ough 208 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or \ name CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or na \ me O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 21 \ 0 through 213)) selection = (chain '21' and (resid 44 through 185 or resid 303 through 305 or (resid 306 thr \ ough 309 and (name NB or name ND or name C1A or name C1B or name C1C or name C1D \ or name C2A or name C2B or name C2C or name C2D or name C3A or name C3B or name \ C3C or name C3D or name C4A or name C4B or name C4C or name C4D or name CAA or \ name CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD \ or name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name \ CHD or name CMA or name CMB or name CMC or name CMD or name NA or name NC or na \ me O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 31 \ 1 through 314)) } ncs_group { reference = (chain 'A' and (resid 11 through 344 or resid 401 through 402)) selection = (chain 'a' and (resid 11 through 344 or resid 401 through 402)) } ncs_group { reference = (chain 'B' and (resid 2 through 485 or resid 601 through 617 or resid 619)) selection = (chain 'b' and (resid 2 through 485 or resid 601 through 617 or resid 619)) } ncs_group { reference = (chain 'C' and (resid 21 through 471 or resid 501 through 515 or resid 517)) selection = (chain 'c' and (resid 21 through 471 or resid 501 through 515 or resid 517)) } ncs_group { reference = (chain 'D' and (resid 11 through 351 or resid 401 through 403 or resid 406)) selection = (chain 'd' and (resid 11 through 351 or resid 401 through 403 or resid 406)) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = (chain 'L' and (resid 1 through 38 or resid 102)) selection = (chain 'l' and (resid 1 through 38 or resid 102)) } ncs_group { reference = chain 'M' selection = (chain 'm' and (resid 2 through 43 or resid 101 through 102)) } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = (chain 'Q' and resid 70 through 206) selection = chain 'q' } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = chain 'U' selection = chain 'u' } ncs_group { reference = chain 'V' selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'w' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = (chain 'Y' and resid 1 through 34) selection = chain 'y' } ncs_group { reference = (chain 'Z' and resid 1 through 59) selection = (chain 'z' and resid 1 through 59) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 160.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.370 Check model and map are aligned: 0.450 Set scattering table: 0.550 Process input model: 119.640 Find NCS groups from input model: 3.880 Set up NCS constraints: 0.870 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 290.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.249 77742 Z= 1.035 Angle : 1.816 39.293 108698 Z= 0.720 Chirality : 0.146 1.679 10276 Planarity : 0.014 0.264 13967 Dihedral : 20.864 155.560 27780 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 0.28 % Allowed : 2.90 % Favored : 96.82 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.07), residues: 6884 helix: -4.10 (0.04), residues: 3588 sheet: -1.77 (0.33), residues: 236 loop : -2.37 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP a 142 HIS 0.018 0.004 HIS F 22 PHE 0.040 0.004 PHE c 282 TYR 0.042 0.003 TYR h 49 ARG 0.016 0.001 ARG17 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1801 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1785 time to evaluate : 5.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.9505 (tp40) cc_final: 0.8948 (tp-100) REVERT: A 238 LYS cc_start: 0.9133 (mmtm) cc_final: 0.8682 (mttt) REVERT: A 314 ILE cc_start: 0.8832 (mm) cc_final: 0.8629 (mm) REVERT: B 55 MET cc_start: 0.8468 (ptp) cc_final: 0.8246 (ptm) REVERT: C 175 ILE cc_start: 0.9205 (mt) cc_final: 0.8947 (mm) REVERT: C 344 SER cc_start: 0.8926 (m) cc_final: 0.8624 (t) REVERT: C 359 LEU cc_start: 0.8510 (tm) cc_final: 0.7156 (tm) REVERT: C 404 SER cc_start: 0.8777 (m) cc_final: 0.8370 (p) REVERT: D 22 LYS cc_start: 0.8796 (mttt) cc_final: 0.8436 (pttp) REVERT: D 243 TYR cc_start: 0.9146 (p90) cc_final: 0.8834 (p90) REVERT: D 272 PHE cc_start: 0.8971 (t80) cc_final: 0.8713 (t80) REVERT: D 325 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7622 (mtm180) REVERT: E 72 SER cc_start: 0.7831 (p) cc_final: 0.7366 (t) REVERT: H 4 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7486 (mmm-85) REVERT: H 31 MET cc_start: 0.8159 (ttp) cc_final: 0.7754 (ttm) REVERT: L 17 SER cc_start: 0.9319 (m) cc_final: 0.9043 (p) REVERT: L 19 TYR cc_start: 0.9102 (m-80) cc_final: 0.8899 (m-80) REVERT: O 124 ASP cc_start: 0.7973 (m-30) cc_final: 0.7671 (t0) REVERT: O 168 MET cc_start: 0.7187 (pp-130) cc_final: 0.6922 (ppp) REVERT: O 202 MET cc_start: 0.8352 (mtm) cc_final: 0.8043 (mtm) REVERT: T 23 PHE cc_start: 0.8684 (m-80) cc_final: 0.8442 (m-80) REVERT: U 14 GLU cc_start: 0.8859 (tp30) cc_final: 0.8522 (tp30) REVERT: U 60 ASP cc_start: 0.8348 (m-30) cc_final: 0.7589 (t0) REVERT: U 100 LEU cc_start: 0.8940 (tt) cc_final: 0.8628 (tt) REVERT: V 49 ASN cc_start: 0.8296 (t0) cc_final: 0.7616 (t0) REVERT: V 112 LEU cc_start: 0.9242 (mt) cc_final: 0.8924 (mt) REVERT: Y 5 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7666 (mm-40) REVERT: Y 33 ASN cc_start: 0.8030 (m-40) cc_final: 0.7830 (p0) REVERT: Z 9 LEU cc_start: 0.8978 (tm) cc_final: 0.8726 (tp) REVERT: Z 55 ASP cc_start: 0.8653 (t0) cc_final: 0.8215 (t0) REVERT: Q 79 THR cc_start: 0.7179 (p) cc_final: 0.6689 (m) REVERT: Q 104 ASP cc_start: 0.8317 (p0) cc_final: 0.8081 (p0) REVERT: Q 105 ASN cc_start: 0.7497 (m-40) cc_final: 0.7230 (m-40) REVERT: W 45 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9113 (mp) REVERT: a 59 ASP cc_start: 0.8580 (t0) cc_final: 0.8380 (t0) REVERT: b 439 SER cc_start: 0.8350 (m) cc_final: 0.8060 (t) REVERT: c 65 MET cc_start: 0.8304 (tpt) cc_final: 0.7944 (tpt) REVERT: c 86 LEU cc_start: 0.9184 (mt) cc_final: 0.8879 (tp) REVERT: c 344 SER cc_start: 0.8985 (m) cc_final: 0.8303 (t) REVERT: c 377 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8005 (mtmt) REVERT: c 381 ASP cc_start: 0.6527 (m-30) cc_final: 0.6138 (p0) REVERT: c 383 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8689 (mm-40) REVERT: d 18 ASP cc_start: 0.8424 (t0) cc_final: 0.7943 (t0) REVERT: d 158 LEU cc_start: 0.9509 (mt) cc_final: 0.9171 (tp) REVERT: d 185 GLN cc_start: 0.8577 (tp40) cc_final: 0.8303 (tp-100) REVERT: d 197 MET cc_start: 0.8621 (mtt) cc_final: 0.8324 (mtt) REVERT: d 245 MET cc_start: 0.8598 (tpt) cc_final: 0.8393 (tpt) REVERT: d 273 VAL cc_start: 0.9547 (t) cc_final: 0.9210 (m) REVERT: d 307 ASP cc_start: 0.8332 (t0) cc_final: 0.8061 (t0) REVERT: e 69 ASP cc_start: 0.6968 (t70) cc_final: 0.6650 (t70) REVERT: f 26 ILE cc_start: 0.9308 (mt) cc_final: 0.9077 (mt) REVERT: h 31 MET cc_start: 0.7868 (ttp) cc_final: 0.7457 (ttp) REVERT: i 17 SER cc_start: 0.9314 (m) cc_final: 0.8913 (p) REVERT: j 31 SER cc_start: 0.9416 (m) cc_final: 0.9100 (t) REVERT: k 17 SER cc_start: 0.9087 (p) cc_final: 0.8599 (t) REVERT: k 41 ILE cc_start: 0.9113 (tt) cc_final: 0.8903 (tp) REVERT: l 9 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8711 (mm-40) REVERT: o 151 THR cc_start: 0.8805 (m) cc_final: 0.8541 (p) REVERT: o 202 MET cc_start: 0.8250 (mtm) cc_final: 0.8044 (mtm) REVERT: t 7 THR cc_start: 0.9581 (m) cc_final: 0.9298 (p) REVERT: t 15 MET cc_start: 0.8315 (mmm) cc_final: 0.8071 (mmt) REVERT: u 10 VAL cc_start: 0.6738 (t) cc_final: 0.6219 (t) REVERT: u 36 LEU cc_start: 0.8936 (tt) cc_final: 0.8723 (mt) REVERT: u 50 VAL cc_start: 0.9035 (t) cc_final: 0.8703 (p) REVERT: u 71 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7301 (mt-10) REVERT: v 32 LEU cc_start: 0.9495 (mt) cc_final: 0.8988 (mp) REVERT: v 67 ASP cc_start: 0.8182 (p0) cc_final: 0.7289 (m-30) REVERT: v 68 ASN cc_start: 0.7618 (m110) cc_final: 0.6774 (m110) REVERT: v 83 ASP cc_start: 0.8165 (p0) cc_final: 0.7815 (p0) REVERT: v 99 ASP cc_start: 0.8455 (p0) cc_final: 0.7919 (p0) REVERT: v 136 TYR cc_start: 0.8531 (m-80) cc_final: 0.8005 (m-80) REVERT: y 2 ILE cc_start: 0.4786 (pt) cc_final: 0.4463 (pt) REVERT: y 7 ILE cc_start: 0.9030 (mt) cc_final: 0.8789 (mt) REVERT: y 27 LEU cc_start: 0.8963 (mt) cc_final: 0.8739 (mt) REVERT: z 4 LEU cc_start: 0.8773 (mt) cc_final: 0.8268 (tt) REVERT: z 55 ASP cc_start: 0.8593 (t0) cc_final: 0.8282 (t70) REVERT: q 107 GLU cc_start: 0.7733 (pm20) cc_final: 0.7176 (tm-30) REVERT: q 121 ASN cc_start: 0.8312 (m110) cc_final: 0.7880 (m110) REVERT: q 141 GLU cc_start: 0.7989 (tp30) cc_final: 0.7337 (tp30) REVERT: q 174 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7092 (tm-30) REVERT: 11 39 GLU cc_start: 0.7832 (tp30) cc_final: 0.7616 (tp30) REVERT: 11 95 ASN cc_start: 0.8750 (m-40) cc_final: 0.8364 (m-40) REVERT: 11 159 LYS cc_start: 0.9133 (mttt) cc_final: 0.8774 (mttp) REVERT: 12 140 ASP cc_start: 0.7445 (p0) cc_final: 0.7117 (p0) REVERT: 12 189 TYR cc_start: 0.8787 (t80) cc_final: 0.8544 (t80) REVERT: 12 196 HIS cc_start: 0.7917 (t-90) cc_final: 0.7710 (t-170) REVERT: 13 72 MET cc_start: 0.8677 (mtp) cc_final: 0.8376 (mtp) REVERT: 13 140 ASP cc_start: 0.7861 (p0) cc_final: 0.6922 (p0) REVERT: 13 156 LYS cc_start: 0.9411 (tttt) cc_final: 0.9120 (ttmm) REVERT: 15 78 THR cc_start: 0.9091 (m) cc_final: 0.8565 (m) REVERT: 15 159 LYS cc_start: 0.9332 (mttt) cc_final: 0.9107 (mttt) REVERT: 15 174 ILE cc_start: 0.8945 (mm) cc_final: 0.8290 (mm) REVERT: 17 94 SER cc_start: 0.9277 (p) cc_final: 0.8766 (t) REVERT: 17 154 GLU cc_start: 0.7764 (mp0) cc_final: 0.7554 (mp0) REVERT: 17 186 GLN cc_start: 0.7846 (mt0) cc_final: 0.7027 (mp10) REVERT: 17 187 THR cc_start: 0.9011 (p) cc_final: 0.7925 (t) REVERT: 18 72 MET cc_start: 0.8417 (mtp) cc_final: 0.8116 (mtp) REVERT: 18 174 ILE cc_start: 0.8028 (mm) cc_final: 0.7774 (mm) REVERT: 18 178 MET cc_start: 0.8076 (mtm) cc_final: 0.7796 (mtp) REVERT: 18 189 TYR cc_start: 0.8052 (t80) cc_final: 0.6962 (t80) outliers start: 16 outliers final: 0 residues processed: 1798 average time/residue: 0.7482 time to fit residues: 2268.3097 Evaluate side-chains 960 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 959 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 45 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 7.9990 chunk 559 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 377 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 578 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 351 optimal weight: 0.6980 chunk 430 optimal weight: 1.9990 chunk 670 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 303 ASN B 53 ASN B 87 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 457 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN C 325 ASN C 330 GLN C 416 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 229 ASN D 254 GLN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN H 47 GLN H 50 ASN M 4 GLN O 190 ASN U 52 HIS V 118 HIS Q 105 ASN Q 121 ASN ** Q 162 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** c 325 ASN c 416 ASN ** d 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 219 ASN d 229 ASN d 254 GLN ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 349 ASN ** o 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN o 222 GLN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN 11 83 ASN 11 96 ASN 11 161 ASN 11 177 ASN 12 82 ASN 12 83 ASN 12 161 ASN ** 13 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 83 ASN 13 161 ASN 14 161 ASN 15 177 ASN ** 15 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 16 96 ASN 16 161 ASN 16 191 GLN 17 177 ASN 18 82 ASN 18 177 ASN 18 196 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 77742 Z= 0.255 Angle : 0.812 18.610 108698 Z= 0.358 Chirality : 0.047 0.569 10276 Planarity : 0.006 0.056 13967 Dihedral : 21.277 166.224 15736 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.40 % Favored : 96.59 % Rotamer: Outliers : 2.49 % Allowed : 11.21 % Favored : 86.30 % 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: -2.57 (0.09), residues: 6884 helix: -1.65 (0.07), residues: 3659 sheet: -1.36 (0.34), residues: 222 loop : -1.64 (0.10), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 131 HIS 0.018 0.002 HIS18 196 PHE 0.028 0.002 PHE c 434 TYR 0.029 0.002 TYR U 42 ARG 0.009 0.001 ARG c 213 *********************** 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 1244 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1104 time to evaluate : 5.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 187 GLN cc_start: 0.9499 (tp40) cc_final: 0.9260 (tp-100) REVERT: A 238 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8652 (mttt) REVERT: B 55 MET cc_start: 0.8454 (ptp) cc_final: 0.8089 (ptm) REVERT: B 266 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7083 (mp0) REVERT: B 352 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6698 (ptt180) REVERT: C 175 ILE cc_start: 0.9388 (mt) cc_final: 0.9179 (mm) REVERT: D 22 LYS cc_start: 0.8845 (mttt) cc_final: 0.8407 (pttp) REVERT: D 158 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9037 (tp) REVERT: D 272 PHE cc_start: 0.9000 (t80) cc_final: 0.8725 (t80) REVERT: E 78 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8170 (mm-30) REVERT: E 79 ASP cc_start: 0.7809 (m-30) cc_final: 0.7140 (m-30) REVERT: K 16 PHE cc_start: 0.8649 (m-80) cc_final: 0.8392 (m-80) REVERT: K 33 LEU cc_start: 0.8940 (tp) cc_final: 0.8489 (tp) REVERT: L 15 ARG cc_start: 0.8468 (ttm170) cc_final: 0.8179 (ttp-170) REVERT: M 28 GLN cc_start: 0.8716 (pp30) cc_final: 0.7875 (pp30) REVERT: M 41 ASP cc_start: 0.8151 (m-30) cc_final: 0.7912 (t0) REVERT: O 124 ASP cc_start: 0.7836 (m-30) cc_final: 0.7601 (t0) REVERT: O 185 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8157 (pp) REVERT: O 222 GLN cc_start: 0.8581 (pt0) cc_final: 0.8372 (pt0) REVERT: T 2 GLU cc_start: 0.7465 (mp0) cc_final: 0.7080 (mp0) REVERT: U 60 ASP cc_start: 0.8287 (m-30) cc_final: 0.7822 (t0) REVERT: U 73 ASP cc_start: 0.9074 (m-30) cc_final: 0.8657 (m-30) REVERT: U 93 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8852 (tp) REVERT: V 49 ASN cc_start: 0.8350 (t0) cc_final: 0.7808 (t0) REVERT: V 74 ASP cc_start: 0.8933 (t0) cc_final: 0.8717 (t0) REVERT: V 111 ASP cc_start: 0.7547 (m-30) cc_final: 0.6911 (m-30) REVERT: Y 5 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7529 (tp40) REVERT: Y 18 LEU cc_start: 0.8572 (mm) cc_final: 0.8208 (pp) REVERT: Y 33 ASN cc_start: 0.7943 (m-40) cc_final: 0.7680 (p0) REVERT: X 9 ILE cc_start: 0.9542 (mt) cc_final: 0.9327 (pt) REVERT: Q 105 ASN cc_start: 0.7596 (m110) cc_final: 0.7287 (m-40) REVERT: Q 122 ARG cc_start: 0.8964 (mmt-90) cc_final: 0.8610 (mmm-85) REVERT: W 34 LEU cc_start: 0.9325 (mp) cc_final: 0.9116 (mp) REVERT: a 37 MET cc_start: 0.9282 (tmm) cc_final: 0.8164 (tmm) REVERT: a 91 MET cc_start: 0.8621 (tpt) cc_final: 0.8354 (tpp) REVERT: a 304 GLN cc_start: 0.7974 (mt0) cc_final: 0.7745 (mt0) REVERT: b 334 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.6973 (p0) REVERT: b 439 SER cc_start: 0.8313 (m) cc_final: 0.7972 (t) REVERT: d 18 ASP cc_start: 0.8269 (t0) cc_final: 0.8041 (t0) REVERT: d 48 MET cc_start: 0.7257 (tpp) cc_final: 0.6932 (tpt) REVERT: d 64 SER cc_start: 0.7656 (p) cc_final: 0.7352 (t) REVERT: d 185 GLN cc_start: 0.9138 (tp40) cc_final: 0.8867 (tp-100) REVERT: d 245 MET cc_start: 0.8547 (tpt) cc_final: 0.8083 (tpt) REVERT: d 307 ASP cc_start: 0.8407 (t0) cc_final: 0.8008 (t70) REVERT: e 60 ASP cc_start: 0.7252 (p0) cc_final: 0.7017 (p0) REVERT: e 76 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7266 (mp0) REVERT: h 31 MET cc_start: 0.7576 (ttp) cc_final: 0.7159 (ttp) REVERT: h 61 ASP cc_start: 0.8290 (t0) cc_final: 0.7992 (t0) REVERT: i 1 MET cc_start: 0.6989 (tmm) cc_final: 0.6707 (tmm) REVERT: i 14 PHE cc_start: 0.8910 (t80) cc_final: 0.8600 (t80) REVERT: i 17 SER cc_start: 0.9322 (m) cc_final: 0.8971 (p) REVERT: j 31 SER cc_start: 0.9525 (m) cc_final: 0.9194 (t) REVERT: k 29 PHE cc_start: 0.8911 (m-10) cc_final: 0.8434 (m-80) REVERT: t 7 THR cc_start: 0.9452 (m) cc_final: 0.9125 (p) REVERT: v 86 GLU cc_start: 0.8191 (pm20) cc_final: 0.7791 (mp0) REVERT: z 4 LEU cc_start: 0.8659 (mt) cc_final: 0.8273 (tt) REVERT: z 46 PHE cc_start: 0.8407 (t80) cc_final: 0.8177 (m-10) REVERT: q 86 TYR cc_start: 0.8095 (t80) cc_final: 0.7893 (t80) REVERT: q 104 ASP cc_start: 0.8311 (p0) cc_final: 0.7962 (t0) REVERT: q 111 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7561 (ttp-170) REVERT: q 137 ASN cc_start: 0.7278 (t0) cc_final: 0.7015 (t0) REVERT: q 138 VAL cc_start: 0.8891 (t) cc_final: 0.8677 (p) REVERT: q 141 GLU cc_start: 0.7936 (tp30) cc_final: 0.7394 (tp30) REVERT: q 144 ARG cc_start: 0.7321 (ttp80) cc_final: 0.6487 (ttp80) REVERT: q 174 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6994 (tm-30) REVERT: w 43 TRP cc_start: 0.8599 (m-10) cc_final: 0.8385 (m-10) REVERT: w 71 ARG cc_start: 0.6211 (mmm160) cc_final: 0.5829 (mmp-170) REVERT: 11 52 SER cc_start: 0.8673 (m) cc_final: 0.8470 (t) REVERT: 12 196 HIS cc_start: 0.8047 (t-90) cc_final: 0.7774 (t-170) REVERT: 15 33 ILE cc_start: 0.8978 (mt) cc_final: 0.8757 (mm) REVERT: 15 172 MET cc_start: 0.8331 (mmm) cc_final: 0.8038 (mmm) REVERT: 18 49 TRP cc_start: 0.7884 (m100) cc_final: 0.7593 (m-10) REVERT: 18 171 MET cc_start: 0.8443 (mmm) cc_final: 0.7874 (mmm) REVERT: 18 189 TYR cc_start: 0.7756 (t80) cc_final: 0.7429 (t80) REVERT: 18 196 HIS cc_start: 0.7335 (t-90) cc_final: 0.6895 (t-90) outliers start: 140 outliers final: 73 residues processed: 1188 average time/residue: 0.6987 time to fit residues: 1442.3788 Evaluate side-chains 991 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 913 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 31 ASN Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 334 ASP Chi-restraints excluded: chain c residue 225 VAL Chi-restraints excluded: chain c residue 242 CYS Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 121 LEU Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 192 ASN Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 11 residue 148 THR Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 12 residue 148 THR Chi-restraints excluded: chain 13 residue 148 THR Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 109 ILE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 164 LEU Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 17 residue 102 ILE Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 557 optimal weight: 4.9990 chunk 456 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 671 optimal weight: 6.9990 chunk 725 optimal weight: 9.9990 chunk 597 optimal weight: 2.9990 chunk 665 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 538 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 315 ASN B 53 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 141 ASN D 188 HIS D 193 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 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** b 457 ASN c 72 HIS c 311 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 219 ASN d 254 GLN ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 139 GLN o 222 GLN u 52 HIS ** y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN w 57 ASN 13 177 ASN 15 82 ASN ** 15 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 196 HIS 17 82 ASN 17 83 ASN 17 161 ASN 18 177 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 77742 Z= 0.345 Angle : 0.793 19.040 108698 Z= 0.348 Chirality : 0.048 0.363 10276 Planarity : 0.005 0.078 13967 Dihedral : 19.649 166.381 15734 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 3.18 % Allowed : 12.97 % Favored : 83.85 % 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: -1.39 (0.09), residues: 6884 helix: -0.52 (0.08), residues: 3684 sheet: -1.19 (0.34), residues: 212 loop : -1.29 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP d 47 HIS 0.016 0.002 HIS13 196 PHE 0.032 0.002 PHE16 124 TYR 0.033 0.002 TYR16 192 ARG 0.012 0.001 ARG c 213 *********************** 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 1119 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 940 time to evaluate : 5.375 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 187 GLN cc_start: 0.9541 (tp40) cc_final: 0.8915 (tm-30) REVERT: A 238 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8635 (mttt) REVERT: C 168 LEU cc_start: 0.9175 (mp) cc_final: 0.8968 (mp) REVERT: D 11 ARG cc_start: 0.5788 (tpt90) cc_final: 0.5089 (ptp-110) REVERT: D 22 LYS cc_start: 0.8837 (mttt) cc_final: 0.8467 (pttp) REVERT: D 70 CYS cc_start: 0.8374 (m) cc_final: 0.7926 (m) REVERT: D 193 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8836 (m110) REVERT: D 307 ASP cc_start: 0.7114 (t0) cc_final: 0.6893 (t0) REVERT: E 68 ASN cc_start: 0.8415 (m-40) cc_final: 0.7949 (p0) REVERT: E 76 GLU cc_start: 0.7420 (tt0) cc_final: 0.6870 (tp30) REVERT: E 79 ASP cc_start: 0.7933 (m-30) cc_final: 0.6659 (m-30) REVERT: K 16 PHE cc_start: 0.8573 (m-80) cc_final: 0.8300 (m-80) REVERT: K 33 LEU cc_start: 0.9005 (tp) cc_final: 0.8551 (tp) REVERT: L 7 ASN cc_start: 0.8743 (m-40) cc_final: 0.8522 (m-40) REVERT: L 19 TYR cc_start: 0.9073 (m-80) cc_final: 0.8791 (m-80) REVERT: M 4 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7003 (mm-40) REVERT: M 28 GLN cc_start: 0.8920 (pp30) cc_final: 0.8056 (pp30) REVERT: M 30 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8094 (tp30) REVERT: O 168 MET cc_start: 0.7543 (ppp) cc_final: 0.6973 (ppp) REVERT: U 60 ASP cc_start: 0.8372 (m-30) cc_final: 0.8163 (t0) REVERT: U 73 ASP cc_start: 0.9114 (m-30) cc_final: 0.8586 (m-30) REVERT: U 93 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8927 (tp) REVERT: U 96 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8808 (tp) REVERT: U 98 ASN cc_start: 0.8537 (p0) cc_final: 0.7976 (p0) REVERT: V 49 ASN cc_start: 0.8401 (t0) cc_final: 0.7879 (t0) REVERT: V 74 ASP cc_start: 0.8890 (t0) cc_final: 0.8544 (t0) REVERT: V 111 ASP cc_start: 0.7795 (m-30) cc_final: 0.7321 (m-30) REVERT: V 125 ILE cc_start: 0.9334 (mm) cc_final: 0.9109 (mt) REVERT: Y 5 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7512 (tp40) REVERT: Y 18 LEU cc_start: 0.8608 (mm) cc_final: 0.8256 (pp) REVERT: X 9 ILE cc_start: 0.9567 (mt) cc_final: 0.9339 (pt) REVERT: Q 105 ASN cc_start: 0.7692 (m110) cc_final: 0.7208 (m-40) REVERT: Q 122 ARG cc_start: 0.8991 (mmt-90) cc_final: 0.8189 (mmm-85) REVERT: a 37 MET cc_start: 0.9219 (tmm) cc_final: 0.8958 (tmm) REVERT: b 256 MET cc_start: 0.9188 (tpt) cc_final: 0.8925 (tpt) REVERT: b 334 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.6956 (p0) REVERT: b 439 SER cc_start: 0.8553 (m) cc_final: 0.8224 (t) REVERT: d 18 ASP cc_start: 0.8087 (t0) cc_final: 0.7789 (t0) REVERT: d 22 LYS cc_start: 0.8878 (mttt) cc_final: 0.8594 (mttt) REVERT: d 158 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.8936 (tp) REVERT: d 245 MET cc_start: 0.8711 (tpt) cc_final: 0.8263 (tpt) REVERT: d 307 ASP cc_start: 0.8374 (t0) cc_final: 0.7976 (t0) REVERT: e 60 ASP cc_start: 0.7456 (p0) cc_final: 0.7190 (p0) REVERT: e 76 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7544 (mp0) REVERT: h 31 MET cc_start: 0.7616 (ttp) cc_final: 0.7185 (ttp) REVERT: i 1 MET cc_start: 0.7019 (tmm) cc_final: 0.6709 (tmm) REVERT: i 14 PHE cc_start: 0.9077 (t80) cc_final: 0.8633 (t80) REVERT: i 17 SER cc_start: 0.9352 (m) cc_final: 0.9014 (p) REVERT: j 31 SER cc_start: 0.9628 (m) cc_final: 0.9204 (t) REVERT: k 29 PHE cc_start: 0.8936 (m-10) cc_final: 0.8416 (m-80) REVERT: m 11 VAL cc_start: 0.9209 (t) cc_final: 0.8962 (p) REVERT: o 202 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7549 (pmm) REVERT: t 7 THR cc_start: 0.9450 (m) cc_final: 0.9132 (p) REVERT: t 25 GLU cc_start: 0.8422 (tp30) cc_final: 0.7882 (pt0) REVERT: v 86 GLU cc_start: 0.8153 (pm20) cc_final: 0.7915 (pm20) REVERT: v 99 ASP cc_start: 0.7948 (p0) cc_final: 0.7692 (p0) REVERT: v 136 TYR cc_start: 0.8489 (m-80) cc_final: 0.8256 (m-80) REVERT: z 4 LEU cc_start: 0.8648 (mt) cc_final: 0.8280 (tt) REVERT: z 46 PHE cc_start: 0.8464 (t80) cc_final: 0.8222 (m-10) REVERT: z 51 ILE cc_start: 0.9306 (tp) cc_final: 0.8881 (tp) REVERT: q 104 ASP cc_start: 0.8443 (p0) cc_final: 0.7637 (t0) REVERT: q 118 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8443 (tm-30) REVERT: q 134 GLU cc_start: 0.8528 (mp0) cc_final: 0.8204 (mp0) REVERT: q 141 GLU cc_start: 0.8021 (tp30) cc_final: 0.7617 (tm-30) REVERT: w 71 ARG cc_start: 0.6311 (mmm160) cc_final: 0.5796 (mmm160) REVERT: 12 32 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7449 (mt-10) REVERT: 12 196 HIS cc_start: 0.8144 (t-90) cc_final: 0.7797 (t-170) REVERT: 13 72 MET cc_start: 0.8287 (mtp) cc_final: 0.8033 (mtm) REVERT: 14 172 MET cc_start: 0.8334 (mtp) cc_final: 0.8087 (mtp) REVERT: 14 178 MET cc_start: 0.8911 (mmm) cc_final: 0.8337 (mmt) REVERT: 15 33 ILE cc_start: 0.9076 (mt) cc_final: 0.8857 (mm) REVERT: 16 140 ASP cc_start: 0.7255 (p0) cc_final: 0.7005 (p0) REVERT: 16 188 MET cc_start: 0.8761 (tpt) cc_final: 0.8014 (tpp) REVERT: 17 78 THR cc_start: 0.9505 (m) cc_final: 0.9102 (p) REVERT: 18 171 MET cc_start: 0.8386 (mmm) cc_final: 0.7941 (mmm) outliers start: 179 outliers final: 115 residues processed: 1044 average time/residue: 0.6867 time to fit residues: 1258.9811 Evaluate side-chains 963 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 841 time to evaluate : 6.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 31 ASP Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 334 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 225 VAL Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain d residue 273 VAL Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 24 LEU Chi-restraints excluded: chain o residue 77 TYR Chi-restraints excluded: chain o residue 140 MET Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain o residue 203 GLU Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 121 LEU Chi-restraints excluded: chain v residue 128 GLU Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 13 THR Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain z residue 18 VAL Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 11 residue 148 THR Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 53 GLU Chi-restraints excluded: chain 13 residue 148 THR Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 13 residue 177 ASN Chi-restraints excluded: chain 14 residue 78 THR Chi-restraints excluded: chain 14 residue 109 ILE Chi-restraints excluded: chain 15 residue 75 VAL Chi-restraints excluded: chain 15 residue 174 ILE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 177 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 17 residue 187 THR Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 114 THR Chi-restraints excluded: chain 18 residue 188 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 0.9980 chunk 504 optimal weight: 0.2980 chunk 348 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 320 optimal weight: 2.9990 chunk 450 optimal weight: 0.9980 chunk 673 optimal weight: 0.6980 chunk 713 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 638 optimal weight: 0.6980 chunk 192 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN d 141 ASN ** d 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 17 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 82 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 83 ASN ** 18 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 77742 Z= 0.163 Angle : 0.661 13.979 108698 Z= 0.290 Chirality : 0.043 0.349 10276 Planarity : 0.004 0.064 13967 Dihedral : 18.652 172.506 15734 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 2.40 % Allowed : 14.48 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.10), residues: 6884 helix: 0.09 (0.08), residues: 3711 sheet: -1.06 (0.33), residues: 222 loop : -1.09 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 33 HIS 0.012 0.001 HIS18 196 PHE 0.028 0.001 PHE13 123 TYR 0.026 0.001 TYR D 41 ARG 0.006 0.000 ARG c 213 *********************** 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 1123 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 988 time to evaluate : 5.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9027 (mt) REVERT: A 133 LEU cc_start: 0.9192 (tp) cc_final: 0.8970 (tp) REVERT: A 187 GLN cc_start: 0.9480 (tp40) cc_final: 0.8777 (tm-30) REVERT: A 238 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8694 (mttt) REVERT: A 254 TYR cc_start: 0.8793 (t80) cc_final: 0.8321 (t80) REVERT: B 42 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8949 (mm) REVERT: B 380 ASP cc_start: 0.8294 (p0) cc_final: 0.7982 (p0) REVERT: C 202 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8316 (mm) REVERT: D 11 ARG cc_start: 0.5721 (tpt90) cc_final: 0.5141 (ptp-110) REVERT: D 22 LYS cc_start: 0.8822 (mttt) cc_final: 0.8401 (pttp) REVERT: E 66 LEU cc_start: 0.8720 (mm) cc_final: 0.8467 (mp) REVERT: E 68 ASN cc_start: 0.8432 (m-40) cc_final: 0.7912 (p0) REVERT: E 76 GLU cc_start: 0.7317 (tt0) cc_final: 0.6967 (tp30) REVERT: E 79 ASP cc_start: 0.7790 (m-30) cc_final: 0.7143 (m-30) REVERT: K 16 PHE cc_start: 0.8299 (m-80) cc_final: 0.8071 (m-80) REVERT: K 33 LEU cc_start: 0.9128 (tp) cc_final: 0.8557 (tp) REVERT: M 28 GLN cc_start: 0.8806 (pp30) cc_final: 0.8410 (pp30) REVERT: M 30 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8050 (tp30) REVERT: O 168 MET cc_start: 0.7740 (ppp) cc_final: 0.6991 (ppp) REVERT: T 1 MET cc_start: 0.6411 (mtp) cc_final: 0.6071 (mpp) REVERT: U 41 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7612 (mtt) REVERT: U 60 ASP cc_start: 0.8571 (m-30) cc_final: 0.8084 (t0) REVERT: U 73 ASP cc_start: 0.9120 (m-30) cc_final: 0.8897 (m-30) REVERT: U 96 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8811 (tp) REVERT: U 98 ASN cc_start: 0.8494 (p0) cc_final: 0.8000 (p0) REVERT: V 49 ASN cc_start: 0.8131 (t0) cc_final: 0.7644 (t0) REVERT: V 55 ASP cc_start: 0.8191 (m-30) cc_final: 0.7708 (m-30) REVERT: V 74 ASP cc_start: 0.8879 (t0) cc_final: 0.8514 (t0) REVERT: V 111 ASP cc_start: 0.7836 (m-30) cc_final: 0.7518 (m-30) REVERT: V 122 SER cc_start: 0.9336 (t) cc_final: 0.8943 (p) REVERT: Y 5 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7436 (tp40) REVERT: Y 18 LEU cc_start: 0.8596 (mm) cc_final: 0.8273 (pp) REVERT: X 9 ILE cc_start: 0.9564 (mt) cc_final: 0.9347 (pt) REVERT: Q 105 ASN cc_start: 0.7511 (m110) cc_final: 0.7084 (m-40) REVERT: Q 122 ARG cc_start: 0.8915 (mmt-90) cc_final: 0.8659 (mmm-85) REVERT: a 91 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7951 (tpt) REVERT: a 262 TYR cc_start: 0.7221 (m-10) cc_final: 0.6925 (t80) REVERT: b 256 MET cc_start: 0.9169 (tpt) cc_final: 0.8927 (tpt) REVERT: b 439 SER cc_start: 0.8411 (m) cc_final: 0.8131 (t) REVERT: b 451 TYR cc_start: 0.9087 (t80) cc_final: 0.8734 (t80) REVERT: c 65 MET cc_start: 0.8198 (tpt) cc_final: 0.7839 (tpp) REVERT: d 18 ASP cc_start: 0.8114 (t0) cc_final: 0.7839 (t0) REVERT: d 22 LYS cc_start: 0.8896 (mttt) cc_final: 0.8689 (mttt) REVERT: d 48 MET cc_start: 0.7786 (mmt) cc_final: 0.7521 (tpp) REVERT: d 158 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8810 (tp) REVERT: d 307 ASP cc_start: 0.8374 (t0) cc_final: 0.8011 (t0) REVERT: d 332 ASP cc_start: 0.7670 (t70) cc_final: 0.7441 (t70) REVERT: d 333 GLN cc_start: 0.8302 (mt0) cc_final: 0.7965 (mp10) REVERT: e 60 ASP cc_start: 0.7505 (p0) cc_final: 0.7295 (p0) REVERT: e 76 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7516 (mp0) REVERT: h 31 MET cc_start: 0.7605 (ttp) cc_final: 0.7287 (ttp) REVERT: i 1 MET cc_start: 0.6997 (tmm) cc_final: 0.6654 (tmm) REVERT: i 14 PHE cc_start: 0.9116 (t80) cc_final: 0.8660 (t80) REVERT: i 17 SER cc_start: 0.9255 (m) cc_final: 0.8984 (p) REVERT: j 31 SER cc_start: 0.9599 (m) cc_final: 0.9209 (t) REVERT: k 8 ARG cc_start: 0.7969 (ptt-90) cc_final: 0.7723 (ptt-90) REVERT: k 29 PHE cc_start: 0.8874 (m-10) cc_final: 0.8439 (m-80) REVERT: m 11 VAL cc_start: 0.9103 (t) cc_final: 0.8885 (p) REVERT: o 202 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7487 (pmm) REVERT: t 7 THR cc_start: 0.9425 (m) cc_final: 0.9106 (p) REVERT: t 25 GLU cc_start: 0.8438 (tp30) cc_final: 0.7879 (pt0) REVERT: v 86 GLU cc_start: 0.8177 (pm20) cc_final: 0.7958 (pm20) REVERT: v 99 ASP cc_start: 0.7935 (p0) cc_final: 0.6005 (p0) REVERT: v 136 TYR cc_start: 0.8428 (m-80) cc_final: 0.8212 (m-80) REVERT: z 4 LEU cc_start: 0.8580 (mt) cc_final: 0.8242 (tt) REVERT: q 104 ASP cc_start: 0.8295 (p0) cc_final: 0.7506 (t0) REVERT: q 111 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7647 (ttp-170) REVERT: q 118 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8430 (tm-30) REVERT: q 134 GLU cc_start: 0.8452 (mp0) cc_final: 0.8068 (mp0) REVERT: q 141 GLU cc_start: 0.8029 (tp30) cc_final: 0.7658 (tm-30) REVERT: q 167 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: w 71 ARG cc_start: 0.5826 (mmm160) cc_final: 0.5316 (mmm160) REVERT: 11 52 SER cc_start: 0.8761 (m) cc_final: 0.8468 (t) REVERT: 11 78 THR cc_start: 0.9271 (m) cc_final: 0.8993 (p) REVERT: 12 32 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7518 (mt-10) REVERT: 12 196 HIS cc_start: 0.8063 (t-90) cc_final: 0.7675 (t-170) REVERT: 13 72 MET cc_start: 0.8240 (mtp) cc_final: 0.7791 (mtm) REVERT: 14 44 TYR cc_start: 0.7435 (t80) cc_final: 0.7129 (t80) REVERT: 14 178 MET cc_start: 0.8818 (mmm) cc_final: 0.8249 (mmt) REVERT: 15 172 MET cc_start: 0.8014 (mmm) cc_final: 0.7807 (mmm) REVERT: 17 172 MET cc_start: 0.8827 (mmm) cc_final: 0.8627 (mmm) REVERT: 18 171 MET cc_start: 0.8071 (mmm) cc_final: 0.7693 (mmm) REVERT: 18 189 TYR cc_start: 0.7805 (t80) cc_final: 0.7604 (t80) outliers start: 135 outliers final: 77 residues processed: 1060 average time/residue: 0.6928 time to fit residues: 1288.6599 Evaluate side-chains 943 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 857 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 13 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain d residue 210 CYS Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain z residue 14 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 78 THR Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 531 optimal weight: 3.9990 chunk 294 optimal weight: 0.0670 chunk 608 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 364 optimal weight: 0.4980 chunk 640 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 394 GLN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 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** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN 11 186 GLN 13 196 HIS ** 15 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 177 ASN 18 196 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 77742 Z= 0.245 Angle : 0.685 11.251 108698 Z= 0.302 Chirality : 0.045 0.314 10276 Planarity : 0.004 0.085 13967 Dihedral : 18.084 173.288 15734 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 2.75 % Allowed : 14.82 % Favored : 82.43 % 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: 0.45 (0.08), residues: 3696 sheet: -0.92 (0.33), residues: 212 loop : -0.97 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP16 49 HIS 0.007 0.001 HIS d 213 PHE 0.026 0.001 PHE13 123 TYR 0.026 0.001 TYR D 41 ARG 0.010 0.000 ARG15 110 *********************** 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 1037 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 882 time to evaluate : 5.313 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: A 91 MET cc_start: 0.8610 (mmm) cc_final: 0.7899 (mmm) REVERT: A 121 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 187 GLN cc_start: 0.9524 (tp40) cc_final: 0.8777 (tm-30) REVERT: A 238 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8633 (mttt) REVERT: A 254 TYR cc_start: 0.8862 (t80) cc_final: 0.8470 (t80) REVERT: C 202 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8396 (mm) REVERT: D 11 ARG cc_start: 0.5927 (tpt90) cc_final: 0.5181 (ptp-110) REVERT: D 22 LYS cc_start: 0.8806 (mttt) cc_final: 0.8453 (pttp) REVERT: D 48 MET cc_start: 0.8930 (mmm) cc_final: 0.8540 (mmm) REVERT: D 70 CYS cc_start: 0.8372 (m) cc_final: 0.8106 (m) REVERT: D 322 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7073 (mp0) REVERT: E 68 ASN cc_start: 0.8372 (m-40) cc_final: 0.7936 (p0) REVERT: E 76 GLU cc_start: 0.7313 (tt0) cc_final: 0.6998 (tp30) REVERT: E 79 ASP cc_start: 0.8101 (m-30) cc_final: 0.6630 (m-30) REVERT: K 33 LEU cc_start: 0.9125 (tp) cc_final: 0.8600 (tp) REVERT: M 8 TYR cc_start: 0.8758 (m-80) cc_final: 0.8511 (m-80) REVERT: M 28 GLN cc_start: 0.8962 (pp30) cc_final: 0.8481 (pp30) REVERT: M 30 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7987 (tp30) REVERT: T 1 MET cc_start: 0.6564 (mtp) cc_final: 0.6248 (mpp) REVERT: U 41 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: U 60 ASP cc_start: 0.8624 (m-30) cc_final: 0.8214 (t0) REVERT: U 73 ASP cc_start: 0.9061 (m-30) cc_final: 0.8542 (m-30) REVERT: U 96 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8842 (tp) REVERT: U 98 ASN cc_start: 0.8564 (p0) cc_final: 0.8149 (p0) REVERT: V 49 ASN cc_start: 0.8116 (t0) cc_final: 0.7643 (t0) REVERT: V 74 ASP cc_start: 0.8891 (t0) cc_final: 0.8554 (t0) REVERT: V 90 GLU cc_start: 0.7650 (pm20) cc_final: 0.7364 (pm20) REVERT: V 111 ASP cc_start: 0.7737 (m-30) cc_final: 0.7460 (m-30) REVERT: V 122 SER cc_start: 0.9353 (t) cc_final: 0.9009 (t) REVERT: Y 5 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7464 (tp40) REVERT: Y 18 LEU cc_start: 0.8620 (mm) cc_final: 0.8334 (pp) REVERT: X 9 ILE cc_start: 0.9583 (mt) cc_final: 0.9344 (pt) REVERT: Z 29 GLU cc_start: 0.6999 (tt0) cc_final: 0.6556 (tt0) REVERT: Q 105 ASN cc_start: 0.7574 (m110) cc_final: 0.7085 (m-40) REVERT: a 91 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8039 (tpt) REVERT: a 262 TYR cc_start: 0.7228 (m-10) cc_final: 0.7007 (t80) REVERT: b 256 MET cc_start: 0.9198 (tpt) cc_final: 0.8899 (tpt) REVERT: b 439 SER cc_start: 0.8495 (m) cc_final: 0.8230 (t) REVERT: c 84 PHE cc_start: 0.7025 (m-80) cc_final: 0.6755 (m-80) REVERT: d 18 ASP cc_start: 0.8016 (t0) cc_final: 0.7584 (t0) REVERT: d 48 MET cc_start: 0.7931 (mmt) cc_final: 0.7707 (tpp) REVERT: d 158 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8936 (tp) REVERT: d 307 ASP cc_start: 0.8236 (t0) cc_final: 0.7929 (t0) REVERT: d 332 ASP cc_start: 0.7752 (t70) cc_final: 0.7477 (t70) REVERT: d 333 GLN cc_start: 0.8408 (mt0) cc_final: 0.7988 (mp10) REVERT: e 60 ASP cc_start: 0.7621 (p0) cc_final: 0.7401 (p0) REVERT: e 76 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7250 (mp0) REVERT: h 31 MET cc_start: 0.7555 (ttp) cc_final: 0.7206 (ttp) REVERT: i 1 MET cc_start: 0.6951 (tmm) cc_final: 0.6593 (tmm) REVERT: i 14 PHE cc_start: 0.9159 (t80) cc_final: 0.8694 (t80) REVERT: i 17 SER cc_start: 0.9299 (m) cc_final: 0.9009 (p) REVERT: j 31 SER cc_start: 0.9646 (m) cc_final: 0.9245 (t) REVERT: k 29 PHE cc_start: 0.8909 (m-10) cc_final: 0.8386 (m-80) REVERT: m 11 VAL cc_start: 0.9151 (t) cc_final: 0.8930 (p) REVERT: o 72 MET cc_start: 0.8602 (mmp) cc_final: 0.8171 (mmt) REVERT: o 202 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7561 (pmm) REVERT: t 7 THR cc_start: 0.9416 (m) cc_final: 0.9064 (p) REVERT: t 25 GLU cc_start: 0.8430 (tp30) cc_final: 0.7909 (pt0) REVERT: u 12 ASP cc_start: 0.7626 (t0) cc_final: 0.6977 (p0) REVERT: v 86 GLU cc_start: 0.8217 (pm20) cc_final: 0.7964 (pm20) REVERT: v 136 TYR cc_start: 0.8406 (m-80) cc_final: 0.8190 (m-80) REVERT: z 4 LEU cc_start: 0.8605 (mt) cc_final: 0.8243 (tt) REVERT: z 55 ASP cc_start: 0.8407 (t0) cc_final: 0.8170 (p0) REVERT: q 104 ASP cc_start: 0.8247 (p0) cc_final: 0.7490 (t0) REVERT: q 118 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8265 (tp30) REVERT: q 122 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8108 (mmm-85) REVERT: q 134 GLU cc_start: 0.8511 (mp0) cc_final: 0.8131 (mp0) REVERT: q 141 GLU cc_start: 0.7993 (tp30) cc_final: 0.7665 (tm-30) REVERT: q 167 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: q 174 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6864 (tm-30) REVERT: w 71 ARG cc_start: 0.6007 (mmm160) cc_final: 0.5730 (mmm160) REVERT: 11 78 THR cc_start: 0.9341 (m) cc_final: 0.9065 (p) REVERT: 12 140 ASP cc_start: 0.7799 (p0) cc_final: 0.7530 (p0) REVERT: 12 196 HIS cc_start: 0.8071 (t-90) cc_final: 0.7724 (t-170) REVERT: 14 44 TYR cc_start: 0.7470 (t80) cc_final: 0.7174 (t80) REVERT: 14 138 ASP cc_start: 0.8541 (p0) cc_final: 0.8171 (p0) REVERT: 14 172 MET cc_start: 0.8515 (mmm) cc_final: 0.8132 (mtp) REVERT: 14 178 MET cc_start: 0.8681 (mmm) cc_final: 0.8247 (mmt) REVERT: 15 107 ASP cc_start: 0.6906 (m-30) cc_final: 0.6610 (p0) REVERT: 15 132 MET cc_start: 0.8899 (mmm) cc_final: 0.8664 (mmm) REVERT: 16 174 ILE cc_start: 0.9220 (tp) cc_final: 0.9017 (tp) REVERT: 16 183 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7905 (pp) REVERT: 17 140 ASP cc_start: 0.7711 (p0) cc_final: 0.7507 (p0) REVERT: 17 172 MET cc_start: 0.8901 (mmm) cc_final: 0.8656 (mmm) REVERT: 18 107 ASP cc_start: 0.7895 (m-30) cc_final: 0.7650 (p0) REVERT: 18 171 MET cc_start: 0.7967 (mmm) cc_final: 0.7596 (mmm) REVERT: 18 189 TYR cc_start: 0.7756 (t80) cc_final: 0.7545 (t80) outliers start: 155 outliers final: 97 residues processed: 972 average time/residue: 0.6930 time to fit residues: 1191.5125 Evaluate side-chains 942 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 836 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 100 ILE Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 31 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 103 ASP Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 399 VAL Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 202 LEU Chi-restraints excluded: chain c residue 225 VAL Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 13 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain f residue 28 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain z residue 9 LEU Chi-restraints excluded: chain z residue 14 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 109 ILE Chi-restraints excluded: chain 11 residue 148 THR Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 109 ILE Chi-restraints excluded: chain 16 residue 37 VAL Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 16 residue 183 LEU Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 177 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 1.9990 chunk 642 optimal weight: 0.4980 chunk 141 optimal weight: 0.9990 chunk 418 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 714 optimal weight: 10.0000 chunk 592 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 374 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Y 33 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN ** d 116 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 57 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 77742 Z= 0.237 Angle : 0.663 11.466 108698 Z= 0.293 Chirality : 0.044 0.311 10276 Planarity : 0.004 0.058 13967 Dihedral : 17.666 175.286 15734 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.95 % Allowed : 15.30 % Favored : 81.75 % 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: -0.16 (0.10), residues: 6884 helix: 0.61 (0.09), residues: 3714 sheet: -0.76 (0.35), residues: 192 loop : -0.92 (0.11), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP16 49 HIS 0.005 0.001 HIS d 213 PHE 0.027 0.001 PHE13 123 TYR 0.022 0.001 TYR m 8 ARG 0.005 0.000 ARG18 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13768 Ramachandran restraints generated. 6884 Oldfield, 0 Emsley, 6884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 890 time to evaluate : 5.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8621 (mmm) cc_final: 0.7735 (mmm) REVERT: A 121 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9058 (mt) REVERT: A 187 GLN cc_start: 0.9525 (tp40) cc_final: 0.8804 (tm-30) REVERT: A 238 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8580 (mttt) REVERT: A 254 TYR cc_start: 0.8854 (t80) cc_final: 0.8490 (t80) REVERT: C 178 MET cc_start: 0.8020 (mmm) cc_final: 0.7769 (mmm) REVERT: C 202 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8453 (mm) REVERT: C 389 ARG cc_start: 0.8268 (tpp80) cc_final: 0.8064 (mmm160) REVERT: D 22 LYS cc_start: 0.8725 (mttt) cc_final: 0.8434 (pttp) REVERT: D 41 TYR cc_start: 0.8479 (t80) cc_final: 0.8203 (t80) REVERT: D 70 CYS cc_start: 0.8387 (m) cc_final: 0.8162 (m) REVERT: E 68 ASN cc_start: 0.8424 (m-40) cc_final: 0.8090 (p0) REVERT: E 75 GLN cc_start: 0.6923 (tp40) cc_final: 0.6604 (tp-100) REVERT: E 76 GLU cc_start: 0.7334 (tt0) cc_final: 0.6909 (tp30) REVERT: E 79 ASP cc_start: 0.7921 (m-30) cc_final: 0.6582 (m-30) REVERT: K 33 LEU cc_start: 0.9153 (tp) cc_final: 0.8682 (tp) REVERT: L 27 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.8973 (p) REVERT: M 28 GLN cc_start: 0.8971 (pp30) cc_final: 0.8463 (pp30) REVERT: M 30 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8007 (tp30) REVERT: O 168 MET cc_start: 0.7846 (ppp) cc_final: 0.7604 (ppp) REVERT: U 60 ASP cc_start: 0.8626 (m-30) cc_final: 0.8243 (t0) REVERT: U 73 ASP cc_start: 0.9068 (m-30) cc_final: 0.8668 (m-30) REVERT: U 96 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8844 (tp) REVERT: U 98 ASN cc_start: 0.8622 (p0) cc_final: 0.8243 (p0) REVERT: V 27 LYS cc_start: 0.8734 (tttp) cc_final: 0.8489 (ttmm) REVERT: V 49 ASN cc_start: 0.8038 (t0) cc_final: 0.7519 (t0) REVERT: V 74 ASP cc_start: 0.8871 (t0) cc_final: 0.8622 (t0) REVERT: V 90 GLU cc_start: 0.7711 (pm20) cc_final: 0.7493 (pm20) REVERT: V 111 ASP cc_start: 0.7855 (m-30) cc_final: 0.7538 (m-30) REVERT: V 122 SER cc_start: 0.9322 (t) cc_final: 0.8969 (p) REVERT: Y 5 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7518 (tp40) REVERT: Y 18 LEU cc_start: 0.8667 (mm) cc_final: 0.8370 (pp) REVERT: X 9 ILE cc_start: 0.9564 (mt) cc_final: 0.9329 (pt) REVERT: Z 29 GLU cc_start: 0.7052 (tt0) cc_final: 0.6639 (tt0) REVERT: Q 105 ASN cc_start: 0.7398 (m110) cc_final: 0.6931 (m-40) REVERT: Q 122 ARG cc_start: 0.8904 (mmt-90) cc_final: 0.8590 (mmm-85) REVERT: W 71 ARG cc_start: 0.5888 (mmp-170) cc_final: 0.5575 (mmp80) REVERT: a 91 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7970 (tpp) REVERT: a 262 TYR cc_start: 0.7216 (m-10) cc_final: 0.6980 (t80) REVERT: b 439 SER cc_start: 0.8463 (m) cc_final: 0.8237 (t) REVERT: b 451 TYR cc_start: 0.9156 (t80) cc_final: 0.8707 (t80) REVERT: d 18 ASP cc_start: 0.8097 (t0) cc_final: 0.7845 (t0) REVERT: d 22 LYS cc_start: 0.8763 (mttt) cc_final: 0.8559 (mttt) REVERT: d 158 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8879 (tp) REVERT: d 307 ASP cc_start: 0.8115 (t0) cc_final: 0.7797 (t0) REVERT: d 332 ASP cc_start: 0.7754 (t70) cc_final: 0.7459 (t70) REVERT: d 333 GLN cc_start: 0.8390 (mt0) cc_final: 0.7930 (mp10) REVERT: e 46 ASP cc_start: 0.8299 (p0) cc_final: 0.8035 (m-30) REVERT: e 60 ASP cc_start: 0.7639 (p0) cc_final: 0.7426 (p0) REVERT: e 76 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7238 (mp0) REVERT: h 31 MET cc_start: 0.7537 (ttp) cc_final: 0.7184 (ttp) REVERT: i 1 MET cc_start: 0.6763 (tmm) cc_final: 0.6366 (tmm) REVERT: i 14 PHE cc_start: 0.9152 (t80) cc_final: 0.8693 (t80) REVERT: i 17 SER cc_start: 0.9292 (m) cc_final: 0.9024 (p) REVERT: j 23 MET cc_start: 0.8114 (mmm) cc_final: 0.7912 (tmm) REVERT: j 31 SER cc_start: 0.9646 (m) cc_final: 0.9262 (t) REVERT: k 8 ARG cc_start: 0.8100 (ptt-90) cc_final: 0.7846 (ptt-90) REVERT: k 29 PHE cc_start: 0.8914 (m-10) cc_final: 0.8328 (m-80) REVERT: m 11 VAL cc_start: 0.9158 (t) cc_final: 0.8935 (p) REVERT: o 72 MET cc_start: 0.8683 (mmp) cc_final: 0.8209 (mmt) REVERT: o 168 MET cc_start: 0.7165 (pmm) cc_final: 0.6418 (ppp) REVERT: o 202 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7564 (pmm) REVERT: t 25 GLU cc_start: 0.8451 (tp30) cc_final: 0.7924 (pt0) REVERT: v 86 GLU cc_start: 0.8169 (pm20) cc_final: 0.7940 (pm20) REVERT: z 4 LEU cc_start: 0.8603 (mt) cc_final: 0.8260 (tt) REVERT: z 44 TRP cc_start: 0.8838 (t60) cc_final: 0.8612 (t60) REVERT: q 104 ASP cc_start: 0.8225 (p0) cc_final: 0.7485 (t0) REVERT: q 118 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8276 (tp30) REVERT: q 122 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8189 (mmm-85) REVERT: q 141 GLU cc_start: 0.7992 (tp30) cc_final: 0.7668 (tm-30) REVERT: q 164 GLU cc_start: 0.8123 (pp20) cc_final: 0.7876 (pp20) REVERT: q 167 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: q 174 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6877 (tm-30) REVERT: w 71 ARG cc_start: 0.5959 (mmm160) cc_final: 0.5669 (mmm160) REVERT: 11 78 THR cc_start: 0.9292 (m) cc_final: 0.9018 (p) REVERT: 12 32 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7538 (mt-10) REVERT: 12 186 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: 12 196 HIS cc_start: 0.8082 (t-90) cc_final: 0.7724 (t-170) REVERT: 13 72 MET cc_start: 0.8356 (mtp) cc_final: 0.8044 (mtm) REVERT: 14 44 TYR cc_start: 0.7399 (t80) cc_final: 0.7043 (t80) REVERT: 14 138 ASP cc_start: 0.8592 (p0) cc_final: 0.8156 (p0) REVERT: 14 140 ASP cc_start: 0.8361 (p0) cc_final: 0.8079 (p0) REVERT: 14 172 MET cc_start: 0.8534 (mmm) cc_final: 0.8104 (mtp) REVERT: 14 178 MET cc_start: 0.8686 (mmm) cc_final: 0.8292 (mmt) REVERT: 15 72 MET cc_start: 0.8313 (ttm) cc_final: 0.8087 (ttm) REVERT: 15 107 ASP cc_start: 0.7072 (m-30) cc_final: 0.6675 (p0) REVERT: 16 110 ARG cc_start: 0.5637 (mtt180) cc_final: 0.5375 (mtt180) REVERT: 16 174 ILE cc_start: 0.9244 (tp) cc_final: 0.9022 (tp) REVERT: 16 183 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7862 (pp) REVERT: 17 72 MET cc_start: 0.6643 (mtp) cc_final: 0.6409 (mtp) REVERT: 17 140 ASP cc_start: 0.7936 (p0) cc_final: 0.7671 (p0) REVERT: 17 172 MET cc_start: 0.8880 (mmm) cc_final: 0.8675 (mmm) REVERT: 18 107 ASP cc_start: 0.7946 (m-30) cc_final: 0.7680 (p0) REVERT: 18 110 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.5838 (mtm-85) REVERT: 18 171 MET cc_start: 0.7879 (mmm) cc_final: 0.7611 (mmm) REVERT: 18 189 TYR cc_start: 0.7724 (t80) cc_final: 0.7516 (t80) outliers start: 166 outliers final: 112 residues processed: 987 average time/residue: 0.6755 time to fit residues: 1175.3434 Evaluate side-chains 959 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 836 time to evaluate : 5.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 100 ILE Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 103 ASP Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 365 THR Chi-restraints excluded: chain b residue 399 VAL Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 202 LEU Chi-restraints excluded: chain c residue 225 VAL Chi-restraints excluded: chain c residue 279 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 13 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain o residue 140 MET Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain o residue 203 GLU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 27 ILE Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 119 ILE Chi-restraints excluded: chain v residue 121 LEU Chi-restraints excluded: chain v residue 128 GLU Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain z residue 14 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 109 ILE Chi-restraints excluded: chain 11 residue 148 THR Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 12 residue 186 GLN Chi-restraints excluded: chain 13 residue 148 THR Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 78 THR Chi-restraints excluded: chain 16 residue 37 VAL Chi-restraints excluded: chain 16 residue 109 ILE Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 16 residue 183 LEU Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 17 residue 186 GLN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 110 ARG Chi-restraints excluded: chain 18 residue 114 THR Chi-restraints excluded: chain 18 residue 166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 406 optimal weight: 0.5980 chunk 521 optimal weight: 0.8980 chunk 404 optimal weight: 2.9990 chunk 601 optimal weight: 6.9990 chunk 398 optimal weight: 0.5980 chunk 711 optimal weight: 9.9990 chunk 445 optimal weight: 0.6980 chunk 433 optimal weight: 4.9990 chunk 328 optimal weight: 0.9990 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 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN D 254 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Q 105 ASN a 181 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 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 57 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 177 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 82 ASN 17 177 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 77742 Z= 0.183 Angle : 0.632 10.835 108698 Z= 0.280 Chirality : 0.043 0.304 10276 Planarity : 0.004 0.059 13967 Dihedral : 17.236 178.336 15734 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.63 % Allowed : 16.15 % Favored : 81.22 % 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: 0.04 (0.10), residues: 6884 helix: 0.79 (0.09), residues: 3721 sheet: -0.64 (0.35), residues: 192 loop : -0.86 (0.12), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 33 HIS 0.005 0.001 HIS c 396 PHE 0.029 0.001 PHE13 123 TYR 0.021 0.001 TYR m 8 ARG 0.006 0.000 ARG12 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 1047 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 899 time to evaluate : 5.384 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 91 MET cc_start: 0.8580 (mmm) cc_final: 0.7731 (mmm) REVERT: A 121 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9014 (mt) REVERT: A 187 GLN cc_start: 0.9494 (tp40) cc_final: 0.8729 (tm-30) REVERT: A 238 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8623 (mttt) REVERT: A 254 TYR cc_start: 0.8854 (t80) cc_final: 0.8569 (t80) REVERT: B 41 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 334 ASP cc_start: 0.7820 (p0) cc_final: 0.7178 (t70) REVERT: B 352 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6702 (ptt180) REVERT: C 178 MET cc_start: 0.8012 (mmm) cc_final: 0.7797 (mmm) REVERT: C 202 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8393 (mm) REVERT: D 22 LYS cc_start: 0.8715 (mttt) cc_final: 0.8311 (pttp) REVERT: D 41 TYR cc_start: 0.8469 (t80) cc_final: 0.8202 (t80) REVERT: D 70 CYS cc_start: 0.8407 (m) cc_final: 0.8094 (m) REVERT: E 75 GLN cc_start: 0.6787 (tp40) cc_final: 0.6437 (tp-100) REVERT: E 76 GLU cc_start: 0.7308 (tt0) cc_final: 0.6833 (tt0) REVERT: E 79 ASP cc_start: 0.7938 (m-30) cc_final: 0.7032 (m-30) REVERT: K 33 LEU cc_start: 0.9163 (tp) cc_final: 0.8742 (tp) REVERT: L 15 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8046 (ttm170) REVERT: M 24 ASN cc_start: 0.8604 (m-40) cc_final: 0.8325 (m-40) REVERT: M 28 GLN cc_start: 0.8920 (pp30) cc_final: 0.8423 (pp30) REVERT: M 30 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7948 (tp30) REVERT: O 168 MET cc_start: 0.7951 (ppp) cc_final: 0.7716 (ppp) REVERT: U 60 ASP cc_start: 0.8632 (m-30) cc_final: 0.8308 (t0) REVERT: U 73 ASP cc_start: 0.9014 (m-30) cc_final: 0.8672 (m-30) REVERT: U 96 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8826 (tp) REVERT: U 98 ASN cc_start: 0.8617 (p0) cc_final: 0.8275 (p0) REVERT: V 49 ASN cc_start: 0.7927 (t0) cc_final: 0.7422 (t0) REVERT: V 74 ASP cc_start: 0.8851 (t0) cc_final: 0.8534 (t0) REVERT: V 111 ASP cc_start: 0.7827 (m-30) cc_final: 0.7533 (m-30) REVERT: V 122 SER cc_start: 0.9279 (t) cc_final: 0.8978 (t) REVERT: Y 5 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7494 (tp40) REVERT: Y 18 LEU cc_start: 0.8665 (mm) cc_final: 0.8391 (pp) REVERT: X 9 ILE cc_start: 0.9561 (mt) cc_final: 0.9332 (pt) REVERT: Z 29 GLU cc_start: 0.7007 (tt0) cc_final: 0.6576 (tt0) REVERT: Q 105 ASN cc_start: 0.7404 (m-40) cc_final: 0.7043 (m-40) REVERT: Q 122 ARG cc_start: 0.8865 (mmt-90) cc_final: 0.8607 (mmm-85) REVERT: Q 200 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: W 71 ARG cc_start: 0.5659 (mmp-170) cc_final: 0.5440 (mmp80) REVERT: a 37 MET cc_start: 0.9248 (tmm) cc_final: 0.8622 (tmm) REVERT: a 262 TYR cc_start: 0.7318 (m-10) cc_final: 0.6970 (t80) REVERT: a 329 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7276 (mt-10) REVERT: b 90 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9049 (mt) REVERT: b 256 MET cc_start: 0.9172 (tpt) cc_final: 0.8904 (tpt) REVERT: b 362 PHE cc_start: 0.8038 (m-80) cc_final: 0.7817 (m-80) REVERT: b 439 SER cc_start: 0.8451 (m) cc_final: 0.8163 (t) REVERT: b 451 TYR cc_start: 0.9142 (t80) cc_final: 0.8654 (t80) REVERT: c 65 MET cc_start: 0.8208 (tpt) cc_final: 0.7853 (tpp) REVERT: c 402 LEU cc_start: 0.9457 (mt) cc_final: 0.9229 (mp) REVERT: d 18 ASP cc_start: 0.8047 (t0) cc_final: 0.7804 (t0) REVERT: d 22 LYS cc_start: 0.8822 (mttt) cc_final: 0.8606 (mttt) REVERT: d 158 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8864 (tp) REVERT: d 307 ASP cc_start: 0.8046 (t0) cc_final: 0.7733 (t0) REVERT: d 332 ASP cc_start: 0.7689 (t70) cc_final: 0.7365 (t70) REVERT: d 333 GLN cc_start: 0.8407 (mt0) cc_final: 0.7945 (mp10) REVERT: e 46 ASP cc_start: 0.8225 (p0) cc_final: 0.7951 (m-30) REVERT: e 60 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7429 (p0) REVERT: e 76 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7377 (mp0) REVERT: e 79 ASP cc_start: 0.8313 (p0) cc_final: 0.8059 (t0) REVERT: h 31 MET cc_start: 0.7463 (ttp) cc_final: 0.7115 (ttp) REVERT: h 61 ASP cc_start: 0.8367 (t0) cc_final: 0.8117 (t0) REVERT: h 64 ASN cc_start: 0.8429 (t0) cc_final: 0.8208 (m110) REVERT: i 17 SER cc_start: 0.9271 (m) cc_final: 0.9038 (p) REVERT: j 31 SER cc_start: 0.9621 (m) cc_final: 0.9256 (t) REVERT: k 8 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7470 (ptt-90) REVERT: k 29 PHE cc_start: 0.8873 (m-10) cc_final: 0.8312 (m-80) REVERT: o 31 SER cc_start: 0.8974 (t) cc_final: 0.8488 (p) REVERT: o 202 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7737 (pmm) REVERT: t 7 THR cc_start: 0.9380 (m) cc_final: 0.9061 (p) REVERT: t 25 GLU cc_start: 0.8409 (tp30) cc_final: 0.7929 (pt0) REVERT: z 4 LEU cc_start: 0.8553 (mt) cc_final: 0.8223 (tt) REVERT: q 73 GLU cc_start: 0.7980 (tp30) cc_final: 0.7582 (tp30) REVERT: q 104 ASP cc_start: 0.8246 (p0) cc_final: 0.7526 (t0) REVERT: q 118 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8285 (tp30) REVERT: q 122 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8222 (mmm-85) REVERT: q 134 GLU cc_start: 0.8343 (mp0) cc_final: 0.8128 (mp0) REVERT: q 141 GLU cc_start: 0.8058 (tp30) cc_final: 0.7710 (tm-30) REVERT: q 167 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: q 174 GLU cc_start: 0.7496 (tm-30) cc_final: 0.6806 (tm-30) REVERT: w 55 ASP cc_start: 0.8144 (t0) cc_final: 0.7814 (t0) REVERT: w 71 ARG cc_start: 0.5850 (mmm160) cc_final: 0.5604 (mmm160) REVERT: 11 78 THR cc_start: 0.9183 (m) cc_final: 0.8925 (p) REVERT: 12 32 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7569 (mt-10) REVERT: 12 178 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: 12 196 HIS cc_start: 0.8042 (t-90) cc_final: 0.7686 (t-170) REVERT: 13 72 MET cc_start: 0.8436 (mtp) cc_final: 0.7953 (mtm) REVERT: 14 44 TYR cc_start: 0.7394 (t80) cc_final: 0.7000 (t80) REVERT: 14 138 ASP cc_start: 0.8521 (p0) cc_final: 0.8089 (p0) REVERT: 14 175 MET cc_start: 0.8845 (mmm) cc_final: 0.8621 (tpp) REVERT: 15 72 MET cc_start: 0.8294 (ttm) cc_final: 0.8014 (ttm) REVERT: 15 107 ASP cc_start: 0.6956 (m-30) cc_final: 0.6740 (p0) REVERT: 16 110 ARG cc_start: 0.5495 (mtt180) cc_final: 0.5236 (mtt180) REVERT: 16 162 VAL cc_start: 0.9557 (t) cc_final: 0.9217 (m) REVERT: 16 174 ILE cc_start: 0.9220 (tp) cc_final: 0.9013 (tp) REVERT: 16 183 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7768 (pp) REVERT: 17 140 ASP cc_start: 0.7997 (p0) cc_final: 0.7722 (p0) REVERT: 17 172 MET cc_start: 0.8834 (mmm) cc_final: 0.8613 (mmm) REVERT: 18 72 MET cc_start: 0.8987 (mtt) cc_final: 0.8769 (mtp) REVERT: 18 137 TYR cc_start: 0.7834 (m-80) cc_final: 0.7622 (m-10) REVERT: 18 171 MET cc_start: 0.7897 (mmm) cc_final: 0.7618 (mmm) REVERT: 18 188 MET cc_start: 0.8288 (tpp) cc_final: 0.7425 (tmm) outliers start: 148 outliers final: 106 residues processed: 988 average time/residue: 0.6896 time to fit residues: 1201.2723 Evaluate side-chains 959 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 841 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 140 MET Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 100 ILE Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 31 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 103 ASP Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 399 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 202 LEU Chi-restraints excluded: chain c residue 225 VAL Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain o residue 140 MET Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain o residue 203 GLU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain o residue 246 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 52 HIS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 128 GLU Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain z residue 9 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 50 LEU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 109 ILE Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 11 residue 148 THR Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 12 residue 178 MET Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 148 THR Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 141 TYR Chi-restraints excluded: chain 16 residue 109 ILE Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 16 residue 183 LEU Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 110 ARG Chi-restraints excluded: chain 18 residue 114 THR Chi-restraints excluded: chain 18 residue 166 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 452 optimal weight: 0.9990 chunk 484 optimal weight: 0.7980 chunk 351 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 559 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 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 349 ASN m 4 GLN ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 68 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 192 ASN 11 177 ASN 14 96 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 177 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 77742 Z= 0.198 Angle : 0.642 11.293 108698 Z= 0.285 Chirality : 0.043 0.331 10276 Planarity : 0.004 0.059 13967 Dihedral : 16.967 179.359 15734 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.45 % Allowed : 16.58 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 6884 helix: 0.88 (0.09), residues: 3721 sheet: -0.58 (0.35), residues: 192 loop : -0.83 (0.12), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP16 49 HIS 0.005 0.001 HIS d 213 PHE 0.028 0.001 PHE13 123 TYR 0.023 0.001 TYR m 8 ARG 0.005 0.000 ARG12 59 *********************** 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 1017 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 879 time to evaluate : 5.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8596 (mmm) cc_final: 0.8052 (mmm) REVERT: A 121 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9005 (mt) REVERT: A 187 GLN cc_start: 0.9498 (tp40) cc_final: 0.8721 (tm-30) REVERT: A 238 LYS cc_start: 0.9181 (mmtm) cc_final: 0.8595 (mttt) REVERT: A 254 TYR cc_start: 0.8871 (t80) cc_final: 0.8577 (t80) REVERT: B 334 ASP cc_start: 0.7802 (p0) cc_final: 0.7167 (t70) REVERT: B 352 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6485 (ptt180) REVERT: C 178 MET cc_start: 0.8006 (mmm) cc_final: 0.7798 (mmm) REVERT: C 202 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8370 (mm) REVERT: D 22 LYS cc_start: 0.8706 (mttt) cc_final: 0.8305 (pttp) REVERT: D 48 MET cc_start: 0.8772 (mmm) cc_final: 0.8448 (mmm) REVERT: E 75 GLN cc_start: 0.7041 (tp40) cc_final: 0.6744 (tp-100) REVERT: E 76 GLU cc_start: 0.7320 (tt0) cc_final: 0.7114 (tt0) REVERT: E 79 ASP cc_start: 0.7963 (m-30) cc_final: 0.7076 (m-30) REVERT: K 33 LEU cc_start: 0.9202 (tp) cc_final: 0.8765 (tp) REVERT: L 15 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8038 (ttm170) REVERT: L 27 VAL cc_start: 0.9361 (t) cc_final: 0.8869 (m) REVERT: M 28 GLN cc_start: 0.8934 (pp30) cc_final: 0.8429 (pp30) REVERT: M 30 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7955 (tp30) REVERT: U 60 ASP cc_start: 0.8654 (m-30) cc_final: 0.8240 (t0) REVERT: U 73 ASP cc_start: 0.9046 (m-30) cc_final: 0.8704 (m-30) REVERT: U 96 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8837 (tp) REVERT: U 98 ASN cc_start: 0.8632 (p0) cc_final: 0.8319 (p0) REVERT: V 27 LYS cc_start: 0.8741 (tttp) cc_final: 0.8394 (ttmt) REVERT: V 49 ASN cc_start: 0.7954 (t0) cc_final: 0.7421 (t0) REVERT: V 74 ASP cc_start: 0.8852 (t0) cc_final: 0.8490 (t0) REVERT: V 111 ASP cc_start: 0.7796 (m-30) cc_final: 0.7537 (m-30) REVERT: V 122 SER cc_start: 0.9231 (t) cc_final: 0.8939 (t) REVERT: V 129 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8707 (mtmm) REVERT: Y 5 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7494 (tp40) REVERT: Y 18 LEU cc_start: 0.8685 (mm) cc_final: 0.8410 (pp) REVERT: X 9 ILE cc_start: 0.9521 (mt) cc_final: 0.9269 (pt) REVERT: Z 29 GLU cc_start: 0.7013 (tt0) cc_final: 0.6665 (tt0) REVERT: Q 105 ASN cc_start: 0.7556 (m-40) cc_final: 0.7217 (m-40) REVERT: Q 122 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8557 (mmm-85) REVERT: Q 140 ASP cc_start: 0.8380 (p0) cc_final: 0.7712 (p0) REVERT: Q 200 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: a 52 PHE cc_start: 0.8961 (t80) cc_final: 0.8751 (t80) REVERT: a 262 TYR cc_start: 0.7308 (m-10) cc_final: 0.6994 (t80) REVERT: a 329 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7269 (mt-10) REVERT: b 37 MET cc_start: 0.8961 (tpt) cc_final: 0.8752 (tpt) REVERT: b 90 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9057 (mt) REVERT: b 256 MET cc_start: 0.9175 (tpt) cc_final: 0.8887 (tpt) REVERT: b 439 SER cc_start: 0.8552 (m) cc_final: 0.8306 (t) REVERT: b 451 TYR cc_start: 0.9155 (t80) cc_final: 0.8681 (t80) REVERT: c 42 ASN cc_start: 0.8526 (m-40) cc_final: 0.8017 (p0) REVERT: c 402 LEU cc_start: 0.9450 (mt) cc_final: 0.9199 (mp) REVERT: d 18 ASP cc_start: 0.8017 (t0) cc_final: 0.7729 (t0) REVERT: d 22 LYS cc_start: 0.8824 (mttt) cc_final: 0.8593 (mttt) REVERT: d 48 MET cc_start: 0.8346 (tpp) cc_final: 0.7925 (mmt) REVERT: d 158 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8865 (tp) REVERT: d 307 ASP cc_start: 0.8026 (t0) cc_final: 0.7739 (t0) REVERT: d 332 ASP cc_start: 0.7683 (t70) cc_final: 0.7369 (t70) REVERT: d 333 GLN cc_start: 0.8402 (mt0) cc_final: 0.7949 (mp10) REVERT: e 46 ASP cc_start: 0.8189 (p0) cc_final: 0.7932 (m-30) REVERT: e 60 ASP cc_start: 0.7686 (p0) cc_final: 0.7460 (p0) REVERT: e 76 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7398 (mp0) REVERT: h 31 MET cc_start: 0.7508 (ttp) cc_final: 0.7157 (ttp) REVERT: h 64 ASN cc_start: 0.8617 (t0) cc_final: 0.8362 (m110) REVERT: i 17 SER cc_start: 0.9277 (m) cc_final: 0.9055 (p) REVERT: j 31 SER cc_start: 0.9592 (m) cc_final: 0.9256 (t) REVERT: k 8 ARG cc_start: 0.8153 (ptt-90) cc_final: 0.7493 (ptt-90) REVERT: k 29 PHE cc_start: 0.8879 (m-10) cc_final: 0.8256 (m-80) REVERT: o 31 SER cc_start: 0.8984 (t) cc_final: 0.8539 (p) REVERT: o 72 MET cc_start: 0.8743 (mmp) cc_final: 0.8276 (mmt) REVERT: o 202 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7737 (pmm) REVERT: t 7 THR cc_start: 0.9375 (m) cc_final: 0.9048 (p) REVERT: t 25 GLU cc_start: 0.8434 (tp30) cc_final: 0.7957 (pt0) REVERT: z 4 LEU cc_start: 0.8588 (mt) cc_final: 0.8252 (tt) REVERT: q 86 TYR cc_start: 0.8322 (t80) cc_final: 0.7570 (t80) REVERT: q 104 ASP cc_start: 0.8279 (p0) cc_final: 0.7567 (t0) REVERT: q 118 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8270 (tp30) REVERT: q 122 ARG cc_start: 0.8601 (mmm160) cc_final: 0.8164 (mmm-85) REVERT: q 134 GLU cc_start: 0.8224 (mp0) cc_final: 0.7954 (mp0) REVERT: q 141 GLU cc_start: 0.8055 (tp30) cc_final: 0.7735 (tm-30) REVERT: q 146 MET cc_start: 0.7805 (mtt) cc_final: 0.7481 (mtt) REVERT: q 164 GLU cc_start: 0.8090 (pp20) cc_final: 0.7691 (pp20) REVERT: q 167 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: q 174 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6811 (tm-30) REVERT: w 55 ASP cc_start: 0.8153 (t0) cc_final: 0.7799 (t0) REVERT: w 71 ARG cc_start: 0.5843 (mmm160) cc_final: 0.5612 (mmm160) REVERT: 11 78 THR cc_start: 0.9166 (m) cc_final: 0.8904 (p) REVERT: 12 32 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7564 (mt-10) REVERT: 12 178 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7954 (mtm) REVERT: 12 186 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7002 (mt0) REVERT: 12 196 HIS cc_start: 0.8038 (t-90) cc_final: 0.7688 (t-170) REVERT: 13 72 MET cc_start: 0.8423 (mtp) cc_final: 0.7962 (mtm) REVERT: 14 44 TYR cc_start: 0.7509 (t80) cc_final: 0.7045 (t80) REVERT: 14 123 PHE cc_start: 0.8932 (t80) cc_final: 0.8690 (t80) REVERT: 14 138 ASP cc_start: 0.8564 (p0) cc_final: 0.8016 (p0) REVERT: 14 175 MET cc_start: 0.8897 (mmm) cc_final: 0.8640 (tpp) REVERT: 16 110 ARG cc_start: 0.5569 (mtt180) cc_final: 0.5314 (mtt180) REVERT: 16 162 VAL cc_start: 0.9571 (t) cc_final: 0.9205 (m) REVERT: 16 174 ILE cc_start: 0.9216 (tp) cc_final: 0.9016 (tp) REVERT: 16 183 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7765 (pp) REVERT: 17 140 ASP cc_start: 0.8062 (p0) cc_final: 0.7799 (p0) REVERT: 17 172 MET cc_start: 0.8791 (mmm) cc_final: 0.8589 (mmm) REVERT: 18 137 TYR cc_start: 0.7804 (m-80) cc_final: 0.7592 (m-10) REVERT: 18 171 MET cc_start: 0.7909 (mmm) cc_final: 0.7697 (mmm) REVERT: 18 188 MET cc_start: 0.8309 (tpp) cc_final: 0.7412 (tmm) outliers start: 138 outliers final: 108 residues processed: 961 average time/residue: 0.7552 time to fit residues: 1290.5913 Evaluate side-chains 960 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 840 time to evaluate : 5.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 85 LEU Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 103 ASP Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 399 VAL Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 202 LEU Chi-restraints excluded: chain c residue 225 VAL Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 13 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain o residue 140 MET Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain o residue 203 GLU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain o residue 246 VAL Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 27 ILE Chi-restraints excluded: chain u residue 52 HIS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 128 GLU Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain z residue 9 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 50 LEU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 109 ILE Chi-restraints excluded: chain 11 residue 135 SER Chi-restraints excluded: chain 11 residue 148 THR Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 12 residue 178 MET Chi-restraints excluded: chain 12 residue 186 GLN Chi-restraints excluded: chain 13 residue 31 SER Chi-restraints excluded: chain 13 residue 148 THR Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 96 ASN Chi-restraints excluded: chain 16 residue 50 LEU Chi-restraints excluded: chain 16 residue 109 ILE Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 16 residue 183 LEU Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 114 THR Chi-restraints excluded: chain 18 residue 166 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 0.6980 chunk 681 optimal weight: 0.7980 chunk 621 optimal weight: 0.0870 chunk 662 optimal weight: 2.9990 chunk 398 optimal weight: 0.8980 chunk 288 optimal weight: 0.6980 chunk 520 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 598 optimal weight: 0.6980 chunk 626 optimal weight: 3.9990 chunk 660 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Q 162 GLN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 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 4 GLN ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 33 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 95 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 196 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 77742 Z= 0.169 Angle : 0.631 15.295 108698 Z= 0.281 Chirality : 0.042 0.311 10276 Planarity : 0.004 0.060 13967 Dihedral : 16.692 177.167 15734 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.24 % Allowed : 17.11 % Favored : 80.65 % 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: 0.97 (0.09), residues: 3718 sheet: -0.57 (0.35), residues: 202 loop : -0.81 (0.12), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP13 131 HIS 0.008 0.001 HIS15 196 PHE 0.030 0.001 PHE13 123 TYR 0.032 0.001 TYR U 55 ARG 0.004 0.000 ARG17 158 *********************** 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 1022 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 896 time to evaluate : 5.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8559 (mmm) cc_final: 0.8019 (mmm) REVERT: A 121 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8968 (mt) REVERT: A 187 GLN cc_start: 0.9482 (tp40) cc_final: 0.8737 (tm-30) REVERT: A 238 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8597 (mttt) REVERT: A 254 TYR cc_start: 0.8861 (t80) cc_final: 0.8588 (t80) REVERT: B 334 ASP cc_start: 0.7802 (p0) cc_final: 0.7226 (t70) REVERT: B 352 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6435 (ptt180) REVERT: C 202 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8336 (mm) REVERT: D 22 LYS cc_start: 0.8694 (mttt) cc_final: 0.8266 (pttp) REVERT: K 33 LEU cc_start: 0.9202 (tp) cc_final: 0.8769 (tp) REVERT: L 15 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7976 (ttp-170) REVERT: L 19 TYR cc_start: 0.8989 (m-80) cc_final: 0.8757 (m-80) REVERT: L 27 VAL cc_start: 0.9317 (t) cc_final: 0.8866 (m) REVERT: M 28 GLN cc_start: 0.8924 (pp30) cc_final: 0.8419 (pp30) REVERT: M 30 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7967 (tp30) REVERT: O 168 MET cc_start: 0.7843 (ppp) cc_final: 0.7489 (ppp) REVERT: U 60 ASP cc_start: 0.8620 (m-30) cc_final: 0.8228 (t0) REVERT: U 73 ASP cc_start: 0.9052 (m-30) cc_final: 0.8728 (m-30) REVERT: U 96 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8825 (tp) REVERT: U 98 ASN cc_start: 0.8629 (p0) cc_final: 0.8331 (p0) REVERT: V 49 ASN cc_start: 0.7926 (t0) cc_final: 0.7361 (t0) REVERT: V 74 ASP cc_start: 0.8780 (t0) cc_final: 0.8406 (t0) REVERT: V 111 ASP cc_start: 0.7752 (m-30) cc_final: 0.7482 (m-30) REVERT: V 122 SER cc_start: 0.9245 (t) cc_final: 0.8963 (t) REVERT: Y 5 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7476 (tp40) REVERT: Y 18 LEU cc_start: 0.8677 (mm) cc_final: 0.8400 (pp) REVERT: X 9 ILE cc_start: 0.9485 (mt) cc_final: 0.9225 (pt) REVERT: Z 1 MET cc_start: 0.6611 (tpp) cc_final: 0.6378 (tpp) REVERT: Z 29 GLU cc_start: 0.7026 (tt0) cc_final: 0.6610 (tt0) REVERT: Q 105 ASN cc_start: 0.7520 (m-40) cc_final: 0.7181 (m-40) REVERT: Q 140 ASP cc_start: 0.8311 (p0) cc_final: 0.7757 (p0) REVERT: Q 200 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: a 37 MET cc_start: 0.9221 (tmm) cc_final: 0.8811 (tmm) REVERT: a 52 PHE cc_start: 0.8909 (t80) cc_final: 0.8690 (t80) REVERT: a 329 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7134 (mt-10) REVERT: b 90 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9055 (mt) REVERT: b 256 MET cc_start: 0.9175 (tpt) cc_final: 0.8906 (tpt) REVERT: b 439 SER cc_start: 0.8569 (m) cc_final: 0.8330 (t) REVERT: b 451 TYR cc_start: 0.9111 (t80) cc_final: 0.8596 (t80) REVERT: c 42 ASN cc_start: 0.8523 (m-40) cc_final: 0.8054 (p0) REVERT: c 402 LEU cc_start: 0.9416 (mt) cc_final: 0.9165 (mp) REVERT: d 18 ASP cc_start: 0.7934 (t0) cc_final: 0.7630 (t0) REVERT: d 22 LYS cc_start: 0.8820 (mttt) cc_final: 0.8619 (mttt) REVERT: d 48 MET cc_start: 0.8325 (tpp) cc_final: 0.7926 (mmt) REVERT: d 158 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8845 (tp) REVERT: d 184 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8945 (mm) REVERT: d 307 ASP cc_start: 0.8058 (t0) cc_final: 0.7768 (t0) REVERT: d 332 ASP cc_start: 0.7707 (t70) cc_final: 0.7408 (t70) REVERT: d 333 GLN cc_start: 0.8379 (mt0) cc_final: 0.7989 (mp10) REVERT: e 46 ASP cc_start: 0.8239 (p0) cc_final: 0.7864 (m-30) REVERT: e 60 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7382 (p0) REVERT: e 76 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7315 (mp0) REVERT: h 31 MET cc_start: 0.7553 (ttp) cc_final: 0.7200 (ttp) REVERT: i 17 SER cc_start: 0.9227 (m) cc_final: 0.8979 (p) REVERT: j 31 SER cc_start: 0.9577 (m) cc_final: 0.9236 (t) REVERT: k 8 ARG cc_start: 0.8179 (ptt-90) cc_final: 0.7591 (ptt-90) REVERT: k 29 PHE cc_start: 0.8852 (m-10) cc_final: 0.8241 (m-80) REVERT: k 44 ARG cc_start: 0.7134 (ppt90) cc_final: 0.5077 (ptt180) REVERT: o 72 MET cc_start: 0.8834 (mmp) cc_final: 0.8566 (mmt) REVERT: o 179 GLU cc_start: 0.8123 (tt0) cc_final: 0.7775 (tm-30) REVERT: o 202 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7783 (pmm) REVERT: t 7 THR cc_start: 0.9345 (m) cc_final: 0.9015 (p) REVERT: t 25 GLU cc_start: 0.8477 (tp30) cc_final: 0.7991 (pt0) REVERT: v 120 MET cc_start: 0.7965 (mtp) cc_final: 0.7725 (mtp) REVERT: x 29 ILE cc_start: 0.8721 (tt) cc_final: 0.8362 (tp) REVERT: z 4 LEU cc_start: 0.8548 (mt) cc_final: 0.8232 (tt) REVERT: q 86 TYR cc_start: 0.8276 (t80) cc_final: 0.7600 (t80) REVERT: q 104 ASP cc_start: 0.8217 (p0) cc_final: 0.7514 (t0) REVERT: q 118 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8278 (tp30) REVERT: q 122 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8167 (mmm-85) REVERT: q 134 GLU cc_start: 0.8175 (mp0) cc_final: 0.7805 (mp0) REVERT: q 141 GLU cc_start: 0.8170 (tp30) cc_final: 0.7840 (tm-30) REVERT: q 146 MET cc_start: 0.7824 (mtt) cc_final: 0.7396 (mtt) REVERT: q 164 GLU cc_start: 0.8088 (pp20) cc_final: 0.7687 (pp20) REVERT: q 167 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: q 174 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6841 (tm-30) REVERT: 12 178 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7919 (mtm) REVERT: 12 186 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7034 (mt0) REVERT: 12 196 HIS cc_start: 0.7941 (t-90) cc_final: 0.7607 (t-170) REVERT: 13 72 MET cc_start: 0.8405 (mtp) cc_final: 0.7965 (mtm) REVERT: 14 44 TYR cc_start: 0.7514 (t80) cc_final: 0.7012 (t80) REVERT: 14 138 ASP cc_start: 0.8594 (p0) cc_final: 0.8040 (p0) REVERT: 14 172 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8066 (ttm) REVERT: 14 175 MET cc_start: 0.8853 (mmm) cc_final: 0.8602 (tpp) REVERT: 16 91 LEU cc_start: 0.7930 (tm) cc_final: 0.7580 (tp) REVERT: 16 110 ARG cc_start: 0.5541 (mtt180) cc_final: 0.5306 (mtt180) REVERT: 16 162 VAL cc_start: 0.9545 (t) cc_final: 0.9166 (m) REVERT: 16 183 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7789 (pp) REVERT: 17 140 ASP cc_start: 0.7969 (p0) cc_final: 0.7755 (p0) REVERT: 17 172 MET cc_start: 0.8747 (mmm) cc_final: 0.8532 (mmm) REVERT: 18 171 MET cc_start: 0.7942 (mmm) cc_final: 0.7685 (mmm) REVERT: 18 188 MET cc_start: 0.8302 (tpp) cc_final: 0.7441 (tmm) outliers start: 126 outliers final: 99 residues processed: 972 average time/residue: 0.6716 time to fit residues: 1148.9489 Evaluate side-chains 960 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 846 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 31 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 103 ASP Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 399 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 202 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 35 MET Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain o residue 140 MET Chi-restraints excluded: chain o residue 202 MET Chi-restraints excluded: chain o residue 203 GLU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain o residue 246 VAL Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 27 ILE Chi-restraints excluded: chain u residue 52 HIS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 68 ASN Chi-restraints excluded: chain v residue 128 GLU Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain z residue 9 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 50 LEU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 109 ILE Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 12 residue 178 MET Chi-restraints excluded: chain 12 residue 186 GLN Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 141 TYR Chi-restraints excluded: chain 14 residue 172 MET Chi-restraints excluded: chain 16 residue 50 LEU Chi-restraints excluded: chain 16 residue 109 ILE Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 16 residue 183 LEU Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 114 THR Chi-restraints excluded: chain 18 residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.9990 chunk 700 optimal weight: 6.9990 chunk 427 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 487 optimal weight: 1.9990 chunk 735 optimal weight: 10.0000 chunk 676 optimal weight: 2.9990 chunk 585 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 452 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 GLN ** d 116 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 h 64 ASN m 4 GLN ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 96 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 83 ASN 16 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 77742 Z= 0.238 Angle : 0.663 12.017 108698 Z= 0.296 Chirality : 0.044 0.325 10276 Planarity : 0.004 0.059 13967 Dihedral : 16.648 176.277 15734 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.22 % Allowed : 17.40 % Favored : 80.38 % 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: 0.20 (0.10), residues: 6884 helix: 0.95 (0.09), residues: 3718 sheet: -0.56 (0.35), residues: 202 loop : -0.81 (0.12), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP11 131 HIS 0.008 0.001 HIS A 195 PHE 0.029 0.001 PHE13 123 TYR 0.027 0.001 TYR U 55 ARG 0.006 0.000 ARG Q 122 ********************** 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 984 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 859 time to evaluate : 5.395 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: A 91 MET cc_start: 0.8566 (mmm) cc_final: 0.8014 (mmm) REVERT: A 121 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9004 (mt) REVERT: A 187 GLN cc_start: 0.9502 (tp40) cc_final: 0.8786 (tm-30) REVERT: A 238 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8547 (mttt) REVERT: A 254 TYR cc_start: 0.8915 (t80) cc_final: 0.8635 (t80) REVERT: A 304 GLN cc_start: 0.8358 (mp10) cc_final: 0.8125 (mm-40) REVERT: B 334 ASP cc_start: 0.7819 (p0) cc_final: 0.7181 (t70) REVERT: B 352 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6418 (ptt180) REVERT: C 202 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8450 (mm) REVERT: D 22 LYS cc_start: 0.8693 (mttt) cc_final: 0.8338 (pttp) REVERT: F 38 MET cc_start: 0.8491 (mtp) cc_final: 0.7995 (mtp) REVERT: K 33 LEU cc_start: 0.9185 (tp) cc_final: 0.8761 (tp) REVERT: L 27 VAL cc_start: 0.9300 (t) cc_final: 0.8851 (m) REVERT: M 28 GLN cc_start: 0.9006 (pp30) cc_final: 0.8474 (pp30) REVERT: M 30 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7911 (tp30) REVERT: M 41 ASP cc_start: 0.8660 (t0) cc_final: 0.8435 (t0) REVERT: O 168 MET cc_start: 0.7866 (ppp) cc_final: 0.7498 (ppp) REVERT: U 60 ASP cc_start: 0.8672 (m-30) cc_final: 0.8262 (t0) REVERT: U 73 ASP cc_start: 0.9036 (m-30) cc_final: 0.8705 (m-30) REVERT: U 96 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8862 (tp) REVERT: U 98 ASN cc_start: 0.8706 (p0) cc_final: 0.8434 (p0) REVERT: V 49 ASN cc_start: 0.7909 (t0) cc_final: 0.7164 (t0) REVERT: V 90 GLU cc_start: 0.7738 (pm20) cc_final: 0.7454 (pm20) REVERT: V 111 ASP cc_start: 0.7763 (m-30) cc_final: 0.7525 (m-30) REVERT: V 122 SER cc_start: 0.9298 (t) cc_final: 0.8983 (p) REVERT: Y 5 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7495 (tp40) REVERT: Y 18 LEU cc_start: 0.8745 (mm) cc_final: 0.8464 (pp) REVERT: X 9 ILE cc_start: 0.9506 (mt) cc_final: 0.9249 (pt) REVERT: Z 1 MET cc_start: 0.6761 (tpp) cc_final: 0.6514 (tpp) REVERT: Z 29 GLU cc_start: 0.7125 (tt0) cc_final: 0.6718 (tt0) REVERT: Q 105 ASN cc_start: 0.7564 (m-40) cc_final: 0.7216 (m-40) REVERT: Q 140 ASP cc_start: 0.8282 (p0) cc_final: 0.7767 (p0) REVERT: Q 200 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: a 37 MET cc_start: 0.9246 (tmm) cc_final: 0.8833 (tmm) REVERT: a 52 PHE cc_start: 0.8964 (t80) cc_final: 0.8742 (t80) REVERT: a 329 GLU cc_start: 0.7785 (tt0) cc_final: 0.7286 (mt-10) REVERT: b 90 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9058 (mt) REVERT: b 256 MET cc_start: 0.9173 (tpt) cc_final: 0.8861 (tpt) REVERT: b 451 TYR cc_start: 0.9193 (t80) cc_final: 0.8682 (t80) REVERT: c 42 ASN cc_start: 0.8518 (m-40) cc_final: 0.8004 (p0) REVERT: c 65 MET cc_start: 0.8170 (tpt) cc_final: 0.7811 (tpp) REVERT: c 354 MET cc_start: 0.8582 (ptm) cc_final: 0.8366 (ptm) REVERT: d 18 ASP cc_start: 0.7933 (t0) cc_final: 0.7598 (t0) REVERT: d 22 LYS cc_start: 0.8836 (mttt) cc_final: 0.8603 (mttt) REVERT: d 158 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8940 (tp) REVERT: d 307 ASP cc_start: 0.8094 (t0) cc_final: 0.7842 (t0) REVERT: d 332 ASP cc_start: 0.7739 (t70) cc_final: 0.7345 (t70) REVERT: d 333 GLN cc_start: 0.8375 (mt0) cc_final: 0.7924 (mp10) REVERT: e 46 ASP cc_start: 0.8253 (p0) cc_final: 0.7851 (m-30) REVERT: e 60 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7311 (p0) REVERT: e 76 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7344 (mp0) REVERT: h 31 MET cc_start: 0.7516 (ttp) cc_final: 0.7170 (ttp) REVERT: i 17 SER cc_start: 0.9262 (m) cc_final: 0.9049 (p) REVERT: j 31 SER cc_start: 0.9598 (m) cc_final: 0.9255 (t) REVERT: k 8 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7628 (ptt-90) REVERT: k 13 TYR cc_start: 0.8238 (m-80) cc_final: 0.7878 (m-80) REVERT: k 29 PHE cc_start: 0.8890 (m-10) cc_final: 0.8282 (m-80) REVERT: o 202 MET cc_start: 0.8210 (mtm) cc_final: 0.7807 (pmm) REVERT: t 25 GLU cc_start: 0.8471 (tp30) cc_final: 0.8001 (pt0) REVERT: v 120 MET cc_start: 0.8007 (mtp) cc_final: 0.7769 (mtp) REVERT: x 29 ILE cc_start: 0.8725 (tt) cc_final: 0.8371 (tp) REVERT: z 4 LEU cc_start: 0.8562 (mt) cc_final: 0.8240 (tt) REVERT: q 104 ASP cc_start: 0.8230 (p0) cc_final: 0.7528 (t0) REVERT: q 118 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8271 (tp30) REVERT: q 122 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8183 (mmm-85) REVERT: q 141 GLU cc_start: 0.8182 (tp30) cc_final: 0.7913 (tm-30) REVERT: q 146 MET cc_start: 0.7846 (mtt) cc_final: 0.7645 (mtt) REVERT: q 164 GLU cc_start: 0.8106 (pp20) cc_final: 0.7709 (pp20) REVERT: q 167 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: q 174 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6861 (tm-30) REVERT: w 55 ASP cc_start: 0.8061 (t0) cc_final: 0.7825 (t70) REVERT: 12 32 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7485 (mt-10) REVERT: 12 186 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: 12 196 HIS cc_start: 0.7951 (t-90) cc_final: 0.7660 (t-170) REVERT: 13 72 MET cc_start: 0.8384 (mtp) cc_final: 0.7952 (mtm) REVERT: 13 98 LYS cc_start: 0.8529 (mttm) cc_final: 0.8315 (mttm) REVERT: 14 44 TYR cc_start: 0.7471 (t80) cc_final: 0.6960 (t80) REVERT: 14 138 ASP cc_start: 0.8573 (p0) cc_final: 0.8008 (p0) REVERT: 14 175 MET cc_start: 0.8897 (mmm) cc_final: 0.8637 (tpp) REVERT: 16 91 LEU cc_start: 0.7960 (tm) cc_final: 0.7616 (tp) REVERT: 16 110 ARG cc_start: 0.5542 (mtt180) cc_final: 0.5253 (mtt180) REVERT: 16 162 VAL cc_start: 0.9586 (t) cc_final: 0.9185 (m) REVERT: 16 183 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7835 (pp) REVERT: 17 172 MET cc_start: 0.8778 (mmm) cc_final: 0.8533 (mmm) REVERT: 18 171 MET cc_start: 0.7948 (mmm) cc_final: 0.7617 (mmm) REVERT: 18 177 ASN cc_start: 0.8542 (m-40) cc_final: 0.7939 (m110) outliers start: 125 outliers final: 106 residues processed: 930 average time/residue: 0.6768 time to fit residues: 1111.3266 Evaluate side-chains 945 residues out of total 5632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 828 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 170 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 96 ILE Chi-restraints excluded: chain V residue 127 SER Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain Q residue 200 ASP Chi-restraints excluded: chain W residue 24 ASN Chi-restraints excluded: chain W residue 31 ASP Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain a residue 103 ASP Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 286 THR Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 208 PHE Chi-restraints excluded: chain b residue 399 VAL Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 116 HIS Chi-restraints excluded: chain c residue 172 LEU Chi-restraints excluded: chain c residue 202 LEU Chi-restraints excluded: chain c residue 359 LEU Chi-restraints excluded: chain c residue 465 LEU Chi-restraints excluded: chain d residue 13 LEU Chi-restraints excluded: chain d residue 24 ASP Chi-restraints excluded: chain d residue 27 VAL Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 35 MET Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 18 LEU Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain o residue 140 MET Chi-restraints excluded: chain o residue 203 GLU Chi-restraints excluded: chain o residue 221 THR Chi-restraints excluded: chain o residue 246 VAL Chi-restraints excluded: chain t residue 30 LEU Chi-restraints excluded: chain u residue 24 ILE Chi-restraints excluded: chain u residue 52 HIS Chi-restraints excluded: chain u residue 61 LEU Chi-restraints excluded: chain u residue 86 THR Chi-restraints excluded: chain u residue 93 ILE Chi-restraints excluded: chain v residue 3 LEU Chi-restraints excluded: chain v residue 68 ASN Chi-restraints excluded: chain v residue 128 GLU Chi-restraints excluded: chain y residue 6 VAL Chi-restraints excluded: chain y residue 18 LEU Chi-restraints excluded: chain x residue 18 VAL Chi-restraints excluded: chain x residue 32 SER Chi-restraints excluded: chain z residue 9 LEU Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 50 LEU Chi-restraints excluded: chain 11 residue 38 THR Chi-restraints excluded: chain 11 residue 109 ILE Chi-restraints excluded: chain 11 residue 150 ILE Chi-restraints excluded: chain 11 residue 171 MET Chi-restraints excluded: chain 11 residue 188 MET Chi-restraints excluded: chain 12 residue 43 VAL Chi-restraints excluded: chain 12 residue 186 GLN Chi-restraints excluded: chain 13 residue 152 ASP Chi-restraints excluded: chain 14 residue 96 ASN Chi-restraints excluded: chain 14 residue 109 ILE Chi-restraints excluded: chain 14 residue 172 MET Chi-restraints excluded: chain 16 residue 50 LEU Chi-restraints excluded: chain 16 residue 109 ILE Chi-restraints excluded: chain 16 residue 123 PHE Chi-restraints excluded: chain 16 residue 141 TYR Chi-restraints excluded: chain 16 residue 177 ASN Chi-restraints excluded: chain 16 residue 183 LEU Chi-restraints excluded: chain 17 residue 91 LEU Chi-restraints excluded: chain 17 residue 114 THR Chi-restraints excluded: chain 17 residue 148 THR Chi-restraints excluded: chain 17 residue 166 ASN Chi-restraints excluded: chain 18 residue 33 ILE Chi-restraints excluded: chain 18 residue 114 THR Chi-restraints excluded: chain 18 residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 0.9980 chunk 623 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 539 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 586 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 602 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** b 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 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 h 64 ASN l 7 ASN m 4 GLN ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 95 ASN ** 14 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 177 ASN 17 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075547 restraints weight = 204603.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077899 restraints weight = 182861.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077791 restraints weight = 93589.177| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 77742 Z= 0.223 Angle : 0.664 20.978 108698 Z= 0.297 Chirality : 0.044 0.321 10276 Planarity : 0.004 0.057 13967 Dihedral : 16.595 175.370 15734 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 2.31 % Allowed : 17.59 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 6884 helix: 0.94 (0.09), residues: 3722 sheet: -0.55 (0.35), residues: 202 loop : -0.81 (0.12), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP11 131 HIS 0.007 0.001 HIS A 195 PHE 0.029 0.001 PHE13 123 TYR 0.032 0.001 TYR D 243 ARG 0.010 0.000 ARG Q 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19191.48 seconds wall clock time: 331 minutes 20.10 seconds (19880.10 seconds total)