Starting phenix.real_space_refine on Thu Sep 26 15:19:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/09_2024/5oqj_3846.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/09_2024/5oqj_3846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/09_2024/5oqj_3846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/09_2024/5oqj_3846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/09_2024/5oqj_3846.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/09_2024/5oqj_3846.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 16 6.06 5 P 148 5.49 5 Mg 1 5.21 5 S 324 5.16 5 C 39122 2.51 5 N 11155 2.21 5 O 12161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62931 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9178 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 51, 'TRANS': 1100} Chain breaks: 7 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "N" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1533 Classifications: {'DNA': 76} Link IDs: {'rna3p': 75} Chain breaks: 1 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 30 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "T" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1440 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain breaks: 1 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 30 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 782 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain breaks: 1 Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "W" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 356 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'TRANS': 66} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 59, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "X" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1004 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 7, 'TRANS': 152} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "0" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1802 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 7, 'TRANS': 263} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 349 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 15, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 257 Chain: "0" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3042 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 2, 'UNK:plan-1': 33, 'TRP:plan': 2, 'HIS:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 227 Chain: "1" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1323 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "1" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'UNK:plan-1': 31, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "1" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1207 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 2, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 623 Unresolved non-hydrogen angles: 858 Unresolved non-hydrogen dihedrals: 428 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 6, 'UNK:plan-1': 139, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 332 Chain: "2" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 548 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 171 Chain: "2" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 840 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'TYR:plan': 3, 'UNK:plan-1': 67, 'HIS:plan': 3, 'ARG:plan': 2, 'PHE:plan': 7, 'GLU:plan': 7, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 236 Chain: "2" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 772 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 40, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "3" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 860 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 178 Chain: "4" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 332 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 63} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "4" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 807 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 606 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 5, 'TYR:plan': 6, 'UNK:plan-1': 21, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 236 Chain: "4" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 336 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 63} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 17, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "6" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1438 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 327 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 59} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2, 'UNK:plan-1': 17, 'HIS:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "6" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 197 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 14, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "6" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 235 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 13, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "7" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 474 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "7" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2674 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 9, 'TRANS': 335} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'UNK:plan-1': 45} Unresolved non-hydrogen planarities: 45 Chain: "Z" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'TRANS': 42} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 813 SG CYS A 107 100.851 117.685 115.078 1.00 0.00 S ATOM 837 SG CYS A 110 100.839 118.916 118.341 1.00 0.00 S ATOM 1142 SG CYS A 148 104.560 118.031 117.299 1.00 0.00 S ATOM 1211 SG CYS A 167 101.990 115.274 117.182 1.00 0.00 S ATOM 508 SG CYS A 67 63.199 143.269 98.435 1.00 0.00 S ATOM 530 SG CYS A 70 65.448 145.824 101.450 1.00 0.00 S ATOM 583 SG CYS A 77 65.905 145.050 97.379 1.00 0.00 S ATOM 19693 SG CYS B1163 75.482 148.202 112.426 1.00 0.00 S ATOM 19711 SG CYS B1166 77.441 144.644 110.627 1.00 0.00 S ATOM 19836 SG CYS B1182 73.676 145.332 110.225 1.00 0.00 S ATOM 19855 SG CYS B1185 75.032 144.963 113.427 1.00 0.00 S ATOM 20822 SG CYS C 86 45.822 183.682 45.846 1.00 0.00 S ATOM 20839 SG CYS C 88 44.819 180.412 46.821 1.00 0.00 S ATOM 20872 SG CYS C 92 44.602 181.557 43.519 1.00 0.00 S ATOM 20895 SG CYS C 95 47.903 180.597 44.039 1.00 0.00 S ATOM 28385 SG CYS I 7 134.353 90.890 59.264 1.00 0.00 S ATOM 28410 SG CYS I 10 131.036 89.020 60.966 1.00 0.00 S ATOM 28576 SG CYS I 29 133.309 92.196 62.560 1.00 0.00 S ATOM 28600 SG CYS I 32 134.356 88.834 62.085 1.00 0.00 S ATOM 28927 SG CYS I 75 138.506 124.939 29.557 1.00 0.00 S ATOM 28949 SG CYS I 78 137.347 123.485 26.073 1.00 0.00 S ATOM 29165 SG CYS I 103 134.500 124.015 27.844 1.00 0.00 S ATOM 29185 SG CYS I 106 137.169 121.064 28.777 1.00 0.00 S ATOM 29330 SG CYS J 7 75.875 169.028 31.922 1.00 0.00 S ATOM 29353 SG CYS J 10 75.836 172.274 30.687 1.00 0.00 S ATOM 29633 SG CYS J 45 79.435 171.564 30.824 1.00 0.00 S ATOM 29639 SG CYS J 46 76.709 170.428 28.459 1.00 0.00 S ATOM 30762 SG CYS L 31 49.649 133.781 41.657 1.00 0.00 S ATOM 30782 SG CYS L 34 47.889 133.859 38.525 1.00 0.00 S ATOM 30886 SG CYS L 48 46.937 132.487 42.581 1.00 0.00 S ATOM 30909 SG CYS L 51 49.227 130.629 40.671 1.00 0.00 S ATOM 31137 SG CYS M 24 49.346 163.558 89.133 1.00 0.00 S ATOM 31159 SG CYS M 27 47.050 164.804 87.543 1.00 0.00 S ATOM 31303 SG CYS M 45 48.295 162.172 85.056 1.00 0.00 S ATOM 31322 SG CYS M 48 49.708 165.933 86.696 1.00 0.00 S ATOM 42521 SG CYS W 124 47.670 139.801 111.049 1.00 0.00 S ATOM 42542 SG CYS W 127 50.260 139.734 108.670 1.00 0.00 S ATOM 42727 SG CYS W 149 49.887 142.961 110.631 1.00 0.00 S ATOM 42747 SG CYS W 152 47.477 141.747 107.484 1.00 0.00 S ATOM 45052 SG CYS 0 115 76.172 92.849 191.353 1.00 0.00 S ATOM 45249 SG CYS 0 156 69.955 91.569 193.435 1.00 0.00 S ATOM 45159 SG CYS 0 133 73.716 96.578 192.038 1.00 0.00 S ATOM 45514 SG CYS 0 191 75.045 93.202 196.095 1.00 0.00 S ATOM 54544 SG CYS 3 13 61.254 123.286 142.461 1.00 0.00 S ATOM 54565 SG CYS 3 16 63.898 122.492 139.168 1.00 0.00 S ATOM 54738 SG CYS 3 39 64.203 125.071 141.144 1.00 0.00 S ATOM 54759 SG CYS 3 42 61.224 125.485 139.440 1.00 0.00 S ATOM 54691 SG CYS 3 34 53.712 128.864 151.091 1.00 0.00 S ATOM 54849 SG CYS 3 54 54.742 126.915 147.774 1.00 0.00 S ATOM 54887 SG CYS 3 59 51.819 126.177 149.902 1.00 0.00 S ATOM 56676 SG CYS 4 289 127.763 47.748 212.149 1.00 0.00 S ATOM 56692 SG CYS 4 292 126.340 50.740 210.783 1.00 0.00 S ATOM 56757 SG CYS 4 305 124.624 49.292 213.346 1.00 0.00 S ATOM 56773 SG CYS 4 308 126.971 51.108 214.053 1.00 0.00 S ATOM 58993 SG CYS 6 349 129.166 31.893 196.025 1.00 0.00 S ATOM 59009 SG CYS 6 352 127.486 29.935 193.728 1.00 0.00 S ATOM 59065 SG CYS 6 363 128.452 33.371 192.846 1.00 0.00 S ATOM 59081 SG CYS 6 366 125.577 32.050 195.758 1.00 0.00 S ATOM 59267 SG CYS 6 403 157.099 66.436 208.131 1.00 0.00 S ATOM 59283 SG CYS 6 406 159.222 65.735 205.423 1.00 0.00 S ATOM 59441 SG CYS 6 437 156.821 68.846 205.444 1.00 0.00 S ATOM 59457 SG CYS 6 440 155.510 65.616 205.017 1.00 0.00 S ATOM 59399 SG CYS 6 429 147.879 64.946 215.027 1.00 0.00 S ATOM 59415 SG CYS 6 432 150.669 63.572 217.144 1.00 0.00 S ATOM 59513 SG CYS 6 451 150.155 62.503 213.931 1.00 0.00 S ATOM 59528 SG CYS 6 454 147.437 61.152 215.961 1.00 0.00 S Time building chain proxies: 25.72, per 1000 atoms: 0.41 Number of scatterers: 62931 At special positions: 0 Unit cell: (217.83, 231.53, 242.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 16 29.99 Fe 4 26.01 S 324 16.00 P 148 15.00 Mg 1 11.99 O 12161 8.00 N 11155 7.00 C 39122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK 0 294 " - " LEU 0 293 " " UNK 1 219 " - " ARG 1 218 " " UNK 1 296 " - " LYS 1 295 " " UNK 2 113 " - " LEU 2 112 " " UNK 4 89 " - " PRO 4 88 " " UNK 4 257 " - " PRO 4 256 " " UNK 6 308 " - " PRO 6 307 " " UNK 6 373 " - " LEU 6 372 " " UNK 6 412 " - " PRO 6 411 " " UNK 7 426 " - " LEU 7 425 " Time building additional restraints: 11.75 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " Number of angles added : 90 15006 Ramachandran restraints generated. 7503 Oldfield, 0 Emsley, 7503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15592 Finding SS restraints... Secondary structure from input PDB file: 310 helices and 0 sheets defined 44.3% alpha, 0.0% beta 69 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 15.13 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 105 removed outlier: 4.594A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.652A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 234 No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 304 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 336 through 341 removed outlier: 4.558A pdb=" N MET A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 418 through 421 No H-bonds generated for 'chain 'A' and resid 418 through 421' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.581A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.906A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.586A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.516A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.550A pdb=" N PHE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 673 through 699 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 845 removed outlier: 3.982A pdb=" N PHE A 815 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 923 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.781A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1026 removed outlier: 5.544A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1035 removed outlier: 3.693A pdb=" N GLU A1034 " --> pdb=" O ARG A1030 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1165 through 1174 removed outlier: 4.774A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1223 removed outlier: 7.821A pdb=" N ASN A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1270 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.537A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 6.794A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 4.165A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1440 No H-bonds generated for 'chain 'A' and resid 1437 through 1440' Processing helix chain 'A' and resid 1447 through 1450 No H-bonds generated for 'chain 'A' and resid 1447 through 1450' Processing helix chain 'B' and resid 28 through 41 removed outlier: 4.308A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 66 removed outlier: 4.425A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 180 through 183 No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 323 removed outlier: 3.559A pdb=" N LYS B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.872A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 438 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 removed outlier: 3.585A pdb=" N SER B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP B 561 " --> pdb=" O PHE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 No H-bonds generated for 'chain 'B' and resid 697 through 700' Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 745 through 748 No H-bonds generated for 'chain 'B' and resid 745 through 748' Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.899A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 4.389A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 787 No H-bonds generated for 'chain 'B' and resid 784 through 787' Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.997A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 928 through 931 No H-bonds generated for 'chain 'B' and resid 928 through 931' Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix No H-bonds generated for 'chain 'B' and resid 1014 through 1020' Processing helix chain 'B' and resid 1024 through 1038 removed outlier: 3.523A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.699A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1102 No H-bonds generated for 'chain 'B' and resid 1099 through 1102' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 76 through 79 No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 4.596A pdb=" N TYR C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 209' Processing helix chain 'C' and resid 240 through 263 Processing helix chain 'D' and resid 54 through 72 removed outlier: 3.516A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.647A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 34 removed outlier: 6.203A pdb=" N GLN G 24 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'I' and resid 60 through 64 removed outlier: 6.150A pdb=" N SER I 64 " --> pdb=" O GLN I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 60 through 64' Processing helix chain 'J' and resid 15 through 28 removed outlier: 5.056A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.177A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 61 Processing helix chain 'K' and resid 6 through 9 No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.771A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 109 Processing helix chain 'M' and resid 60 through 65 removed outlier: 4.706A pdb=" N THR M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 88 No H-bonds generated for 'chain 'M' and resid 85 through 88' Processing helix chain 'M' and resid 104 through 116 Processing helix chain 'M' and resid 118 through 120 No H-bonds generated for 'chain 'M' and resid 118 through 120' Processing helix chain 'M' and resid 124 through 140 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 170 through 182 Processing helix chain 'M' and resid 189 through 195 Processing helix chain 'M' and resid 201 through 216 Processing helix chain 'M' and resid 236 through 246 Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 266 Processing helix chain 'M' and resid 274 through 288 Processing helix chain 'M' and resid 294 through 301 removed outlier: 4.116A pdb=" N VAL M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 319 removed outlier: 3.790A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 236 Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 108 through 113 Processing helix chain 'Q' and resid 338 through 345 Processing helix chain 'Q' and resid 407 through 414 removed outlier: 3.968A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 81 Processing helix chain 'R' and resid 234 through 245 removed outlier: 4.199A pdb=" N LYS R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.704A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 28 removed outlier: 4.388A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 46 Processing helix chain 'V' and resid 9 through 12 No H-bonds generated for 'chain 'V' and resid 9 through 12' Processing helix chain 'V' and resid 14 through 28 Processing helix chain 'V' and resid 36 through 54 Processing helix chain 'W' and resid 5 through 20 Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 115 removed outlier: 3.805A pdb=" N ASP W 112 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS W 115 " --> pdb=" O ASP W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 139 Processing helix chain 'W' and resid 162 through 191 removed outlier: 4.142A pdb=" N LYS W 166 " --> pdb=" O GLY W 162 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU W 167 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS W 168 " --> pdb=" O LYS W 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP W 170 " --> pdb=" O LYS W 166 " (cutoff:3.500A) Proline residue: W 181 - end of helix removed outlier: 3.759A pdb=" N ASP W 191 " --> pdb=" O LYS W 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 270 through 286 removed outlier: 3.803A pdb=" N UNK W 274 " --> pdb=" O UNK W 270 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK W 275 " --> pdb=" O UNK W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 351 through 372 Processing helix chain 'X' and resid 125 through 138 Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 Processing helix chain 'X' and resid 189 through 199 removed outlier: 3.851A pdb=" N GLN X 199 " --> pdb=" O LEU X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 213 Processing helix chain 'X' and resid 217 through 223 Processing helix chain 'X' and resid 257 through 264 Processing helix chain 'X' and resid 271 through 281 Proline residue: X 275 - end of helix removed outlier: 3.661A pdb=" N LEU X 281 " --> pdb=" O LYS X 277 " (cutoff:3.500A) Processing helix chain '0' and resid 19 through 33 removed outlier: 3.611A pdb=" N TYR 0 24 " --> pdb=" O GLU 0 20 " (cutoff:3.500A) Processing helix chain '0' and resid 48 through 62 removed outlier: 4.253A pdb=" N LEU 0 52 " --> pdb=" O LYS 0 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU 0 53 " --> pdb=" O THR 0 49 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR 0 56 " --> pdb=" O LEU 0 52 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS 0 62 " --> pdb=" O ALA 0 58 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 95 Processing helix chain '0' and resid 111 through 114 No H-bonds generated for 'chain '0' and resid 111 through 114' Processing helix chain '0' and resid 117 through 122 Processing helix chain '0' and resid 129 through 145 Processing helix chain '0' and resid 165 through 173 removed outlier: 4.300A pdb=" N LEU 0 171 " --> pdb=" O VAL 0 167 " (cutoff:3.500A) Proline residue: 0 172 - end of helix Processing helix chain '0' and resid 179 through 188 Processing helix chain '0' and resid 192 through 202 removed outlier: 4.402A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU 0 202 " --> pdb=" O ARG 0 198 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 213 No H-bonds generated for 'chain '0' and resid 210 through 213' Processing helix chain '0' and resid 219 through 225 Processing helix chain '0' and resid 240 through 246 Processing helix chain '0' and resid 255 through 276 Processing helix chain '0' and resid 280 through 300 Processing helix chain '0' and resid 312 through 315 No H-bonds generated for 'chain '0' and resid 312 through 315' Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 373 through 387 removed outlier: 3.531A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG 0 380 " --> pdb=" O PHE 0 376 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER 0 382 " --> pdb=" O SER 0 378 " (cutoff:3.500A) Processing helix chain '0' and resid 393 through 410 Processing helix chain '0' and resid 442 through 452 Proline residue: 0 448 - end of helix removed outlier: 4.093A pdb=" N GLU 0 451 " --> pdb=" O LYS 0 447 " (cutoff:3.500A) Processing helix chain '0' and resid 468 through 471 No H-bonds generated for 'chain '0' and resid 468 through 471' Processing helix chain '0' and resid 488 through 490 No H-bonds generated for 'chain '0' and resid 488 through 490' Processing helix chain '0' and resid 504 through 509 removed outlier: 4.370A pdb=" N ARG 0 509 " --> pdb=" O ALA 0 505 " (cutoff:3.500A) Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 551 Processing helix chain '0' and resid 558 through 562 Processing helix chain '0' and resid 576 through 592 Processing helix chain '0' and resid 633 through 646 Processing helix chain '0' and resid 653 through 669 removed outlier: 4.888A pdb=" N ASP 0 657 " --> pdb=" O PHE 0 653 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA 0 658 " --> pdb=" O LEU 0 654 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS 0 665 " --> pdb=" O HIS 0 661 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 688 removed outlier: 4.367A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 684 through 688' Processing helix chain '0' and resid 701 through 722 removed outlier: 3.726A pdb=" N LEU 0 706 " --> pdb=" O SER 0 702 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA 0 713 " --> pdb=" O SER 0 709 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN 0 716 " --> pdb=" O MET 0 712 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN 0 719 " --> pdb=" O SER 0 715 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE 0 720 " --> pdb=" O ASN 0 716 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 0 721 " --> pdb=" O THR 0 717 " (cutoff:3.500A) Processing helix chain '1' and resid 94 through 120 removed outlier: 3.940A pdb=" N GLN 1 106 " --> pdb=" O MET 1 102 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE 1 107 " --> pdb=" O THR 1 103 " (cutoff:3.500A) Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 189 through 199 Processing helix chain '1' and resid 206 through 224 removed outlier: 3.594A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) Proline residue: 1 215 - end of helix Processing helix chain '1' and resid 230 through 239 removed outlier: 4.414A pdb=" N UNK 1 238 " --> pdb=" O UNK 1 234 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N UNK 1 239 " --> pdb=" O UNK 1 235 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 262 Processing helix chain '1' and resid 264 through 273 Processing helix chain '1' and resid 280 through 295 removed outlier: 4.039A pdb=" N ARG 1 286 " --> pdb=" O GLU 1 282 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 329 removed outlier: 4.402A pdb=" N UNK 1 319 " --> pdb=" O UNK 1 315 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) Processing helix chain '1' and resid 371 through 393 removed outlier: 4.099A pdb=" N UNK 1 390 " --> pdb=" O UNK 1 386 " (cutoff:3.500A) Processing helix chain '1' and resid 467 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 495 through 517 removed outlier: 3.749A pdb=" N UNK 1 499 " --> pdb=" O UNK 1 495 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N UNK 1 517 " --> pdb=" O UNK 1 513 " (cutoff:3.500A) Processing helix chain '1' and resid 542 through 570 removed outlier: 3.872A pdb=" N LEU 1 546 " --> pdb=" O LEU 1 542 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 603 Processing helix chain '1' and resid 607 through 638 Proline residue: 1 618 - end of helix Processing helix chain '2' and resid 4 through 16 Processing helix chain '2' and resid 19 through 25 Processing helix chain '2' and resid 28 through 37 removed outlier: 3.996A pdb=" N CYS 2 32 " --> pdb=" O SER 2 28 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU 2 33 " --> pdb=" O PRO 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 52 removed outlier: 4.028A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 66 Processing helix chain '2' and resid 71 through 83 Processing helix chain '2' and resid 102 through 112 Processing helix chain '2' and resid 117 through 122 Processing helix chain '2' and resid 132 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 194 Processing helix chain '2' and resid 197 through 210 removed outlier: 3.614A pdb=" N UNK 2 210 " --> pdb=" O UNK 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 226 removed outlier: 3.752A pdb=" N PHE 2 226 " --> pdb=" O LEU 2 222 " (cutoff:3.500A) Processing helix chain '2' and resid 237 through 240 No H-bonds generated for 'chain '2' and resid 237 through 240' Processing helix chain '2' and resid 244 through 256 removed outlier: 3.688A pdb=" N GLN 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 280 Processing helix chain '2' and resid 380 through 388 removed outlier: 4.001A pdb=" N UNK 2 384 " --> pdb=" O UNK 2 380 " (cutoff:3.500A) Processing helix chain '2' and resid 394 through 403 Processing helix chain '2' and resid 408 through 418 Processing helix chain '2' and resid 435 through 449 Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 495 through 507 removed outlier: 5.157A pdb=" N SER 2 499 " --> pdb=" O LYS 2 495 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN 2 500 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) Processing helix chain '3' and resid 20 through 22 No H-bonds generated for 'chain '3' and resid 20 through 22' Processing helix chain '3' and resid 40 through 49 removed outlier: 3.948A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 76 through 92 Processing helix chain '3' and resid 104 through 122 Processing helix chain '3' and resid 128 through 144 Processing helix chain '4' and resid 34 through 41 Processing helix chain '4' and resid 50 through 67 Processing helix chain '4' and resid 90 through 96 Processing helix chain '4' and resid 108 through 111 No H-bonds generated for 'chain '4' and resid 108 through 111' Processing helix chain '4' and resid 116 through 135 Processing helix chain '4' and resid 138 through 142 Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 206 removed outlier: 4.415A pdb=" N ILE 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 244 through 255 removed outlier: 3.953A pdb=" N ILE 4 254 " --> pdb=" O THR 4 250 " (cutoff:3.500A) Processing helix chain '4' and resid 314 through 322 removed outlier: 3.909A pdb=" N ARG 4 322 " --> pdb=" O ALA 4 318 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 44 through 62 removed outlier: 4.702A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE 5 62 " --> pdb=" O LEU 5 58 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 201 removed outlier: 3.731A pdb=" N ILE 6 199 " --> pdb=" O ALA 6 195 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG 6 200 " --> pdb=" O LEU 6 196 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 221 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 281 removed outlier: 3.733A pdb=" N ASN 6 281 " --> pdb=" O CYS 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 305 Processing helix chain '6' and resid 373 through 383 Processing helix chain '6' and resid 394 through 397 No H-bonds generated for 'chain '6' and resid 394 through 397' Processing helix chain '6' and resid 418 through 421 No H-bonds generated for 'chain '6' and resid 418 through 421' Processing helix chain '6' and resid 438 through 446 Processing helix chain '6' and resid 452 through 455 No H-bonds generated for 'chain '6' and resid 452 through 455' Processing helix chain '7' and resid 364 through 375 removed outlier: 4.432A pdb=" N LYS 7 372 " --> pdb=" O LYS 7 368 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET 7 373 " --> pdb=" O SER 7 369 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 427 Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 470 through 478 removed outlier: 3.638A pdb=" N UNK 7 476 " --> pdb=" O UNK 7 472 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 496 through 504 Processing helix chain '7' and resid 524 through 530 removed outlier: 4.582A pdb=" N ASN 7 528 " --> pdb=" O ILE 7 524 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE 7 529 " --> pdb=" O GLY 7 525 " (cutoff:3.500A) Processing helix chain '7' and resid 540 through 546 Processing helix chain '7' and resid 563 through 571 Processing helix chain '7' and resid 574 through 581 removed outlier: 4.375A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 601 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 660 Processing helix chain '7' and resid 680 through 693 Processing helix chain '7' and resid 716 through 728 removed outlier: 4.054A pdb=" N LYS 7 721 " --> pdb=" O TYR 7 717 " (cutoff:3.500A) Processing helix chain '7' and resid 742 through 744 No H-bonds generated for 'chain '7' and resid 742 through 744' Processing helix chain '7' and resid 753 through 769 Processing helix chain 'Z' and resid 19 through 28 removed outlier: 3.731A pdb=" N UNK Z 27 " --> pdb=" O UNK Z 23 " (cutoff:3.500A) 1964 hydrogen bonds defined for protein. 5892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 164 hydrogen bonds 328 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 20.12 Time building geometry restraints manager: 14.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.54: 63221 1.54 - 1.87: 922 1.87 - 2.20: 0 2.20 - 2.53: 12 2.53 - 2.86: 1 Bond restraints: 64156 Sorted by residual: bond pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 1.332 2.865 -1.532 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C UNK 0 321 " pdb=" N UNK 0 322 " ideal model delta sigma weight residual 1.329 1.401 -0.072 1.40e-02 5.10e+03 2.62e+01 bond pdb=" C THR 0 533 " pdb=" N PRO 0 534 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.34e-02 1.83e+03 1.76e+01 bond pdb=" C THR B1213 " pdb=" N PRO B1214 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.43e+01 bond pdb=" CA MET 1 88 " pdb=" C MET 1 88 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.03e-02 9.43e+03 1.28e+01 ... (remaining 64151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 87394 4.60 - 9.20: 74 9.20 - 13.80: 1 13.80 - 18.40: 0 18.40 - 23.00: 1 Bond angle restraints: 87470 Sorted by residual: angle pdb=" O LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 122.59 99.59 23.00 1.33e+00 5.65e-01 2.99e+02 angle pdb=" C ILE E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta sigma weight residual 119.66 124.41 -4.75 7.20e-01 1.93e+00 4.36e+01 angle pdb=" C VAL A1146 " pdb=" N THR A1147 " pdb=" CA THR A1147 " ideal model delta sigma weight residual 122.77 114.37 8.40 1.33e+00 5.65e-01 3.99e+01 angle pdb=" C ILE 4 288 " pdb=" N CYS 4 289 " pdb=" CA CYS 4 289 " ideal model delta sigma weight residual 120.63 113.51 7.12 1.36e+00 5.41e-01 2.74e+01 angle pdb=" N CYS I 29 " pdb=" CA CYS I 29 " pdb=" C CYS I 29 " ideal model delta sigma weight residual 108.34 100.59 7.75 1.64e+00 3.72e-01 2.24e+01 ... (remaining 87465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 37774 31.92 - 63.84: 971 63.84 - 95.75: 71 95.75 - 127.67: 0 127.67 - 159.59: 2 Dihedral angle restraints: 38818 sinusoidal: 14910 harmonic: 23908 Sorted by residual: dihedral pdb=" CA LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " pdb=" CA THR X 183 " ideal model delta harmonic sigma weight residual -180.00 -96.03 -83.97 0 5.00e+00 4.00e-02 2.82e+02 dihedral pdb=" CA LEU 2 39 " pdb=" C LEU 2 39 " pdb=" N PRO 2 40 " pdb=" CA PRO 2 40 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA UNK 1 350 " pdb=" C UNK 1 350 " pdb=" N UNK 1 351 " pdb=" CA UNK 1 351 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 38815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 8466 0.050 - 0.101: 1385 0.101 - 0.151: 338 0.151 - 0.202: 11 0.202 - 0.252: 5 Chirality restraints: 10205 Sorted by residual: chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C4' DG N 45 " pdb=" C5' DG N 45 " pdb=" O4' DG N 45 " pdb=" C3' DG N 45 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS I 29 " pdb=" N CYS I 29 " pdb=" C CYS I 29 " pdb=" CB CYS I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 10202 not shown) Planarity restraints: 10902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU X 181 " 0.126 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C LEU X 181 " -0.313 2.00e-02 2.50e+03 pdb=" O LEU X 181 " 0.141 2.00e-02 2.50e+03 pdb=" N THR X 183 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 43 " 0.046 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" N1 DT N 43 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DT N 43 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT N 43 " -0.048 2.00e-02 2.50e+03 pdb=" N3 DT N 43 " 0.051 2.00e-02 2.50e+03 pdb=" C4 DT N 43 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT N 43 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT N 43 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT N 43 " -0.020 2.00e-02 2.50e+03 pdb=" C6 DT N 43 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 44 " 0.033 2.00e-02 2.50e+03 2.03e-02 9.28e+00 pdb=" N1 DC N 44 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DC N 44 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC N 44 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC N 44 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC N 44 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC N 44 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC N 44 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC N 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 10899 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 9467 2.76 - 3.47: 86135 3.47 - 4.19: 147810 4.19 - 4.90: 250813 Nonbonded interactions: 494227 Sorted by model distance: nonbonded pdb=" N UNK 2 380 " pdb=" C UNK Z 43 " model vdw 1.336 3.350 nonbonded pdb=" O GLU I 54 " pdb=" N GLN I 89 " model vdw 1.928 3.120 nonbonded pdb=" NH1 ARG 0 594 " pdb=" O THR 6 241 " model vdw 2.080 3.120 nonbonded pdb=" NH1 ARG C 11 " pdb=" OH TYR C 209 " model vdw 2.121 3.120 nonbonded pdb=" O ARG J 48 " pdb=" OG1 THR J 52 " model vdw 2.145 3.040 ... (remaining 494222 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.840 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 132.630 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.210 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 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 : 0.007 1.532 64156 Z= 0.462 Angle : 0.541 23.000 87470 Z= 0.317 Chirality : 0.040 0.252 10205 Planarity : 0.004 0.184 10892 Dihedral : 12.583 159.590 23196 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 1.23 % Allowed : 6.46 % Favored : 92.31 % Rotamer: Outliers : 0.30 % Allowed : 4.17 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -3.41 (0.08), residues: 7503 helix: -2.15 (0.07), residues: 3174 sheet: -1.76 (0.14), residues: 1220 loop : -2.44 (0.09), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 81 HIS 0.014 0.001 HIS A 80 PHE 0.023 0.001 PHE 0 437 TYR 0.012 0.001 TYR Q 401 ARG 0.006 0.000 ARG A1055 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15006 Ramachandran restraints generated. 7503 Oldfield, 0 Emsley, 7503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15006 Ramachandran restraints generated. 7503 Oldfield, 0 Emsley, 7503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2085 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 2068 time to evaluate : 5.301 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 14 VAL cc_start: 0.8236 (t) cc_final: 0.7499 (p) REVERT: A 27 VAL cc_start: 0.8969 (t) cc_final: 0.8618 (t) REVERT: A 58 LEU cc_start: 0.8582 (mt) cc_final: 0.8369 (mt) REVERT: A 99 ILE cc_start: 0.8588 (mt) cc_final: 0.8090 (mm) REVERT: A 222 LEU cc_start: 0.9235 (mt) cc_final: 0.8946 (mm) REVERT: A 266 LEU cc_start: 0.8895 (mt) cc_final: 0.8692 (mt) REVERT: A 297 GLN cc_start: 0.8395 (tp40) cc_final: 0.8086 (tm-30) REVERT: A 455 MET cc_start: 0.6691 (mtp) cc_final: 0.5961 (mtt) REVERT: A 456 MET cc_start: 0.6067 (mtm) cc_final: 0.5488 (mtp) REVERT: A 577 ILE cc_start: 0.9179 (pp) cc_final: 0.8838 (pp) REVERT: A 586 ILE cc_start: 0.8862 (mm) cc_final: 0.8494 (mt) REVERT: A 662 PHE cc_start: 0.8360 (t80) cc_final: 0.7912 (t80) REVERT: A 676 MET cc_start: 0.8134 (mmt) cc_final: 0.7926 (mmm) REVERT: A 715 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7505 (mt-10) REVERT: A 762 SER cc_start: 0.9382 (m) cc_final: 0.9027 (t) REVERT: A 784 LEU cc_start: 0.8765 (mt) cc_final: 0.8403 (mm) REVERT: A 873 MET cc_start: 0.8349 (mmt) cc_final: 0.7414 (mpp) REVERT: A 997 LEU cc_start: 0.9308 (mt) cc_final: 0.9071 (mt) REVERT: A 1056 SER cc_start: 0.9236 (m) cc_final: 0.8427 (t) REVERT: A 1105 LEU cc_start: 0.9288 (mt) cc_final: 0.8939 (mm) REVERT: A 1193 LEU cc_start: 0.7757 (tp) cc_final: 0.6868 (tt) REVERT: A 1224 LEU cc_start: 0.7872 (tp) cc_final: 0.7499 (tt) REVERT: A 1313 LEU cc_start: 0.7909 (tp) cc_final: 0.7388 (tp) REVERT: A 1361 SER cc_start: 0.8810 (p) cc_final: 0.8595 (m) REVERT: A 1375 MET cc_start: 0.7331 (mtp) cc_final: 0.7071 (mtp) REVERT: A 1409 LEU cc_start: 0.9069 (mt) cc_final: 0.8740 (mp) REVERT: A 1433 MET cc_start: 0.6970 (mmm) cc_final: 0.6569 (tpp) REVERT: B 97 VAL cc_start: 0.7758 (p) cc_final: 0.7381 (p) REVERT: B 396 ASP cc_start: 0.4422 (t0) cc_final: 0.4141 (t0) REVERT: B 412 LEU cc_start: 0.8637 (mt) cc_final: 0.7970 (mm) REVERT: B 436 VAL cc_start: 0.6170 (p) cc_final: 0.5786 (p) REVERT: B 466 TRP cc_start: 0.5327 (t-100) cc_final: 0.4663 (t-100) REVERT: B 495 LEU cc_start: 0.7733 (mt) cc_final: 0.7518 (mt) REVERT: B 514 LEU cc_start: 0.9340 (tp) cc_final: 0.8518 (tt) REVERT: B 541 LEU cc_start: 0.7136 (mt) cc_final: 0.6748 (tp) REVERT: B 615 MET cc_start: 0.4626 (ptp) cc_final: 0.4360 (tmm) REVERT: B 800 GLN cc_start: 0.7627 (mt0) cc_final: 0.7030 (mm-40) REVERT: B 829 CYS cc_start: 0.7778 (m) cc_final: 0.7029 (p) REVERT: B 851 PHE cc_start: 0.8716 (m-80) cc_final: 0.8475 (m-10) REVERT: B 853 SER cc_start: 0.5474 (p) cc_final: 0.4058 (p) REVERT: B 1082 MET cc_start: 0.8101 (tpp) cc_final: 0.7825 (tpp) REVERT: B 1168 LEU cc_start: 0.6933 (mt) cc_final: 0.6680 (mm) REVERT: B 1207 LEU cc_start: 0.8813 (mt) cc_final: 0.8446 (mm) REVERT: B 1208 MET cc_start: 0.8033 (mtp) cc_final: 0.7625 (mtt) REVERT: B 1210 MET cc_start: 0.7882 (ttt) cc_final: 0.7590 (ttt) REVERT: C 25 VAL cc_start: 0.8970 (t) cc_final: 0.8769 (t) REVERT: C 49 VAL cc_start: 0.8406 (t) cc_final: 0.8037 (p) REVERT: C 69 LEU cc_start: 0.7757 (mp) cc_final: 0.7539 (mp) REVERT: C 101 LEU cc_start: 0.8912 (tt) cc_final: 0.8165 (tp) REVERT: C 124 LEU cc_start: 0.8191 (mt) cc_final: 0.7417 (mt) REVERT: C 125 MET cc_start: 0.5873 (mpt) cc_final: 0.5637 (mpp) REVERT: C 143 LEU cc_start: 0.9128 (tp) cc_final: 0.8882 (tt) REVERT: C 167 HIS cc_start: 0.6593 (t-90) cc_final: 0.5021 (t70) REVERT: D 58 VAL cc_start: 0.8554 (t) cc_final: 0.8305 (p) REVERT: D 64 VAL cc_start: 0.7927 (t) cc_final: 0.7713 (t) REVERT: D 123 LEU cc_start: 0.7053 (tp) cc_final: 0.6660 (tp) REVERT: D 128 VAL cc_start: 0.8043 (t) cc_final: 0.6872 (t) REVERT: D 164 ILE cc_start: 0.8191 (mm) cc_final: 0.7902 (pt) REVERT: D 198 LEU cc_start: 0.6663 (mt) cc_final: 0.6272 (pp) REVERT: E 140 LEU cc_start: 0.8733 (mt) cc_final: 0.8171 (mm) REVERT: F 77 ASP cc_start: 0.7948 (p0) cc_final: 0.7601 (p0) REVERT: F 138 LEU cc_start: 0.9082 (mp) cc_final: 0.8824 (mp) REVERT: F 140 ASP cc_start: 0.8291 (p0) cc_final: 0.7911 (p0) REVERT: F 145 ASP cc_start: 0.6061 (m-30) cc_final: 0.5613 (m-30) REVERT: G 6 ASP cc_start: 0.7385 (m-30) cc_final: 0.6767 (m-30) REVERT: G 88 ASP cc_start: 0.5934 (m-30) cc_final: 0.5394 (m-30) REVERT: G 127 PRO cc_start: 0.7383 (Cg_endo) cc_final: 0.7105 (Cg_exo) REVERT: G 143 ILE cc_start: 0.7633 (mp) cc_final: 0.7295 (mm) REVERT: G 160 ILE cc_start: 0.7165 (mp) cc_final: 0.6229 (mp) REVERT: H 46 LEU cc_start: 0.8190 (mp) cc_final: 0.7876 (mp) REVERT: H 94 ASP cc_start: 0.7337 (m-30) cc_final: 0.7104 (m-30) REVERT: H 97 MET cc_start: 0.6514 (mtm) cc_final: 0.6241 (mtm) REVERT: H 116 TYR cc_start: 0.5528 (m-80) cc_final: 0.5176 (m-80) REVERT: H 137 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7661 (pp30) REVERT: I 14 LEU cc_start: 0.8864 (mt) cc_final: 0.8158 (mt) REVERT: I 25 LEU cc_start: 0.7039 (tp) cc_final: 0.6674 (tp) REVERT: I 26 LEU cc_start: 0.7161 (mt) cc_final: 0.6716 (mt) REVERT: I 83 ASN cc_start: 0.8002 (p0) cc_final: 0.7688 (p0) REVERT: I 95 THR cc_start: 0.7827 (m) cc_final: 0.7456 (p) REVERT: I 104 LEU cc_start: 0.8972 (mt) cc_final: 0.8107 (mt) REVERT: J 30 LEU cc_start: 0.8478 (mt) cc_final: 0.8235 (mt) REVERT: K 58 PHE cc_start: 0.8627 (t80) cc_final: 0.7990 (t80) REVERT: K 101 LEU cc_start: 0.8326 (tp) cc_final: 0.8056 (tp) REVERT: L 43 THR cc_start: 0.7925 (m) cc_final: 0.7613 (p) REVERT: M 64 ARG cc_start: 0.7081 (mmt180) cc_final: 0.5827 (ptt90) REVERT: M 146 VAL cc_start: 0.7788 (t) cc_final: 0.7077 (t) REVERT: M 172 MET cc_start: 0.6600 (mtp) cc_final: 0.5730 (mtp) REVERT: M 176 ILE cc_start: 0.8443 (mt) cc_final: 0.8214 (mt) REVERT: M 208 ASN cc_start: 0.7097 (t0) cc_final: 0.6798 (t0) REVERT: M 317 TYR cc_start: 0.5765 (t80) cc_final: 0.5419 (t80) REVERT: O 84 THR cc_start: 0.7494 (m) cc_final: 0.6662 (m) REVERT: O 169 PRO cc_start: 0.6383 (Cg_exo) cc_final: 0.5872 (Cg_endo) REVERT: O 205 LEU cc_start: 0.7062 (mt) cc_final: 0.6293 (mt) REVERT: O 213 VAL cc_start: 0.8539 (t) cc_final: 0.8268 (t) REVERT: O 223 ILE cc_start: 0.6669 (mm) cc_final: 0.6336 (mm) REVERT: Q 111 LEU cc_start: 0.6057 (mt) cc_final: 0.5765 (mp) REVERT: Q 377 SER cc_start: 0.5022 (t) cc_final: 0.4802 (t) REVERT: R 122 LEU cc_start: 0.5543 (tt) cc_final: 0.4967 (tp) REVERT: U 17 VAL cc_start: 0.8029 (t) cc_final: 0.7384 (p) REVERT: U 262 LEU cc_start: 0.6633 (mt) cc_final: 0.5966 (mt) REVERT: W 98 ILE cc_start: 0.8572 (mt) cc_final: 0.8325 (mt) REVERT: 0 86 LEU cc_start: 0.8540 (tp) cc_final: 0.7966 (tp) REVERT: 0 257 LEU cc_start: 0.7689 (mt) cc_final: 0.7454 (mt) REVERT: 0 400 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7847 (mtpt) REVERT: 0 457 ILE cc_start: 0.5332 (mm) cc_final: 0.5065 (mm) REVERT: 0 666 LEU cc_start: 0.8461 (mt) cc_final: 0.7497 (tp) REVERT: 1 27 LEU cc_start: 0.6554 (tp) cc_final: 0.6302 (tp) REVERT: 3 72 ILE cc_start: 0.4113 (OUTLIER) cc_final: 0.3749 (pp) REVERT: 6 156 PHE cc_start: 0.6950 (t80) cc_final: 0.5891 (t80) REVERT: 6 157 VAL cc_start: 0.8223 (t) cc_final: 0.7533 (t) REVERT: 6 161 PHE cc_start: 0.7054 (m-80) cc_final: 0.6623 (m-10) REVERT: 6 193 ILE cc_start: 0.8861 (mt) cc_final: 0.8478 (mt) REVERT: 6 233 LEU cc_start: 0.5951 (tp) cc_final: 0.5639 (tp) REVERT: 6 250 THR cc_start: 0.8297 (m) cc_final: 0.7955 (p) REVERT: 6 263 VAL cc_start: 0.7108 (t) cc_final: 0.6432 (t) REVERT: 6 301 PHE cc_start: 0.7461 (m-80) cc_final: 0.7032 (m-10) outliers start: 17 outliers final: 5 residues processed: 2079 average time/residue: 0.6803 time to fit residues: 2351.4296 Evaluate side-chains 1086 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1080 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 618 optimal weight: 20.0000 chunk 554 optimal weight: 0.3980 chunk 307 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 374 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 573 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 427 optimal weight: 9.9990 chunk 664 optimal weight: 0.7980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 64 ASN A 92 HIS A 256 GLN A 311 GLN A 313 GLN A 339 ASN A 525 GLN A 548 ASN A 576 GLN A 640 GLN A 659 HIS A 698 GLN A 745 GLN A 760 GLN A 953 ASN A 965 GLN A 968 GLN A1130 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 433 GLN B 440 HIS B 573 GLN B 657 HIS B 667 GLN B 770 GLN B 822 ASN B1193 GLN B1195 HIS C 73 GLN C 224 GLN C 231 ASN C 242 GLN C 252 GLN E 54 GLN G 10 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN I 12 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN K 112 GLN L 53 HIS M 90 ASN M 124 ASN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN R 223 GLN ** U 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN X 199 GLN X 223 GLN X 279 GLN 0 88 ASN ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 3 HIS 1 75 ASN ** 1 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 92 ASN 5 11 GLN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 64156 Z= 0.290 Angle : 0.660 13.858 87470 Z= 0.345 Chirality : 0.043 0.252 10205 Planarity : 0.005 0.072 10892 Dihedral : 14.005 161.007 10322 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.60 % Favored : 95.08 % Rotamer: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.54 (0.09), residues: 7505 helix: -0.10 (0.09), residues: 3204 sheet: -1.28 (0.14), residues: 1147 loop : -1.82 (0.10), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1191 HIS 0.015 0.002 HIS I 108 PHE 0.032 0.002 PHE A 22 TYR 0.030 0.002 TYR H 129 ARG 0.021 0.001 ARG X 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1233 time to evaluate : 5.324 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 40 THR cc_start: 0.7753 (p) cc_final: 0.7460 (p) REVERT: A 53 LEU cc_start: 0.8939 (mm) cc_final: 0.8606 (mm) REVERT: A 103 CYS cc_start: 0.8091 (m) cc_final: 0.7888 (t) REVERT: A 142 CYS cc_start: 0.8436 (m) cc_final: 0.8061 (p) REVERT: A 174 ILE cc_start: 0.8552 (mp) cc_final: 0.7717 (mp) REVERT: A 453 MET cc_start: 0.7549 (mpp) cc_final: 0.7101 (mpp) REVERT: A 577 ILE cc_start: 0.9157 (pt) cc_final: 0.8951 (pt) REVERT: A 702 LEU cc_start: 0.7496 (pt) cc_final: 0.7133 (pt) REVERT: A 748 MET cc_start: 0.8044 (mtp) cc_final: 0.7779 (mtm) REVERT: A 1224 LEU cc_start: 0.7434 (tp) cc_final: 0.7109 (tt) REVERT: A 1336 MET cc_start: 0.8109 (tmm) cc_final: 0.7886 (tmm) REVERT: A 1370 LEU cc_start: 0.8156 (tt) cc_final: 0.7910 (tp) REVERT: B 167 ILE cc_start: 0.8847 (pt) cc_final: 0.8613 (mm) REVERT: B 308 TRP cc_start: 0.7814 (p-90) cc_final: 0.7480 (p-90) REVERT: B 310 MET cc_start: 0.7027 (mtm) cc_final: 0.6645 (mtt) REVERT: B 313 MET cc_start: 0.7293 (mmm) cc_final: 0.7025 (tpp) REVERT: B 425 THR cc_start: 0.8954 (p) cc_final: 0.8548 (p) REVERT: B 542 MET cc_start: 0.6374 (mtm) cc_final: 0.5879 (mtm) REVERT: B 760 ASP cc_start: 0.8779 (p0) cc_final: 0.8382 (p0) REVERT: B 829 CYS cc_start: 0.8129 (m) cc_final: 0.6441 (p) REVERT: B 978 ASP cc_start: 0.6955 (m-30) cc_final: 0.6450 (m-30) REVERT: B 1006 ILE cc_start: 0.7802 (mp) cc_final: 0.7593 (mm) REVERT: B 1194 ILE cc_start: 0.8966 (pt) cc_final: 0.8753 (pt) REVERT: B 1206 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6618 (mt-10) REVERT: B 1212 ILE cc_start: 0.9160 (mm) cc_final: 0.8622 (mm) REVERT: C 37 MET cc_start: 0.7920 (mtp) cc_final: 0.7559 (mtp) REVERT: C 40 GLU cc_start: 0.7931 (tp30) cc_final: 0.7662 (tp30) REVERT: C 167 HIS cc_start: 0.6846 (t-90) cc_final: 0.6165 (t-90) REVERT: C 177 GLU cc_start: 0.7820 (tt0) cc_final: 0.7366 (tt0) REVERT: D 160 VAL cc_start: 0.8658 (t) cc_final: 0.8401 (t) REVERT: D 198 LEU cc_start: 0.6124 (mt) cc_final: 0.5653 (mp) REVERT: E 198 ILE cc_start: 0.9386 (mp) cc_final: 0.9149 (mm) REVERT: F 100 GLN cc_start: 0.8639 (mp10) cc_final: 0.8235 (mp10) REVERT: F 140 ASP cc_start: 0.8557 (p0) cc_final: 0.8356 (p0) REVERT: G 3 PHE cc_start: 0.5109 (m-10) cc_final: 0.3837 (m-10) REVERT: G 51 TYR cc_start: 0.3874 (t80) cc_final: 0.3471 (t80) REVERT: G 52 ASP cc_start: 0.6664 (p0) cc_final: 0.5830 (p0) REVERT: G 101 VAL cc_start: 0.6384 (t) cc_final: 0.5735 (t) REVERT: G 135 ASP cc_start: 0.6114 (p0) cc_final: 0.5774 (p0) REVERT: H 26 ILE cc_start: 0.9242 (tp) cc_final: 0.8896 (tp) REVERT: H 34 ASP cc_start: 0.7216 (p0) cc_final: 0.6459 (p0) REVERT: H 64 ASN cc_start: 0.8003 (t0) cc_final: 0.7706 (t0) REVERT: H 76 THR cc_start: 0.5740 (p) cc_final: 0.5533 (p) REVERT: H 94 ASP cc_start: 0.7804 (m-30) cc_final: 0.7532 (m-30) REVERT: H 117 SER cc_start: 0.8473 (t) cc_final: 0.7958 (p) REVERT: H 123 MET cc_start: 0.8494 (tmm) cc_final: 0.8153 (tmm) REVERT: I 104 LEU cc_start: 0.9176 (mt) cc_final: 0.8468 (tt) REVERT: J 12 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7211 (ttmm) REVERT: J 49 MET cc_start: 0.9066 (mtp) cc_final: 0.8791 (mtt) REVERT: J 56 LEU cc_start: 0.7596 (mm) cc_final: 0.7347 (mm) REVERT: J 57 ILE cc_start: 0.9081 (tp) cc_final: 0.8746 (tp) REVERT: K 21 ILE cc_start: 0.8504 (tt) cc_final: 0.8178 (tt) REVERT: K 58 PHE cc_start: 0.9023 (t80) cc_final: 0.8076 (t80) REVERT: K 106 GLU cc_start: 0.6922 (pp20) cc_final: 0.6682 (pp20) REVERT: M 94 THR cc_start: 0.6246 (m) cc_final: 0.5865 (p) REVERT: M 138 ASP cc_start: 0.7945 (m-30) cc_final: 0.7572 (t0) REVERT: M 172 MET cc_start: 0.7119 (mtp) cc_final: 0.6670 (mtt) REVERT: M 189 PHE cc_start: 0.6802 (m-80) cc_final: 0.5895 (m-80) REVERT: M 283 TYR cc_start: 0.5881 (t80) cc_final: 0.5605 (t80) REVERT: M 315 ILE cc_start: 0.7323 (mp) cc_final: 0.6486 (mp) REVERT: O 84 THR cc_start: 0.7958 (m) cc_final: 0.6626 (m) REVERT: O 240 MET cc_start: 0.0682 (ttt) cc_final: -0.0937 (mmp) REVERT: Q 336 ASP cc_start: 0.7457 (p0) cc_final: 0.6794 (p0) REVERT: Q 393 TYR cc_start: 0.6047 (m-80) cc_final: 0.5518 (m-80) REVERT: R 97 ILE cc_start: 0.6413 (pt) cc_final: 0.6123 (pt) REVERT: R 131 ASN cc_start: 0.6980 (m-40) cc_final: 0.6650 (m110) REVERT: U 17 VAL cc_start: 0.8117 (t) cc_final: 0.7654 (p) REVERT: V 87 VAL cc_start: 0.5685 (m) cc_final: 0.5251 (m) REVERT: W 135 GLU cc_start: 0.7193 (pt0) cc_final: 0.6685 (pt0) REVERT: X 208 LYS cc_start: 0.7931 (mppt) cc_final: 0.7634 (mmtm) REVERT: 0 86 LEU cc_start: 0.8504 (tp) cc_final: 0.7967 (tp) REVERT: 0 404 THR cc_start: 0.8484 (p) cc_final: 0.8193 (p) REVERT: 0 496 ILE cc_start: 0.7760 (pt) cc_final: 0.7223 (pt) REVERT: 0 597 ILE cc_start: 0.6082 (mm) cc_final: 0.5857 (mm) REVERT: 0 659 MET cc_start: 0.5932 (mmm) cc_final: 0.5717 (mmm) REVERT: 0 666 LEU cc_start: 0.8862 (mt) cc_final: 0.7705 (tp) REVERT: 0 681 LEU cc_start: 0.5457 (mm) cc_final: 0.4965 (mm) REVERT: 1 28 THR cc_start: 0.5409 (p) cc_final: 0.4894 (t) REVERT: 3 43 VAL cc_start: 0.8115 (p) cc_final: 0.7809 (p) REVERT: 3 56 TYR cc_start: 0.2437 (t80) cc_final: 0.0776 (t80) REVERT: 6 126 LEU cc_start: 0.7931 (tp) cc_final: 0.7560 (tp) REVERT: 6 156 PHE cc_start: 0.6754 (t80) cc_final: 0.6354 (t80) REVERT: 6 157 VAL cc_start: 0.8151 (t) cc_final: 0.7733 (t) REVERT: 6 161 PHE cc_start: 0.6952 (m-80) cc_final: 0.6703 (m-10) REVERT: 6 261 VAL cc_start: 0.7908 (t) cc_final: 0.7562 (t) outliers start: 11 outliers final: 3 residues processed: 1243 average time/residue: 0.5832 time to fit residues: 1227.2630 Evaluate side-chains 851 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 848 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 369 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 553 optimal weight: 10.0000 chunk 452 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 665 optimal weight: 5.9990 chunk 719 optimal weight: 6.9990 chunk 593 optimal weight: 7.9990 chunk 660 optimal weight: 30.0000 chunk 227 optimal weight: 0.5980 chunk 534 optimal weight: 0.8980 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 802 ASN A1218 GLN A1270 ASN A1390 ASN B 60 GLN B 887 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS C 206 ASN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 GLN U 36 GLN V 17 ASN ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 182 GLN 6 146 HIS ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 211 GLN 6 248 HIS ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 64156 Z= 0.220 Angle : 0.582 13.228 87470 Z= 0.303 Chirality : 0.041 0.267 10205 Planarity : 0.004 0.126 10892 Dihedral : 14.014 161.418 10322 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.09 % Favored : 94.66 % Rotamer: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.93 (0.09), residues: 7505 helix: 0.54 (0.09), residues: 3202 sheet: -1.04 (0.15), residues: 1147 loop : -1.63 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 1 210 HIS 0.016 0.001 HIS B 300 PHE 0.030 0.002 PHE D 175 TYR 0.019 0.001 TYR Q 393 ARG 0.039 0.001 ARG 3 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1097 time to evaluate : 5.298 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 40 THR cc_start: 0.7975 (p) cc_final: 0.7488 (p) REVERT: A 53 LEU cc_start: 0.8551 (mm) cc_final: 0.8215 (mm) REVERT: A 103 CYS cc_start: 0.8133 (m) cc_final: 0.7878 (t) REVERT: A 142 CYS cc_start: 0.8045 (m) cc_final: 0.7448 (t) REVERT: A 174 ILE cc_start: 0.8701 (mp) cc_final: 0.7972 (mp) REVERT: A 234 MET cc_start: 0.8964 (tpp) cc_final: 0.8714 (tpp) REVERT: A 304 MET cc_start: 0.8994 (mmm) cc_final: 0.8518 (mmt) REVERT: A 453 MET cc_start: 0.7488 (mpp) cc_final: 0.6640 (mpp) REVERT: A 577 ILE cc_start: 0.9175 (pt) cc_final: 0.8961 (pt) REVERT: A 748 MET cc_start: 0.8162 (mtp) cc_final: 0.7822 (mtm) REVERT: A 903 ASN cc_start: 0.5474 (t0) cc_final: 0.5162 (t0) REVERT: A 962 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6569 (mtm180) REVERT: A 1224 LEU cc_start: 0.7467 (tp) cc_final: 0.7102 (tt) REVERT: A 1336 MET cc_start: 0.8009 (tmm) cc_final: 0.7716 (tmm) REVERT: B 199 MET cc_start: 0.6692 (mmp) cc_final: 0.6474 (mmm) REVERT: B 308 TRP cc_start: 0.7732 (p-90) cc_final: 0.7325 (p-90) REVERT: B 310 MET cc_start: 0.7364 (mtm) cc_final: 0.6852 (mtt) REVERT: B 542 MET cc_start: 0.6769 (mtm) cc_final: 0.6221 (mtm) REVERT: B 596 LEU cc_start: 0.8172 (tp) cc_final: 0.7741 (tt) REVERT: B 760 ASP cc_start: 0.8901 (p0) cc_final: 0.8125 (p0) REVERT: B 829 CYS cc_start: 0.7615 (m) cc_final: 0.6516 (p) REVERT: B 955 THR cc_start: 0.7156 (m) cc_final: 0.6816 (m) REVERT: B 978 ASP cc_start: 0.6936 (m-30) cc_final: 0.6489 (m-30) REVERT: B 1138 MET cc_start: 0.8450 (mmm) cc_final: 0.8248 (mmm) REVERT: B 1149 GLU cc_start: 0.6121 (tp30) cc_final: 0.5918 (tp30) REVERT: B 1168 LEU cc_start: 0.6423 (mp) cc_final: 0.6004 (mp) REVERT: B 1194 ILE cc_start: 0.8950 (pt) cc_final: 0.8465 (pt) REVERT: C 43 THR cc_start: 0.8022 (m) cc_final: 0.7666 (p) REVERT: C 85 ASP cc_start: 0.7655 (m-30) cc_final: 0.7234 (m-30) REVERT: C 167 HIS cc_start: 0.6687 (t-90) cc_final: 0.6198 (t-90) REVERT: D 57 LEU cc_start: 0.8307 (mt) cc_final: 0.7687 (tp) REVERT: D 65 GLU cc_start: 0.7529 (mp0) cc_final: 0.6694 (mp0) REVERT: D 141 LEU cc_start: 0.8614 (tp) cc_final: 0.7940 (tt) REVERT: E 198 ILE cc_start: 0.9518 (mp) cc_final: 0.9254 (mm) REVERT: E 208 TYR cc_start: 0.8634 (t80) cc_final: 0.8426 (t80) REVERT: F 77 ASP cc_start: 0.7926 (p0) cc_final: 0.7130 (p0) REVERT: F 100 GLN cc_start: 0.8603 (mp10) cc_final: 0.8192 (mp10) REVERT: G 52 ASP cc_start: 0.6735 (p0) cc_final: 0.6038 (p0) REVERT: G 135 ASP cc_start: 0.5619 (p0) cc_final: 0.5245 (p0) REVERT: G 160 ILE cc_start: 0.6648 (mp) cc_final: 0.6046 (mp) REVERT: H 34 ASP cc_start: 0.7031 (p0) cc_final: 0.6166 (p0) REVERT: H 37 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7768 (mtmm) REVERT: H 64 ASN cc_start: 0.7946 (t0) cc_final: 0.7742 (t0) REVERT: H 117 SER cc_start: 0.8425 (t) cc_final: 0.7761 (p) REVERT: I 104 LEU cc_start: 0.9191 (mt) cc_final: 0.8358 (tt) REVERT: J 49 MET cc_start: 0.9120 (mtp) cc_final: 0.8778 (mtp) REVERT: K 58 PHE cc_start: 0.8980 (t80) cc_final: 0.7891 (t80) REVERT: M 138 ASP cc_start: 0.7895 (m-30) cc_final: 0.7485 (t0) REVERT: M 172 MET cc_start: 0.7059 (mtp) cc_final: 0.6259 (mtp) REVERT: M 189 PHE cc_start: 0.6433 (m-80) cc_final: 0.5797 (m-80) REVERT: M 315 ILE cc_start: 0.7378 (mp) cc_final: 0.6925 (mp) REVERT: O 84 THR cc_start: 0.7528 (m) cc_final: 0.6436 (m) REVERT: O 190 PHE cc_start: 0.7041 (t80) cc_final: 0.6806 (t80) REVERT: O 193 LEU cc_start: 0.6800 (tp) cc_final: 0.6543 (tt) REVERT: O 205 LEU cc_start: 0.7042 (mm) cc_final: 0.6825 (mm) REVERT: O 213 VAL cc_start: 0.7972 (t) cc_final: 0.7735 (t) REVERT: O 240 MET cc_start: 0.0849 (ttt) cc_final: -0.0853 (mmp) REVERT: Q 336 ASP cc_start: 0.7098 (p0) cc_final: 0.6663 (p0) REVERT: R 97 ILE cc_start: 0.6180 (pt) cc_final: 0.5684 (pt) REVERT: R 131 ASN cc_start: 0.6927 (m-40) cc_final: 0.6687 (m110) REVERT: R 215 VAL cc_start: 0.5706 (t) cc_final: 0.5363 (t) REVERT: V 87 VAL cc_start: 0.5568 (m) cc_final: 0.5149 (m) REVERT: V 111 LEU cc_start: 0.5035 (tp) cc_final: 0.4026 (tp) REVERT: V 114 VAL cc_start: 0.7476 (t) cc_final: 0.7196 (m) REVERT: W 135 GLU cc_start: 0.6839 (pt0) cc_final: 0.6393 (pt0) REVERT: X 208 LYS cc_start: 0.8087 (mppt) cc_final: 0.7711 (mmtm) REVERT: 0 86 LEU cc_start: 0.8318 (tp) cc_final: 0.7974 (tp) REVERT: 0 400 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7765 (mttt) REVERT: 0 532 ILE cc_start: 0.7277 (pt) cc_final: 0.6994 (pt) REVERT: 0 680 VAL cc_start: 0.6095 (m) cc_final: 0.5854 (m) REVERT: 1 28 THR cc_start: 0.5490 (p) cc_final: 0.5186 (t) REVERT: 3 43 VAL cc_start: 0.8397 (p) cc_final: 0.7642 (m) REVERT: 6 156 PHE cc_start: 0.6686 (t80) cc_final: 0.5999 (t80) REVERT: 6 157 VAL cc_start: 0.8135 (t) cc_final: 0.7590 (t) REVERT: 6 261 VAL cc_start: 0.7029 (t) cc_final: 0.6822 (t) REVERT: 6 278 LYS cc_start: 0.7170 (ptpp) cc_final: 0.6862 (pttm) REVERT: 6 301 PHE cc_start: 0.7603 (m-80) cc_final: 0.7298 (m-80) REVERT: 7 673 ILE cc_start: 0.8184 (pt) cc_final: 0.7789 (pt) REVERT: 7 708 LEU cc_start: 0.7277 (tp) cc_final: 0.6776 (tp) outliers start: 6 outliers final: 3 residues processed: 1102 average time/residue: 0.5696 time to fit residues: 1074.4496 Evaluate side-chains 832 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 829 time to evaluate : 6.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 657 optimal weight: 40.0000 chunk 500 optimal weight: 20.0000 chunk 345 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 317 optimal weight: 0.8980 chunk 447 optimal weight: 8.9990 chunk 668 optimal weight: 7.9990 chunk 707 optimal weight: 0.8980 chunk 349 optimal weight: 0.4980 chunk 633 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 451 HIS A 802 ASN A 968 GLN B 53 GLN B 590 HIS B 951 GLN ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN F 78 GLN G 10 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN I 90 GLN ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 88 ASN ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 242 ASN 6 146 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 64156 Z= 0.160 Angle : 0.555 13.599 87470 Z= 0.287 Chirality : 0.041 0.309 10205 Planarity : 0.004 0.133 10892 Dihedral : 14.003 162.003 10322 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.38 % Favored : 95.36 % Rotamer: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.59 (0.10), residues: 7505 helix: 0.84 (0.09), residues: 3204 sheet: -0.87 (0.15), residues: 1136 loop : -1.47 (0.11), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 1 210 HIS 0.014 0.001 HIS M 158 PHE 0.027 0.001 PHE Q 395 TYR 0.017 0.001 TYR D 147 ARG 0.009 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1112 time to evaluate : 5.334 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.8483 (mm) cc_final: 0.8099 (mm) REVERT: A 103 CYS cc_start: 0.8013 (m) cc_final: 0.7805 (t) REVERT: A 105 CYS cc_start: 0.5967 (m) cc_final: 0.5748 (m) REVERT: A 142 CYS cc_start: 0.8042 (m) cc_final: 0.7660 (p) REVERT: A 174 ILE cc_start: 0.8792 (mp) cc_final: 0.8182 (mp) REVERT: A 234 MET cc_start: 0.8949 (tpp) cc_final: 0.8734 (tpt) REVERT: A 295 LEU cc_start: 0.9165 (tp) cc_final: 0.8907 (tt) REVERT: A 304 MET cc_start: 0.8876 (mmm) cc_final: 0.8447 (mmt) REVERT: A 453 MET cc_start: 0.7325 (mpp) cc_final: 0.6788 (mpp) REVERT: A 541 ILE cc_start: 0.8909 (mp) cc_final: 0.8592 (mm) REVERT: A 547 LEU cc_start: 0.9202 (mt) cc_final: 0.8833 (mt) REVERT: A 748 MET cc_start: 0.8142 (mtp) cc_final: 0.7779 (mtm) REVERT: A 962 ARG cc_start: 0.7200 (mtm180) cc_final: 0.6975 (mtm110) REVERT: A 1022 LEU cc_start: 0.8149 (mm) cc_final: 0.7938 (mm) REVERT: A 1224 LEU cc_start: 0.7135 (tp) cc_final: 0.6855 (tp) REVERT: B 199 MET cc_start: 0.6759 (mmp) cc_final: 0.6480 (mmm) REVERT: B 308 TRP cc_start: 0.7653 (p-90) cc_final: 0.7347 (p-90) REVERT: B 542 MET cc_start: 0.6702 (mtm) cc_final: 0.6224 (mtm) REVERT: B 596 LEU cc_start: 0.8009 (tp) cc_final: 0.7694 (tt) REVERT: B 760 ASP cc_start: 0.8902 (p0) cc_final: 0.8047 (p0) REVERT: B 829 CYS cc_start: 0.7575 (m) cc_final: 0.6874 (p) REVERT: B 885 MET cc_start: 0.7295 (tpp) cc_final: 0.7069 (tpp) REVERT: B 955 THR cc_start: 0.7288 (m) cc_final: 0.7065 (m) REVERT: B 978 ASP cc_start: 0.7041 (m-30) cc_final: 0.6698 (m-30) REVERT: B 1045 SER cc_start: 0.8817 (m) cc_final: 0.8512 (m) REVERT: B 1082 MET cc_start: 0.8199 (tpp) cc_final: 0.7855 (tpp) REVERT: B 1168 LEU cc_start: 0.6362 (mp) cc_final: 0.6009 (mp) REVERT: C 43 THR cc_start: 0.7899 (m) cc_final: 0.7602 (p) REVERT: C 85 ASP cc_start: 0.7533 (m-30) cc_final: 0.7249 (m-30) REVERT: C 167 HIS cc_start: 0.6711 (t-90) cc_final: 0.6089 (t-90) REVERT: D 29 LEU cc_start: 0.7392 (mm) cc_final: 0.7000 (mm) REVERT: D 128 VAL cc_start: 0.7878 (t) cc_final: 0.7665 (p) REVERT: D 148 LEU cc_start: 0.8848 (mt) cc_final: 0.8421 (mt) REVERT: D 151 PHE cc_start: 0.7322 (m-80) cc_final: 0.6954 (m-10) REVERT: E 198 ILE cc_start: 0.9493 (mp) cc_final: 0.9268 (mm) REVERT: F 100 GLN cc_start: 0.8962 (mp10) cc_final: 0.8039 (mp10) REVERT: F 124 GLU cc_start: 0.6627 (tt0) cc_final: 0.6363 (tt0) REVERT: G 7 LEU cc_start: 0.6351 (tp) cc_final: 0.6113 (tp) REVERT: G 52 ASP cc_start: 0.6384 (p0) cc_final: 0.5728 (p0) REVERT: G 135 ASP cc_start: 0.6134 (p0) cc_final: 0.5678 (p0) REVERT: H 26 ILE cc_start: 0.8968 (tp) cc_final: 0.8761 (tp) REVERT: H 64 ASN cc_start: 0.7882 (t0) cc_final: 0.7668 (t0) REVERT: H 117 SER cc_start: 0.8561 (t) cc_final: 0.7968 (p) REVERT: I 104 LEU cc_start: 0.9102 (mt) cc_final: 0.8440 (tt) REVERT: K 58 PHE cc_start: 0.8962 (t80) cc_final: 0.7966 (t80) REVERT: K 106 GLU cc_start: 0.6535 (pp20) cc_final: 0.6261 (pp20) REVERT: M 138 ASP cc_start: 0.7847 (m-30) cc_final: 0.7607 (t0) REVERT: M 172 MET cc_start: 0.6624 (mtp) cc_final: 0.6004 (mtp) REVERT: M 315 ILE cc_start: 0.7385 (mp) cc_final: 0.6876 (mp) REVERT: O 84 THR cc_start: 0.7556 (m) cc_final: 0.6361 (m) REVERT: O 157 ILE cc_start: 0.4953 (mt) cc_final: 0.4636 (mt) REVERT: O 190 PHE cc_start: 0.7138 (t80) cc_final: 0.6907 (t80) REVERT: O 193 LEU cc_start: 0.6258 (tp) cc_final: 0.6006 (tt) REVERT: O 205 LEU cc_start: 0.7042 (mm) cc_final: 0.6778 (mm) REVERT: O 240 MET cc_start: 0.0749 (ttt) cc_final: -0.0982 (mmp) REVERT: Q 336 ASP cc_start: 0.7247 (p0) cc_final: 0.6949 (p0) REVERT: Q 365 TYR cc_start: 0.5929 (t80) cc_final: 0.5636 (t80) REVERT: R 68 VAL cc_start: 0.7007 (t) cc_final: 0.6774 (t) REVERT: R 97 ILE cc_start: 0.6270 (pt) cc_final: 0.5917 (pt) REVERT: R 131 ASN cc_start: 0.7424 (m-40) cc_final: 0.7152 (m-40) REVERT: U 21 VAL cc_start: 0.8305 (m) cc_final: 0.7496 (m) REVERT: U 243 LEU cc_start: 0.5280 (mt) cc_final: 0.4883 (mt) REVERT: V 87 VAL cc_start: 0.5447 (m) cc_final: 0.5041 (m) REVERT: W 135 GLU cc_start: 0.6701 (pt0) cc_final: 0.6344 (pt0) REVERT: W 167 GLU cc_start: 0.7307 (pm20) cc_final: 0.6984 (pm20) REVERT: X 208 LYS cc_start: 0.8123 (mppt) cc_final: 0.7822 (mmtm) REVERT: 0 86 LEU cc_start: 0.8305 (tp) cc_final: 0.7959 (tp) REVERT: 0 171 LEU cc_start: 0.4112 (tp) cc_final: 0.3628 (tp) REVERT: 0 404 THR cc_start: 0.8353 (p) cc_final: 0.8140 (p) REVERT: 1 28 THR cc_start: 0.5516 (p) cc_final: 0.5166 (t) REVERT: 6 149 ILE cc_start: 0.7605 (pt) cc_final: 0.7372 (pt) REVERT: 6 156 PHE cc_start: 0.6585 (t80) cc_final: 0.5839 (t80) REVERT: 6 157 VAL cc_start: 0.7948 (t) cc_final: 0.7656 (t) REVERT: 6 261 VAL cc_start: 0.7643 (t) cc_final: 0.7438 (t) REVERT: 6 288 TYR cc_start: 0.6302 (t80) cc_final: 0.5753 (t80) REVERT: 6 301 PHE cc_start: 0.7532 (m-80) cc_final: 0.7266 (m-80) REVERT: 7 708 LEU cc_start: 0.6906 (tp) cc_final: 0.6686 (tp) outliers start: 2 outliers final: 0 residues processed: 1114 average time/residue: 0.5755 time to fit residues: 1098.8479 Evaluate side-chains 817 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 817 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 589 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 chunk 603 optimal weight: 8.9990 chunk 489 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 635 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A 640 GLN A 654 ASN A 736 ASN A 742 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 996 ASN A1211 GLN A1218 GLN B 53 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 494 HIS B 572 HIS B 862 GLN B 932 HIS B 951 GLN B 958 GLN B 986 GLN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 HIS ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS ** W 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 64156 Z= 0.483 Angle : 0.813 13.434 87470 Z= 0.425 Chirality : 0.046 0.267 10205 Planarity : 0.005 0.081 10892 Dihedral : 14.355 161.387 10322 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.67 % Rotamer: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.76 (0.10), residues: 7505 helix: 0.72 (0.09), residues: 3160 sheet: -1.11 (0.15), residues: 1116 loop : -1.48 (0.11), residues: 3229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 13 HIS 0.016 0.002 HIS J 53 PHE 0.036 0.003 PHE B1130 TYR 0.031 0.003 TYR J 44 ARG 0.032 0.001 ARG V 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 964 time to evaluate : 5.360 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.8879 (mm) cc_final: 0.8465 (mm) REVERT: A 105 CYS cc_start: 0.6827 (m) cc_final: 0.6441 (m) REVERT: A 174 ILE cc_start: 0.9011 (mp) cc_final: 0.8490 (mm) REVERT: A 266 LEU cc_start: 0.8680 (mt) cc_final: 0.8283 (mm) REVERT: A 304 MET cc_start: 0.9275 (mmm) cc_final: 0.7489 (mmm) REVERT: A 453 MET cc_start: 0.7216 (mpp) cc_final: 0.6682 (mpp) REVERT: A 668 ASP cc_start: 0.8709 (m-30) cc_final: 0.8255 (m-30) REVERT: A 748 MET cc_start: 0.8168 (mtp) cc_final: 0.7911 (mtm) REVERT: A 761 MET cc_start: 0.6839 (mtp) cc_final: 0.6607 (mtp) REVERT: A 802 ASN cc_start: 0.8324 (m110) cc_final: 0.7871 (t0) REVERT: A 864 ILE cc_start: 0.9170 (mp) cc_final: 0.8945 (mm) REVERT: A 871 ASP cc_start: 0.8636 (p0) cc_final: 0.7817 (p0) REVERT: A 1062 GLU cc_start: 0.5961 (mt-10) cc_final: 0.5743 (mt-10) REVERT: A 1195 LEU cc_start: 0.5192 (pt) cc_final: 0.4797 (pp) REVERT: B 760 ASP cc_start: 0.9186 (p0) cc_final: 0.8461 (p0) REVERT: B 806 THR cc_start: 0.8122 (m) cc_final: 0.7756 (m) REVERT: B 809 MET cc_start: 0.7790 (mmp) cc_final: 0.6797 (mtp) REVERT: B 829 CYS cc_start: 0.7539 (m) cc_final: 0.6952 (p) REVERT: B 868 MET cc_start: 0.7612 (tmm) cc_final: 0.7244 (tpt) REVERT: B 978 ASP cc_start: 0.7529 (m-30) cc_final: 0.6968 (m-30) REVERT: B 1009 ASP cc_start: 0.7911 (m-30) cc_final: 0.7658 (m-30) REVERT: B 1045 SER cc_start: 0.9032 (m) cc_final: 0.8778 (m) REVERT: B 1111 MET cc_start: 0.7789 (mpp) cc_final: 0.7534 (mpp) REVERT: B 1152 MET cc_start: 0.7358 (tpp) cc_final: 0.7055 (tpp) REVERT: C 37 MET cc_start: 0.8355 (mtm) cc_final: 0.8062 (mtm) REVERT: C 43 THR cc_start: 0.8819 (m) cc_final: 0.8565 (p) REVERT: C 85 ASP cc_start: 0.7606 (m-30) cc_final: 0.6944 (m-30) REVERT: D 59 ILE cc_start: 0.8523 (mm) cc_final: 0.8256 (mm) REVERT: D 138 ASN cc_start: 0.7689 (t0) cc_final: 0.6635 (t0) REVERT: D 141 LEU cc_start: 0.8335 (tp) cc_final: 0.7790 (tp) REVERT: D 151 PHE cc_start: 0.7104 (m-80) cc_final: 0.5649 (m-10) REVERT: D 163 VAL cc_start: 0.9392 (t) cc_final: 0.9144 (t) REVERT: E 22 MET cc_start: 0.8669 (ttt) cc_final: 0.8157 (ttt) REVERT: E 58 MET cc_start: 0.6794 (tpt) cc_final: 0.6074 (tpt) REVERT: E 198 ILE cc_start: 0.9588 (mp) cc_final: 0.9323 (tp) REVERT: E 208 TYR cc_start: 0.8475 (t80) cc_final: 0.8110 (t80) REVERT: F 77 ASP cc_start: 0.7435 (p0) cc_final: 0.6859 (p0) REVERT: F 100 GLN cc_start: 0.9069 (mp10) cc_final: 0.8441 (mp10) REVERT: F 140 ASP cc_start: 0.8817 (p0) cc_final: 0.8548 (p0) REVERT: G 52 ASP cc_start: 0.6985 (p0) cc_final: 0.5937 (p0) REVERT: G 55 ASP cc_start: 0.7697 (p0) cc_final: 0.7293 (p0) REVERT: G 135 ASP cc_start: 0.6073 (p0) cc_final: 0.5644 (p0) REVERT: H 34 ASP cc_start: 0.6843 (p0) cc_final: 0.6498 (p0) REVERT: H 59 ILE cc_start: 0.9107 (mm) cc_final: 0.8901 (mm) REVERT: H 117 SER cc_start: 0.8942 (t) cc_final: 0.8443 (p) REVERT: M 138 ASP cc_start: 0.8030 (m-30) cc_final: 0.7719 (t0) REVERT: M 172 MET cc_start: 0.7542 (mtp) cc_final: 0.5423 (mtp) REVERT: O 84 THR cc_start: 0.7810 (m) cc_final: 0.6725 (m) REVERT: O 175 LEU cc_start: 0.6626 (tp) cc_final: 0.6221 (tp) REVERT: O 190 PHE cc_start: 0.7354 (t80) cc_final: 0.6994 (t80) REVERT: O 240 MET cc_start: 0.1355 (ttt) cc_final: -0.0116 (mmp) REVERT: Q 336 ASP cc_start: 0.7100 (p0) cc_final: 0.6593 (p0) REVERT: R 131 ASN cc_start: 0.7121 (m-40) cc_final: 0.6891 (m-40) REVERT: U 262 LEU cc_start: 0.6227 (mm) cc_final: 0.5333 (mm) REVERT: V 111 LEU cc_start: 0.5209 (tp) cc_final: 0.4307 (tp) REVERT: W 135 GLU cc_start: 0.7670 (pt0) cc_final: 0.6849 (pt0) REVERT: 0 76 MET cc_start: 0.6468 (mtp) cc_final: 0.6003 (mtp) REVERT: 0 495 MET cc_start: 0.6044 (ppp) cc_final: 0.5743 (ppp) REVERT: 0 680 VAL cc_start: 0.6220 (m) cc_final: 0.5935 (m) REVERT: 1 28 THR cc_start: 0.5392 (p) cc_final: 0.5111 (t) REVERT: 3 43 VAL cc_start: 0.8469 (p) cc_final: 0.8185 (p) REVERT: 6 156 PHE cc_start: 0.6205 (t80) cc_final: 0.5831 (t80) REVERT: 6 261 VAL cc_start: 0.7736 (t) cc_final: 0.7506 (t) REVERT: 7 708 LEU cc_start: 0.6919 (tp) cc_final: 0.6680 (tp) outliers start: 2 outliers final: 2 residues processed: 966 average time/residue: 0.5764 time to fit residues: 952.5933 Evaluate side-chains 696 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 694 time to evaluate : 5.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 238 optimal weight: 1.9990 chunk 637 optimal weight: 3.9990 chunk 139 optimal weight: 0.0670 chunk 415 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 708 optimal weight: 9.9990 chunk 587 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 371 optimal weight: 0.0670 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN A 510 GLN A 545 GLN A 786 HIS A1211 GLN A1218 GLN ** B 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 52 GLN I 22 ASN J 53 HIS ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 285 ASN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 280 GLN ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 176 ASN ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 64156 Z= 0.162 Angle : 0.584 14.323 87470 Z= 0.302 Chirality : 0.042 0.242 10205 Planarity : 0.004 0.070 10892 Dihedral : 14.213 160.506 10322 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.28 % Rotamer: Outliers : 0.02 % Allowed : 1.81 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.28 (0.10), residues: 7505 helix: 1.19 (0.09), residues: 3176 sheet: -0.87 (0.16), residues: 1095 loop : -1.33 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 1 210 HIS 0.015 0.001 HIS 7 598 PHE 0.029 0.001 PHE I 100 TYR 0.015 0.001 TYR D 147 ARG 0.013 0.000 ARG R 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1013 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.8836 (mm) cc_final: 0.8545 (mm) REVERT: A 103 CYS cc_start: 0.6302 (t) cc_final: 0.6027 (t) REVERT: A 174 ILE cc_start: 0.8943 (mp) cc_final: 0.8636 (mm) REVERT: A 266 LEU cc_start: 0.8711 (mt) cc_final: 0.8310 (mm) REVERT: A 304 MET cc_start: 0.8888 (mmm) cc_final: 0.8464 (mmm) REVERT: A 391 LEU cc_start: 0.9104 (mt) cc_final: 0.8779 (mt) REVERT: A 453 MET cc_start: 0.7411 (mpp) cc_final: 0.6769 (mpp) REVERT: A 547 LEU cc_start: 0.9287 (mt) cc_final: 0.9064 (mt) REVERT: A 668 ASP cc_start: 0.8610 (m-30) cc_final: 0.8297 (m-30) REVERT: A 871 ASP cc_start: 0.8758 (p0) cc_final: 0.7902 (m-30) REVERT: A 903 ASN cc_start: 0.5840 (t0) cc_final: 0.5544 (t0) REVERT: A 949 ASP cc_start: 0.7450 (p0) cc_final: 0.7204 (p0) REVERT: A 1062 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5935 (mt-10) REVERT: A 1195 LEU cc_start: 0.5110 (pt) cc_final: 0.4848 (pt) REVERT: A 1224 LEU cc_start: 0.7108 (tp) cc_final: 0.6630 (tp) REVERT: A 1336 MET cc_start: 0.8323 (tmm) cc_final: 0.8101 (tmm) REVERT: B 760 ASP cc_start: 0.9114 (p0) cc_final: 0.8231 (p0) REVERT: B 809 MET cc_start: 0.7798 (mmp) cc_final: 0.6594 (mtp) REVERT: B 829 CYS cc_start: 0.7547 (m) cc_final: 0.6483 (p) REVERT: B 868 MET cc_start: 0.7497 (tmm) cc_final: 0.7246 (tpt) REVERT: B 978 ASP cc_start: 0.7175 (m-30) cc_final: 0.6750 (m-30) REVERT: B 1009 ASP cc_start: 0.7830 (m-30) cc_final: 0.7467 (m-30) REVERT: B 1045 SER cc_start: 0.8971 (m) cc_final: 0.8712 (m) REVERT: B 1111 MET cc_start: 0.7926 (mpp) cc_final: 0.7650 (mpp) REVERT: B 1138 MET cc_start: 0.8191 (mmp) cc_final: 0.7346 (mmm) REVERT: B 1150 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7446 (tpp80) REVERT: B 1210 MET cc_start: 0.8297 (tpp) cc_final: 0.8044 (tpp) REVERT: C 37 MET cc_start: 0.8163 (mtm) cc_final: 0.7935 (mtp) REVERT: C 43 THR cc_start: 0.8647 (m) cc_final: 0.8386 (p) REVERT: D 59 ILE cc_start: 0.8022 (mm) cc_final: 0.7814 (mm) REVERT: D 141 LEU cc_start: 0.8243 (tp) cc_final: 0.7675 (tp) REVERT: D 163 VAL cc_start: 0.9188 (t) cc_final: 0.8937 (t) REVERT: D 175 PHE cc_start: 0.7604 (t80) cc_final: 0.7059 (t80) REVERT: F 77 ASP cc_start: 0.7442 (p0) cc_final: 0.7008 (p0) REVERT: F 140 ASP cc_start: 0.8831 (p0) cc_final: 0.8535 (p0) REVERT: G 7 LEU cc_start: 0.7031 (tp) cc_final: 0.6660 (tp) REVERT: G 52 ASP cc_start: 0.6908 (p0) cc_final: 0.5942 (p0) REVERT: G 55 ASP cc_start: 0.6902 (p0) cc_final: 0.6597 (p0) REVERT: G 79 PHE cc_start: 0.6497 (t80) cc_final: 0.6104 (t80) REVERT: G 109 PHE cc_start: 0.6898 (t80) cc_final: 0.6545 (t80) REVERT: G 115 MET cc_start: 0.7276 (mmm) cc_final: 0.6827 (mmt) REVERT: G 135 ASP cc_start: 0.6199 (p0) cc_final: 0.5664 (p0) REVERT: H 26 ILE cc_start: 0.8832 (tp) cc_final: 0.8551 (tp) REVERT: H 104 PHE cc_start: 0.7582 (m-10) cc_final: 0.7221 (m-80) REVERT: H 117 SER cc_start: 0.8755 (t) cc_final: 0.8290 (p) REVERT: H 122 LEU cc_start: 0.9275 (mt) cc_final: 0.8931 (pp) REVERT: I 47 GLU cc_start: 0.5384 (tm-30) cc_final: 0.4985 (tm-30) REVERT: K 106 GLU cc_start: 0.6389 (pp20) cc_final: 0.6143 (pp20) REVERT: L 68 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7084 (tm-30) REVERT: M 286 ILE cc_start: 0.6801 (tt) cc_final: 0.6592 (tt) REVERT: O 73 THR cc_start: 0.6454 (p) cc_final: 0.6084 (p) REVERT: O 84 THR cc_start: 0.7680 (m) cc_final: 0.6547 (m) REVERT: O 190 PHE cc_start: 0.7186 (t80) cc_final: 0.6844 (t80) REVERT: O 193 LEU cc_start: 0.6957 (tp) cc_final: 0.6690 (tt) REVERT: O 240 MET cc_start: 0.1552 (ttt) cc_final: -0.0248 (mmp) REVERT: Q 336 ASP cc_start: 0.7148 (p0) cc_final: 0.6938 (p0) REVERT: R 270 MET cc_start: 0.7687 (mpp) cc_final: 0.6956 (mpp) REVERT: U 21 VAL cc_start: 0.8148 (m) cc_final: 0.7917 (m) REVERT: U 242 ASN cc_start: 0.2511 (m-40) cc_final: 0.1994 (m-40) REVERT: U 255 LYS cc_start: 0.6297 (mmtt) cc_final: 0.6005 (mmmt) REVERT: V 109 ASP cc_start: 0.1205 (t0) cc_final: 0.0760 (t0) REVERT: W 135 GLU cc_start: 0.7213 (pt0) cc_final: 0.6688 (pt0) REVERT: X 208 LYS cc_start: 0.8163 (mppt) cc_final: 0.7928 (mmtm) REVERT: 0 400 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7077 (mtpt) REVERT: 0 496 ILE cc_start: 0.7859 (pt) cc_final: 0.7575 (pt) REVERT: 0 518 ILE cc_start: 0.8532 (pt) cc_final: 0.8246 (pt) REVERT: 1 28 THR cc_start: 0.5893 (p) cc_final: 0.5234 (t) REVERT: 3 43 VAL cc_start: 0.8495 (p) cc_final: 0.8073 (p) REVERT: 6 156 PHE cc_start: 0.6145 (t80) cc_final: 0.5437 (t80) REVERT: 6 301 PHE cc_start: 0.7677 (m-80) cc_final: 0.7282 (m-80) outliers start: 1 outliers final: 0 residues processed: 1014 average time/residue: 0.5908 time to fit residues: 1018.9079 Evaluate side-chains 750 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 750 time to evaluate : 5.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 682 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 403 optimal weight: 9.9990 chunk 517 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 596 optimal weight: 0.9990 chunk 395 optimal weight: 9.9990 chunk 705 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 430 optimal weight: 0.9990 chunk 325 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN A1211 GLN A1218 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 179 GLN D 216 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 ASN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 64156 Z= 0.299 Angle : 0.647 12.965 87470 Z= 0.337 Chirality : 0.043 0.261 10205 Planarity : 0.004 0.068 10892 Dihedral : 14.226 159.692 10322 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.88 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.31 (0.10), residues: 7505 helix: 1.15 (0.09), residues: 3174 sheet: -0.84 (0.16), residues: 1074 loop : -1.34 (0.11), residues: 3257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 1 210 HIS 0.009 0.001 HIS B 300 PHE 0.028 0.002 PHE I 100 TYR 0.027 0.002 TYR B 666 ARG 0.012 0.001 ARG 6 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 937 time to evaluate : 5.366 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.8939 (mm) cc_final: 0.8639 (mm) REVERT: A 266 LEU cc_start: 0.8746 (mt) cc_final: 0.8373 (mm) REVERT: A 304 MET cc_start: 0.9281 (mmm) cc_final: 0.8412 (mmm) REVERT: A 453 MET cc_start: 0.7644 (mpp) cc_final: 0.6934 (mpp) REVERT: A 668 ASP cc_start: 0.8777 (m-30) cc_final: 0.8214 (m-30) REVERT: A 748 MET cc_start: 0.8211 (mtp) cc_final: 0.7933 (mtm) REVERT: A 871 ASP cc_start: 0.8642 (p0) cc_final: 0.7935 (m-30) REVERT: A 949 ASP cc_start: 0.7378 (p0) cc_final: 0.7153 (p0) REVERT: A 1062 GLU cc_start: 0.6082 (mt-10) cc_final: 0.5751 (mt-10) REVERT: A 1195 LEU cc_start: 0.5100 (pt) cc_final: 0.4814 (pt) REVERT: A 1433 MET cc_start: 0.8057 (tpp) cc_final: 0.7349 (tpp) REVERT: B 310 MET cc_start: 0.7692 (mtp) cc_final: 0.7476 (mtp) REVERT: B 360 PHE cc_start: 0.8706 (t80) cc_final: 0.8372 (t80) REVERT: B 543 SER cc_start: 0.8722 (m) cc_final: 0.8343 (m) REVERT: B 760 ASP cc_start: 0.8946 (p0) cc_final: 0.8188 (p0) REVERT: B 806 THR cc_start: 0.7783 (m) cc_final: 0.7496 (m) REVERT: B 809 MET cc_start: 0.7747 (mmp) cc_final: 0.6612 (mtp) REVERT: B 829 CYS cc_start: 0.7575 (m) cc_final: 0.6790 (p) REVERT: B 978 ASP cc_start: 0.7292 (m-30) cc_final: 0.6736 (m-30) REVERT: B 1009 ASP cc_start: 0.7962 (m-30) cc_final: 0.7677 (m-30) REVERT: B 1021 MET cc_start: 0.9027 (mmm) cc_final: 0.8574 (mmm) REVERT: B 1210 MET cc_start: 0.8293 (tpp) cc_final: 0.7841 (mmm) REVERT: C 37 MET cc_start: 0.8272 (mtm) cc_final: 0.7696 (ttp) REVERT: D 138 ASN cc_start: 0.7536 (t0) cc_final: 0.6692 (t0) REVERT: D 163 VAL cc_start: 0.9355 (t) cc_final: 0.9037 (t) REVERT: D 198 LEU cc_start: 0.7429 (mt) cc_final: 0.7164 (mt) REVERT: D 205 ASP cc_start: 0.8192 (p0) cc_final: 0.7952 (p0) REVERT: F 77 ASP cc_start: 0.7264 (p0) cc_final: 0.6743 (p0) REVERT: F 100 GLN cc_start: 0.9235 (mp10) cc_final: 0.8321 (mp10) REVERT: F 140 ASP cc_start: 0.8940 (p0) cc_final: 0.8598 (p0) REVERT: G 7 LEU cc_start: 0.7215 (tp) cc_final: 0.6834 (tp) REVERT: G 52 ASP cc_start: 0.6861 (p0) cc_final: 0.5842 (p0) REVERT: G 135 ASP cc_start: 0.6254 (p0) cc_final: 0.5750 (p0) REVERT: H 34 ASP cc_start: 0.6761 (p0) cc_final: 0.6430 (p0) REVERT: H 122 LEU cc_start: 0.9273 (mt) cc_final: 0.8945 (pp) REVERT: H 123 MET cc_start: 0.9143 (ppp) cc_final: 0.8751 (ppp) REVERT: I 47 GLU cc_start: 0.5052 (tm-30) cc_final: 0.4728 (tm-30) REVERT: L 68 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7241 (tm-30) REVERT: M 172 MET cc_start: 0.7637 (mtp) cc_final: 0.6758 (mmm) REVERT: M 176 ILE cc_start: 0.8658 (mt) cc_final: 0.8424 (mt) REVERT: M 189 PHE cc_start: 0.6461 (m-80) cc_final: 0.6248 (m-80) REVERT: O 73 THR cc_start: 0.6545 (p) cc_final: 0.6125 (p) REVERT: O 84 THR cc_start: 0.7759 (m) cc_final: 0.6720 (m) REVERT: O 175 LEU cc_start: 0.6326 (tp) cc_final: 0.5984 (tp) REVERT: O 190 PHE cc_start: 0.7539 (t80) cc_final: 0.7169 (t80) REVERT: O 193 LEU cc_start: 0.7335 (tp) cc_final: 0.7046 (tp) REVERT: Q 336 ASP cc_start: 0.7061 (p0) cc_final: 0.6680 (p0) REVERT: Q 371 ASP cc_start: 0.5708 (p0) cc_final: 0.5487 (p0) REVERT: U 262 LEU cc_start: 0.6380 (mm) cc_final: 0.5627 (mm) REVERT: W 167 GLU cc_start: 0.8159 (pm20) cc_final: 0.7762 (pm20) REVERT: 0 76 MET cc_start: 0.6442 (mtp) cc_final: 0.6013 (mtp) REVERT: 0 404 THR cc_start: 0.8561 (p) cc_final: 0.8360 (p) REVERT: 0 518 ILE cc_start: 0.8735 (pt) cc_final: 0.8477 (pt) REVERT: 0 664 GLN cc_start: 0.7803 (mp10) cc_final: 0.6998 (mm-40) REVERT: 1 28 THR cc_start: 0.5971 (p) cc_final: 0.5380 (t) REVERT: 1 95 THR cc_start: 0.8066 (p) cc_final: 0.7838 (p) REVERT: 3 43 VAL cc_start: 0.8505 (p) cc_final: 0.7966 (p) REVERT: 6 156 PHE cc_start: 0.6099 (t80) cc_final: 0.5808 (t80) REVERT: 6 261 VAL cc_start: 0.7638 (t) cc_final: 0.7437 (t) outliers start: 0 outliers final: 0 residues processed: 937 average time/residue: 0.6515 time to fit residues: 1051.9409 Evaluate side-chains 682 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 436 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 421 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 448 optimal weight: 4.9990 chunk 480 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 554 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A1211 GLN A1218 GLN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN E 101 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 285 ASN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 64156 Z= 0.179 Angle : 0.587 13.372 87470 Z= 0.303 Chirality : 0.042 0.235 10205 Planarity : 0.004 0.109 10892 Dihedral : 14.149 159.265 10322 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.00 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.11 (0.10), residues: 7505 helix: 1.37 (0.09), residues: 3176 sheet: -0.76 (0.16), residues: 1081 loop : -1.29 (0.11), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 1 210 HIS 0.009 0.001 HIS 7 598 PHE 0.027 0.001 PHE G 82 TYR 0.016 0.001 TYR O 139 ARG 0.040 0.001 ARG 1 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 960 time to evaluate : 5.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.8986 (mm) cc_final: 0.8657 (mm) REVERT: A 266 LEU cc_start: 0.8775 (mt) cc_final: 0.8402 (mm) REVERT: A 291 GLU cc_start: 0.7206 (mp0) cc_final: 0.6934 (mp0) REVERT: A 295 LEU cc_start: 0.9205 (tp) cc_final: 0.8960 (tt) REVERT: A 304 MET cc_start: 0.8990 (mmm) cc_final: 0.8517 (mmm) REVERT: A 453 MET cc_start: 0.7495 (mpp) cc_final: 0.6805 (mpp) REVERT: A 668 ASP cc_start: 0.8777 (m-30) cc_final: 0.8230 (m-30) REVERT: A 748 MET cc_start: 0.8140 (mtp) cc_final: 0.7934 (mtm) REVERT: A 838 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 871 ASP cc_start: 0.8647 (p0) cc_final: 0.7998 (m-30) REVERT: A 1195 LEU cc_start: 0.5053 (pt) cc_final: 0.4681 (pt) REVERT: A 1336 MET cc_start: 0.8413 (tmm) cc_final: 0.8145 (tmm) REVERT: A 1433 MET cc_start: 0.8184 (tpp) cc_final: 0.7386 (tpp) REVERT: B 199 MET cc_start: 0.7057 (mmp) cc_final: 0.6809 (mmm) REVERT: B 360 PHE cc_start: 0.8723 (t80) cc_final: 0.8300 (t80) REVERT: B 760 ASP cc_start: 0.8992 (p0) cc_final: 0.8247 (p0) REVERT: B 778 MET cc_start: 0.7941 (ttm) cc_final: 0.7535 (ttt) REVERT: B 806 THR cc_start: 0.7660 (m) cc_final: 0.6512 (m) REVERT: B 809 MET cc_start: 0.7908 (mmp) cc_final: 0.6645 (mpp) REVERT: B 829 CYS cc_start: 0.7454 (m) cc_final: 0.6635 (p) REVERT: B 860 MET cc_start: 0.8275 (tmm) cc_final: 0.7967 (ttt) REVERT: B 978 ASP cc_start: 0.7052 (m-30) cc_final: 0.6769 (m-30) REVERT: B 1009 ASP cc_start: 0.8033 (m-30) cc_final: 0.7657 (m-30) REVERT: B 1021 MET cc_start: 0.8669 (mmm) cc_final: 0.7816 (mmm) REVERT: B 1059 LEU cc_start: 0.8915 (tp) cc_final: 0.8680 (tp) REVERT: C 37 MET cc_start: 0.8288 (mtm) cc_final: 0.8046 (ttp) REVERT: D 163 VAL cc_start: 0.9305 (t) cc_final: 0.9045 (t) REVERT: D 198 LEU cc_start: 0.7257 (mt) cc_final: 0.6999 (mt) REVERT: F 77 ASP cc_start: 0.7395 (p0) cc_final: 0.6894 (p0) REVERT: F 100 GLN cc_start: 0.9185 (mp10) cc_final: 0.8355 (mp10) REVERT: F 140 ASP cc_start: 0.8975 (p0) cc_final: 0.8655 (p0) REVERT: G 3 PHE cc_start: 0.4719 (m-10) cc_final: 0.4166 (m-10) REVERT: G 7 LEU cc_start: 0.7043 (tp) cc_final: 0.6698 (tp) REVERT: G 52 ASP cc_start: 0.6693 (p0) cc_final: 0.5730 (p0) REVERT: G 109 PHE cc_start: 0.6564 (t80) cc_final: 0.6300 (t80) REVERT: G 115 MET cc_start: 0.7205 (mmt) cc_final: 0.6768 (mmm) REVERT: G 135 ASP cc_start: 0.6428 (p0) cc_final: 0.5950 (p0) REVERT: H 34 ASP cc_start: 0.6672 (p0) cc_final: 0.6332 (p0) REVERT: H 122 LEU cc_start: 0.9227 (mt) cc_final: 0.8964 (pp) REVERT: H 146 ARG cc_start: 0.6617 (pmt170) cc_final: 0.6188 (ptt-90) REVERT: I 47 GLU cc_start: 0.4698 (tm-30) cc_final: 0.4373 (tm-30) REVERT: K 106 GLU cc_start: 0.6269 (pp20) cc_final: 0.6040 (pp20) REVERT: L 56 LEU cc_start: 0.9154 (mt) cc_final: 0.8947 (mp) REVERT: L 68 GLU cc_start: 0.7600 (tm-30) cc_final: 0.6887 (tm-30) REVERT: M 172 MET cc_start: 0.7366 (mtp) cc_final: 0.5130 (mtp) REVERT: O 73 THR cc_start: 0.6627 (p) cc_final: 0.6348 (p) REVERT: O 190 PHE cc_start: 0.7248 (t80) cc_final: 0.6730 (t80) REVERT: O 193 LEU cc_start: 0.6915 (tp) cc_final: 0.6569 (tt) REVERT: Q 371 ASP cc_start: 0.5801 (p0) cc_final: 0.5497 (p0) REVERT: R 272 SER cc_start: 0.7992 (p) cc_final: 0.7598 (t) REVERT: W 167 GLU cc_start: 0.8014 (pm20) cc_final: 0.7632 (pm20) REVERT: 0 78 GLU cc_start: 0.7309 (pt0) cc_final: 0.6848 (mp0) REVERT: 0 404 THR cc_start: 0.8562 (p) cc_final: 0.8356 (p) REVERT: 0 518 ILE cc_start: 0.8656 (pt) cc_final: 0.8383 (pt) REVERT: 1 28 THR cc_start: 0.5620 (p) cc_final: 0.5263 (t) REVERT: 1 95 THR cc_start: 0.8093 (p) cc_final: 0.7363 (p) REVERT: 3 43 VAL cc_start: 0.8534 (p) cc_final: 0.7591 (p) REVERT: 6 126 LEU cc_start: 0.7642 (tp) cc_final: 0.7425 (mp) REVERT: 6 156 PHE cc_start: 0.6112 (t80) cc_final: 0.5555 (t80) REVERT: 6 233 LEU cc_start: 0.5863 (pp) cc_final: 0.5480 (pp) outliers start: 0 outliers final: 0 residues processed: 960 average time/residue: 0.5824 time to fit residues: 959.1087 Evaluate side-chains 709 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 709 time to evaluate : 5.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 641 optimal weight: 5.9990 chunk 675 optimal weight: 10.0000 chunk 616 optimal weight: 9.9990 chunk 657 optimal weight: 9.9990 chunk 395 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 516 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 594 optimal weight: 4.9990 chunk 621 optimal weight: 10.0000 chunk 655 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN A1211 GLN A1218 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN E 5 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 144 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 64156 Z= 0.411 Angle : 0.735 12.363 87470 Z= 0.384 Chirality : 0.045 0.337 10205 Planarity : 0.005 0.101 10892 Dihedral : 14.332 157.416 10322 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.48 % Favored : 93.30 % Rotamer: Outliers : 0.02 % Allowed : 0.72 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 7505 helix: 1.02 (0.09), residues: 3150 sheet: -1.06 (0.15), residues: 1068 loop : -1.41 (0.11), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 7 558 HIS 0.012 0.002 HIS M 245 PHE 0.026 0.002 PHE I 100 TYR 0.032 0.002 TYR B 797 ARG 0.012 0.001 ARG 1 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 876 time to evaluate : 5.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.9055 (mm) cc_final: 0.8774 (mm) REVERT: A 266 LEU cc_start: 0.8773 (mt) cc_final: 0.8399 (mm) REVERT: A 295 LEU cc_start: 0.9292 (tp) cc_final: 0.9036 (tt) REVERT: A 304 MET cc_start: 0.9219 (mmm) cc_final: 0.8131 (mmm) REVERT: A 453 MET cc_start: 0.7712 (mpp) cc_final: 0.7013 (mpp) REVERT: A 526 ASP cc_start: 0.6740 (t0) cc_final: 0.5223 (t0) REVERT: A 668 ASP cc_start: 0.8714 (m-30) cc_final: 0.8212 (m-30) REVERT: A 748 MET cc_start: 0.8141 (mtp) cc_final: 0.7877 (mtm) REVERT: A 949 ASP cc_start: 0.7626 (p0) cc_final: 0.7350 (p0) REVERT: A 1195 LEU cc_start: 0.5406 (pt) cc_final: 0.5177 (pt) REVERT: A 1336 MET cc_start: 0.8434 (tmm) cc_final: 0.8206 (tmm) REVERT: A 1433 MET cc_start: 0.8058 (tpp) cc_final: 0.7231 (tpp) REVERT: B 299 GLU cc_start: 0.7418 (tt0) cc_final: 0.6957 (tp30) REVERT: B 542 MET cc_start: 0.7871 (mmm) cc_final: 0.7374 (mmm) REVERT: B 543 SER cc_start: 0.9102 (m) cc_final: 0.8887 (m) REVERT: B 760 ASP cc_start: 0.9152 (p0) cc_final: 0.8462 (p0) REVERT: B 809 MET cc_start: 0.7905 (mmp) cc_final: 0.6960 (mtp) REVERT: B 860 MET cc_start: 0.8339 (tmm) cc_final: 0.7890 (ttt) REVERT: B 978 ASP cc_start: 0.7260 (m-30) cc_final: 0.6724 (m-30) REVERT: B 1210 MET cc_start: 0.8072 (tpp) cc_final: 0.7867 (tpp) REVERT: C 37 MET cc_start: 0.8229 (mtm) cc_final: 0.7884 (mtm) REVERT: C 40 GLU cc_start: 0.7767 (tp30) cc_final: 0.7541 (tp30) REVERT: D 65 GLU cc_start: 0.6460 (tp30) cc_final: 0.5644 (tp30) REVERT: D 138 ASN cc_start: 0.7009 (t0) cc_final: 0.6017 (t0) REVERT: D 163 VAL cc_start: 0.9389 (t) cc_final: 0.9061 (t) REVERT: D 198 LEU cc_start: 0.7729 (mt) cc_final: 0.7445 (mt) REVERT: D 200 ASN cc_start: 0.7789 (p0) cc_final: 0.7587 (p0) REVERT: F 77 ASP cc_start: 0.7389 (p0) cc_final: 0.6877 (p0) REVERT: F 100 GLN cc_start: 0.9135 (mp10) cc_final: 0.8446 (mp10) REVERT: F 140 ASP cc_start: 0.9179 (p0) cc_final: 0.8869 (p0) REVERT: G 52 ASP cc_start: 0.6909 (p0) cc_final: 0.5990 (p0) REVERT: G 115 MET cc_start: 0.7285 (mmt) cc_final: 0.6873 (mmm) REVERT: G 135 ASP cc_start: 0.6359 (p0) cc_final: 0.5935 (p0) REVERT: H 34 ASP cc_start: 0.7178 (p0) cc_final: 0.6869 (p0) REVERT: H 123 MET cc_start: 0.9256 (ppp) cc_final: 0.8689 (ppp) REVERT: I 47 GLU cc_start: 0.4870 (tm-30) cc_final: 0.4586 (tm-30) REVERT: L 56 LEU cc_start: 0.8987 (mt) cc_final: 0.8757 (mt) REVERT: L 68 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6740 (tm-30) REVERT: M 176 ILE cc_start: 0.8689 (mt) cc_final: 0.8437 (mt) REVERT: O 73 THR cc_start: 0.6661 (p) cc_final: 0.6196 (p) REVERT: Q 371 ASP cc_start: 0.6739 (p0) cc_final: 0.6265 (p0) REVERT: R 272 SER cc_start: 0.8109 (p) cc_final: 0.7651 (t) REVERT: U 262 LEU cc_start: 0.6230 (mm) cc_final: 0.5701 (mm) REVERT: V 60 LEU cc_start: 0.6801 (mm) cc_final: 0.6472 (mm) REVERT: V 111 LEU cc_start: 0.5486 (tp) cc_final: 0.4942 (tp) REVERT: W 167 GLU cc_start: 0.8275 (pm20) cc_final: 0.7826 (pm20) REVERT: 0 518 ILE cc_start: 0.8538 (pt) cc_final: 0.8250 (pt) REVERT: 0 527 VAL cc_start: 0.8546 (t) cc_final: 0.8333 (t) REVERT: 0 659 MET cc_start: 0.6883 (mmm) cc_final: 0.6571 (mmm) REVERT: 1 28 THR cc_start: 0.5949 (p) cc_final: 0.5445 (t) REVERT: 1 95 THR cc_start: 0.8395 (p) cc_final: 0.8073 (p) REVERT: 1 113 ASP cc_start: 0.5025 (m-30) cc_final: 0.4694 (m-30) REVERT: 3 43 VAL cc_start: 0.8702 (p) cc_final: 0.7770 (p) REVERT: 3 70 THR cc_start: 0.7502 (m) cc_final: 0.7183 (m) REVERT: 6 156 PHE cc_start: 0.6103 (t80) cc_final: 0.5388 (t80) REVERT: 6 157 VAL cc_start: 0.7988 (t) cc_final: 0.7698 (t) REVERT: 6 263 VAL cc_start: 0.6536 (t) cc_final: 0.6317 (t) REVERT: 6 301 PHE cc_start: 0.7608 (m-80) cc_final: 0.7248 (m-10) outliers start: 1 outliers final: 0 residues processed: 877 average time/residue: 0.5894 time to fit residues: 883.7584 Evaluate side-chains 634 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 5.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 431 optimal weight: 0.0270 chunk 695 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 483 optimal weight: 7.9990 chunk 729 optimal weight: 30.0000 chunk 671 optimal weight: 7.9990 chunk 580 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 448 optimal weight: 0.5980 chunk 356 optimal weight: 3.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN A1218 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 ASN ** 1 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 64156 Z= 0.176 Angle : 0.621 12.822 87470 Z= 0.320 Chirality : 0.043 0.259 10205 Planarity : 0.004 0.085 10892 Dihedral : 14.225 157.170 10322 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.90 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 7505 helix: 1.38 (0.10), residues: 3123 sheet: -0.84 (0.15), residues: 1074 loop : -1.33 (0.11), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP 1 210 HIS 0.009 0.001 HIS 7 598 PHE 0.022 0.002 PHE 7 424 TYR 0.026 0.001 TYR M 154 ARG 0.022 0.001 ARG 1 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 929 time to evaluate : 6.912 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 LEU cc_start: 0.9086 (mm) cc_final: 0.8797 (mm) REVERT: A 266 LEU cc_start: 0.8701 (mt) cc_final: 0.8361 (mm) REVERT: A 295 LEU cc_start: 0.9195 (tp) cc_final: 0.8927 (tt) REVERT: A 304 MET cc_start: 0.9034 (mmm) cc_final: 0.8148 (mmm) REVERT: A 453 MET cc_start: 0.7787 (mpp) cc_final: 0.7047 (mpp) REVERT: A 455 MET cc_start: 0.7827 (ptm) cc_final: 0.6509 (ptm) REVERT: A 500 GLU cc_start: 0.8794 (pt0) cc_final: 0.8533 (tt0) REVERT: A 668 ASP cc_start: 0.8704 (m-30) cc_final: 0.8254 (m-30) REVERT: A 761 MET cc_start: 0.6652 (mpp) cc_final: 0.6263 (mpp) REVERT: A 1195 LEU cc_start: 0.5200 (pt) cc_final: 0.4767 (pt) REVERT: A 1224 LEU cc_start: 0.7453 (tp) cc_final: 0.7179 (tp) REVERT: A 1336 MET cc_start: 0.8391 (tmm) cc_final: 0.8145 (tmm) REVERT: A 1433 MET cc_start: 0.8073 (tpp) cc_final: 0.7388 (tpp) REVERT: B 167 ILE cc_start: 0.8955 (pt) cc_final: 0.8734 (pt) REVERT: B 240 ILE cc_start: 0.9355 (tt) cc_final: 0.9096 (tt) REVERT: B 760 ASP cc_start: 0.9126 (p0) cc_final: 0.8424 (p0) REVERT: B 806 THR cc_start: 0.7681 (m) cc_final: 0.6685 (m) REVERT: B 809 MET cc_start: 0.7968 (mmp) cc_final: 0.6798 (mtp) REVERT: B 829 CYS cc_start: 0.7796 (m) cc_final: 0.6929 (p) REVERT: B 841 MET cc_start: 0.7960 (tpp) cc_final: 0.7666 (tpp) REVERT: B 860 MET cc_start: 0.8148 (tmm) cc_final: 0.7819 (ttt) REVERT: B 978 ASP cc_start: 0.7055 (m-30) cc_final: 0.6701 (m-30) REVERT: B 1152 MET cc_start: 0.7292 (tpp) cc_final: 0.6881 (tpp) REVERT: C 37 MET cc_start: 0.8029 (mtm) cc_final: 0.7619 (ttm) REVERT: D 40 HIS cc_start: 0.7006 (m-70) cc_final: 0.6565 (m-70) REVERT: D 64 VAL cc_start: 0.7655 (t) cc_final: 0.7143 (t) REVERT: D 147 TYR cc_start: 0.5903 (t80) cc_final: 0.5558 (t80) REVERT: D 163 VAL cc_start: 0.9374 (t) cc_final: 0.9076 (t) REVERT: D 198 LEU cc_start: 0.7420 (mt) cc_final: 0.7124 (mt) REVERT: F 77 ASP cc_start: 0.7305 (p0) cc_final: 0.6913 (p0) REVERT: F 100 GLN cc_start: 0.8980 (mp10) cc_final: 0.8436 (mp10) REVERT: F 140 ASP cc_start: 0.9158 (p0) cc_final: 0.8719 (p0) REVERT: G 52 ASP cc_start: 0.6494 (p0) cc_final: 0.5892 (p0) REVERT: G 53 ASN cc_start: 0.7004 (m110) cc_final: 0.6520 (m110) REVERT: G 79 PHE cc_start: 0.5486 (t80) cc_final: 0.5067 (t80) REVERT: G 115 MET cc_start: 0.7138 (mmt) cc_final: 0.6903 (mmm) REVERT: G 135 ASP cc_start: 0.6465 (p0) cc_final: 0.5967 (p0) REVERT: H 34 ASP cc_start: 0.7043 (p0) cc_final: 0.6690 (p0) REVERT: H 122 LEU cc_start: 0.9170 (mt) cc_final: 0.8949 (pp) REVERT: H 123 MET cc_start: 0.9324 (ppp) cc_final: 0.8820 (ppp) REVERT: I 47 GLU cc_start: 0.4809 (tm-30) cc_final: 0.4585 (tm-30) REVERT: L 56 LEU cc_start: 0.9060 (mt) cc_final: 0.8822 (mp) REVERT: L 68 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6632 (tm-30) REVERT: M 286 ILE cc_start: 0.6697 (tt) cc_final: 0.6463 (tt) REVERT: O 73 THR cc_start: 0.6527 (p) cc_final: 0.6204 (p) REVERT: O 190 PHE cc_start: 0.6652 (t80) cc_final: 0.6278 (t80) REVERT: O 205 LEU cc_start: 0.7292 (mm) cc_final: 0.7042 (mm) REVERT: Q 369 ASN cc_start: 0.6050 (t0) cc_final: 0.5714 (t0) REVERT: Q 370 SER cc_start: 0.5869 (t) cc_final: 0.5424 (t) REVERT: Q 371 ASP cc_start: 0.6598 (p0) cc_final: 0.6015 (p0) REVERT: R 272 SER cc_start: 0.7896 (p) cc_final: 0.7527 (t) REVERT: U 19 ASN cc_start: 0.7471 (m-40) cc_final: 0.7264 (m-40) REVERT: 0 76 MET cc_start: 0.6131 (mtp) cc_final: 0.5518 (mtp) REVERT: 0 78 GLU cc_start: 0.6891 (pt0) cc_final: 0.6454 (pt0) REVERT: 0 404 THR cc_start: 0.8595 (p) cc_final: 0.8343 (p) REVERT: 0 659 MET cc_start: 0.6765 (mmm) cc_final: 0.6237 (mmm) REVERT: 1 28 THR cc_start: 0.5450 (p) cc_final: 0.5140 (t) REVERT: 3 43 VAL cc_start: 0.8707 (p) cc_final: 0.7742 (p) REVERT: 6 156 PHE cc_start: 0.5998 (t80) cc_final: 0.5181 (t80) REVERT: 6 301 PHE cc_start: 0.7598 (m-80) cc_final: 0.7221 (m-10) outliers start: 0 outliers final: 0 residues processed: 929 average time/residue: 0.6043 time to fit residues: 967.7051 Evaluate side-chains 686 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 5.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 461 optimal weight: 7.9990 chunk 618 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 535 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 581 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 597 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 399 HIS A1211 GLN A1218 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.067655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.045083 restraints weight = 354742.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.046336 restraints weight = 224995.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.047189 restraints weight = 163944.793| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 64156 Z= 0.297 Angle : 0.650 12.316 87470 Z= 0.339 Chirality : 0.043 0.279 10205 Planarity : 0.004 0.075 10892 Dihedral : 14.209 156.536 10322 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.18 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -0.26 (0.10), residues: 7505 helix: 1.29 (0.10), residues: 3151 sheet: -0.92 (0.16), residues: 1041 loop : -1.37 (0.11), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 1 210 HIS 0.010 0.001 HIS 5 52 PHE 0.020 0.002 PHE A 814 TYR 0.019 0.001 TYR J 44 ARG 0.015 0.001 ARG D 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16823.75 seconds wall clock time: 290 minutes 14.91 seconds (17414.91 seconds total)