Starting phenix.real_space_refine on Mon Sep 30 08:45:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/09_2024/6id0_9646.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/09_2024/6id0_9646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/09_2024/6id0_9646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/09_2024/6id0_9646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/09_2024/6id0_9646.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/09_2024/6id0_9646.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 416 5.49 5 Mg 7 5.21 5 S 220 5.16 5 C 47074 2.51 5 N 14255 2.21 5 O 16025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78004 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 16477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1981, 16477 Classifications: {'peptide': 1981} Link IDs: {'PTRANS': 106, 'TRANS': 1874} Chain breaks: 1 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2060 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 33, 'rna3p_pyr': 43} Link IDs: {'rna2p': 21, 'rna3p': 76} Chain: "C" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 888, 7022 Classifications: {'peptide': 888} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 833} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2366 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 10, 'TRANS': 292} Chain: "F" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 45, 'rna3p_pyr': 35} Link IDs: {'rna2p': 17, 'rna3p': 79} Chain: "J" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 3758 Classifications: {'peptide': 556} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 254} Link IDs: {'PTRANS': 16, 'TRANS': 539} Chain breaks: 17 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1087 Unresolved non-hydrogen angles: 1380 Unresolved non-hydrogen dihedrals: 918 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 15, 'PHE:plan': 15, 'GLU:plan': 44, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 688 Chain: "L" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3237 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 7 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 716 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 591 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 407 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1098 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "N" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "O" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2340 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 17, 'TRANS': 272} Chain: "P" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 985 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain breaks: 1 Chain: "R" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2165 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 22, 'TRANS': 249} Chain: "S" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "T" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2496 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain: "W" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3008 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 313} Link IDs: {'PTRANS': 24, 'TRANS': 484} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1199 Unresolved non-hydrogen angles: 1538 Unresolved non-hydrogen dihedrals: 1051 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 13, 'ASN:plan1': 13, 'TRP:plan': 12, 'ASP:plan': 23, 'PHE:plan': 15, 'GLU:plan': 17, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 667 Chain: "G" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1246 Classifications: {'RNA': 70} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 29} Link IDs: {'rna2p': 21, 'rna3p': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {' G%rna3p_pur:plan2': 7, ' C%rna3p_pyr:plan': 6, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 8, ' C%rna3p_pyr:plan2': 6, ' G%rna3p_pur:plan': 7, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 263 Chain: "H" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2968 Classifications: {'RNA': 140} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 23, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 33, 'rna3p': 106} Chain breaks: 6 Chain: "U" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2864 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 334} Chain breaks: 1 Chain: "I" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 2822 Classifications: {'peptide': 568} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 471} Link IDs: {'PTRANS': 18, 'TRANS': 549} Chain breaks: 19 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2450 Unresolved non-hydrogen dihedrals: 1599 Unresolved non-hydrogen chiralities: 150 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 15, 'TYR:plan': 25, 'ASN:plan1': 16, 'TRP:plan': 9, 'ASP:plan': 36, 'PHE:plan': 22, 'GLU:plan': 54, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 1179 Chain: "a" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 399 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 424 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "c" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "d" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 480 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "f" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "g" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 363 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "q" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 659 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 10, 'TRANS': 121} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "r" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 654 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "s" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "t" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "K" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 757 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 320 Chain: "h" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 398 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "i" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 424 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "j" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "k" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 422 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "m" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "n" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 329 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "o" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 804 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 272 Chain: "p" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 464 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 163 Chain: "Q" Number of atoms: 6562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 42, 'PHE:plan': 76, 'GLU:plan': 97, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2621 Conformer: "B" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 42, 'PHE:plan': 76, 'GLU:plan': 97, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2621 bond proxies already assigned to first conformer: 6533 Chain: "y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 390 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "N" 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} Chain: "O" 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} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38990 SG CYS N 105 66.336 188.626 113.310 1.00 8.68 S ATOM 39084 SG CYS N 117 66.371 185.531 111.054 1.00 17.85 S ATOM 39098 SG CYS N 119 63.169 187.073 111.887 1.00 19.81 S ATOM 39217 SG CYS N 134 65.533 185.247 114.466 1.00 14.21 S ATOM 38959 SG CYS N 101 63.190 190.633 112.738 1.00 15.09 S ATOM 38965 SG CYS N 102 66.244 191.947 115.081 1.00 11.38 S ATOM 38990 SG CYS N 105 66.336 188.626 113.310 1.00 8.68 S ATOM 39240 SG CYS N 137 63.627 190.215 116.020 1.00 16.22 S ATOM 38959 SG CYS N 101 63.190 190.633 112.738 1.00 15.09 S ATOM 39098 SG CYS N 119 63.169 187.073 111.887 1.00 19.81 S ATOM 39250 SG CYS N 139 60.060 188.430 113.073 1.00 18.20 S ATOM 39271 SG CYS N 142 61.769 189.802 109.817 1.00 17.20 S ATOM 39369 SG CYS O 24 73.458 155.005 114.474 1.00 18.87 S ATOM 39391 SG CYS O 27 72.152 157.509 116.697 1.00 23.08 S ATOM 39834 SG CYS O 81 76.630 156.153 115.934 1.00 17.29 S ATOM 39856 SG CYS O 84 74.001 154.031 117.912 1.00 21.80 S ATOM 39540 SG CYS O 45 85.686 159.260 124.543 1.00 9.52 S ATOM 39759 SG CYS O 71 88.460 159.918 121.913 1.00 10.42 S ATOM 39781 SG CYS O 74 87.922 155.602 123.573 1.00 12.58 S ATOM 40502 SG CYS O 165 59.653 172.395 129.190 1.00 26.64 S ATOM 40568 SG CYS O 173 57.115 174.866 128.494 1.00 26.82 S ATOM 40616 SG CYS O 179 60.067 173.723 125.798 1.00 26.30 S ATOM 56767 SG CYS U 675 130.794 192.154 197.141 1.00 39.50 S ATOM 56793 SG CYS U 678 126.819 194.052 199.655 1.00 48.11 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N MET Q 79 " occ=0.50 ... (3 atoms not shown) pdb=" CB MET Q 79 " occ=0.50 residue: pdb=" N MET Q 326 " occ=0.58 ... (3 atoms not shown) pdb=" CB MET Q 326 " occ=0.58 Time building chain proxies: 37.32, per 1000 atoms: 0.48 Number of scatterers: 78004 At special positions: 0 Unit cell: (242.178, 276.966, 266.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 220 16.00 P 416 15.00 Mg 7 11.99 O 16025 8.00 N 14255 7.00 C 47074 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.60 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 134 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 117 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 119 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 137 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 102 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 101 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 105 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 119 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 101 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 142 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 139 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 27 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 84 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 24 " pdb=" ZN O 502 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 45 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 74 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 71 " pdb=" ZN O 503 " pdb="ZN ZN O 503 " - pdb=" NE2 HIS O 183 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 179 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 173 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 165 " pdb=" ZN U 900 " pdb="ZN ZN U 900 " - pdb=" ND1 HIS U 765 " pdb="ZN ZN U 900 " - pdb=" NE2 HIS U 718 " pdb="ZN ZN U 900 " - pdb=" SG CYS U 675 " pdb="ZN ZN U 900 " - pdb=" SG CYS U 678 " Number of angles added : 29 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19710 Finding SS restraints... Secondary structure from input PDB file: 368 helices and 66 sheets defined 45.1% alpha, 14.5% beta 70 base pairs and 169 stacking pairs defined. Time for finding SS restraints: 21.67 Creating SS restraints... Processing helix chain 'A' and resid 26 through 45 removed outlier: 5.374A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 4.051A pdb=" N LYS A 50 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.861A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.704A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.846A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.899A pdb=" N ASN A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.087A pdb=" N TYR A 254 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.723A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.608A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.541A pdb=" N LYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 489 through 511 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.530A pdb=" N ARG A 593 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.541A pdb=" N MET A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 661 removed outlier: 3.524A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 676 through 697 removed outlier: 3.523A pdb=" N ARG A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 722 removed outlier: 3.611A pdb=" N ILE A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 797 removed outlier: 3.673A pdb=" N ARG A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.743A pdb=" N ALA A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 849 through 852 removed outlier: 4.325A pdb=" N VAL A 852 " --> pdb=" O ALA A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 852' Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 removed outlier: 3.526A pdb=" N ALA A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 933 Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 1001 Processing helix chain 'A' and resid 1002 through 1013 removed outlier: 3.642A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1054 removed outlier: 3.564A pdb=" N ILE A1040 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1103 through 1117 Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 4.043A pdb=" N ILE A1125 " --> pdb=" O ASN A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 3.702A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1249 Processing helix chain 'A' and resid 1257 through 1274 Processing helix chain 'A' and resid 1281 through 1303 removed outlier: 3.518A pdb=" N LEU A1285 " --> pdb=" O THR A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1339 Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.581A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1399 removed outlier: 3.972A pdb=" N GLN A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1411 removed outlier: 4.098A pdb=" N SER A1411 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 3.679A pdb=" N GLN A1424 " --> pdb=" O THR A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1443 removed outlier: 3.601A pdb=" N ARG A1439 " --> pdb=" O GLY A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1468 through 1479 Processing helix chain 'A' and resid 1479 through 1485 removed outlier: 3.697A pdb=" N GLY A1483 " --> pdb=" O GLY A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1494 Processing helix chain 'A' and resid 1519 through 1524 removed outlier: 3.571A pdb=" N SER A1524 " --> pdb=" O ALA A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1530 No H-bonds generated for 'chain 'A' and resid 1528 through 1530' Processing helix chain 'A' and resid 1531 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.510A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1598 Processing helix chain 'A' and resid 1600 through 1604 removed outlier: 4.026A pdb=" N ALA A1603 " --> pdb=" O GLU A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1722 through 1734 removed outlier: 3.827A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1767 through 1773 removed outlier: 3.573A pdb=" N PHE A1772 " --> pdb=" O GLY A1769 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A1773 " --> pdb=" O GLU A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1827 Processing helix chain 'A' and resid 1835 through 1852 removed outlier: 4.359A pdb=" N TRP A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1867 No H-bonds generated for 'chain 'A' and resid 1865 through 1867' Processing helix chain 'A' and resid 1868 through 1876 removed outlier: 3.561A pdb=" N GLU A1873 " --> pdb=" O LEU A1869 " (cutoff:3.500A) Processing helix chain 'A' and resid 1894 through 1898 Processing helix chain 'A' and resid 1899 through 1908 removed outlier: 3.605A pdb=" N LYS A1908 " --> pdb=" O ASP A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1926 removed outlier: 3.708A pdb=" N LYS A1925 " --> pdb=" O ASP A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1948 through 1955 Processing helix chain 'A' and resid 1972 through 1996 removed outlier: 3.607A pdb=" N ASP A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2012 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 116 through 124 removed outlier: 4.050A pdb=" N ALA C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.870A pdb=" N GLY C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.922A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 260 through 266 removed outlier: 3.788A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.696A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.509A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 391 through 398 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.547A pdb=" N LEU C 410 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.667A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.576A pdb=" N LYS C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.609A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 633 through 648 removed outlier: 3.740A pdb=" N TYR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 701 Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.583A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.616A pdb=" N ARG C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 754 removed outlier: 3.960A pdb=" N VAL C 754 " --> pdb=" O PRO C 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 751 through 754' Processing helix chain 'C' and resid 755 through 777 removed outlier: 4.108A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 777 " --> pdb=" O GLY C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 822 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 852 removed outlier: 3.753A pdb=" N SER C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 941 removed outlier: 3.614A pdb=" N LYS C 941 " --> pdb=" O THR C 937 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 200 Processing helix chain 'J' and resid 216 through 239 removed outlier: 3.989A pdb=" N LEU J 220 " --> pdb=" O ASP J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 255 removed outlier: 3.570A pdb=" N LEU J 255 " --> pdb=" O TRP J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 272 removed outlier: 3.672A pdb=" N ALA J 261 " --> pdb=" O GLU J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 289 removed outlier: 3.641A pdb=" N TRP J 279 " --> pdb=" O ASN J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 306 Processing helix chain 'J' and resid 309 through 323 removed outlier: 4.073A pdb=" N TRP J 313 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 338 Processing helix chain 'J' and resid 342 through 357 removed outlier: 3.697A pdb=" N TRP J 346 " --> pdb=" O GLU J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 373 Processing helix chain 'J' and resid 375 through 389 Processing helix chain 'J' and resid 391 through 407 removed outlier: 3.605A pdb=" N GLU J 404 " --> pdb=" O GLU J 400 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY J 407 " --> pdb=" O VAL J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 426 Processing helix chain 'J' and resid 429 through 440 removed outlier: 3.566A pdb=" N ARG J 433 " --> pdb=" O PHE J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 467 Processing helix chain 'J' and resid 477 through 491 removed outlier: 3.799A pdb=" N GLU J 481 " --> pdb=" O ARG J 477 " (cutoff:3.500A) Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 496 through 513 Processing helix chain 'J' and resid 521 through 534 Processing helix chain 'J' and resid 540 through 555 removed outlier: 3.794A pdb=" N LEU J 546 " --> pdb=" O LEU J 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU J 547 " --> pdb=" O TYR J 543 " (cutoff:3.500A) Proline residue: J 551 - end of helix Processing helix chain 'J' and resid 560 through 569 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 593 through 597 Processing helix chain 'J' and resid 609 through 624 removed outlier: 3.503A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG J 624 " --> pdb=" O ARG J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 643 removed outlier: 3.894A pdb=" N TRP J 643 " --> pdb=" O ASN J 639 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 660 removed outlier: 3.677A pdb=" N LEU J 653 " --> pdb=" O LEU J 649 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 659 " --> pdb=" O ASP J 655 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG J 660 " --> pdb=" O ILE J 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 679 removed outlier: 3.507A pdb=" N ARG J 671 " --> pdb=" O ILE J 667 " (cutoff:3.500A) Proline residue: J 675 - end of helix Processing helix chain 'J' and resid 684 through 696 Processing helix chain 'J' and resid 700 through 708 Processing helix chain 'J' and resid 719 through 730 Processing helix chain 'J' and resid 741 through 755 Processing helix chain 'J' and resid 764 through 775 Processing helix chain 'J' and resid 781 through 800 Processing helix chain 'L' and resid 12 through 27 Processing helix chain 'L' and resid 30 through 35 removed outlier: 3.572A pdb=" N ILE L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 54 Processing helix chain 'L' and resid 64 through 78 removed outlier: 3.774A pdb=" N GLU L 68 " --> pdb=" O SER L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 90 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 92 through 112 removed outlier: 3.512A pdb=" N ALA L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG L 110 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN L 112 " --> pdb=" O ALA L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 135 removed outlier: 3.764A pdb=" N THR L 134 " --> pdb=" O ASN L 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS L 135 " --> pdb=" O PRO L 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 131 through 135' Processing helix chain 'L' and resid 145 through 161 removed outlier: 3.561A pdb=" N ASN L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 195 Processing helix chain 'L' and resid 208 through 213 removed outlier: 3.759A pdb=" N ALA L 212 " --> pdb=" O VAL L 208 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU L 213 " --> pdb=" O ASP L 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 208 through 213' Processing helix chain 'L' and resid 243 through 249 removed outlier: 3.612A pdb=" N ASP L 248 " --> pdb=" O GLN L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 269 removed outlier: 3.534A pdb=" N LYS L 255 " --> pdb=" O LEU L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 526 removed outlier: 3.799A pdb=" N ILE L 525 " --> pdb=" O ARG L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 534 Processing helix chain 'L' and resid 545 through 552 Processing helix chain 'L' and resid 557 through 571 Proline residue: L 563 - end of helix removed outlier: 3.835A pdb=" N SER L 571 " --> pdb=" O ASP L 567 " (cutoff:3.500A) Processing helix chain 'L' and resid 594 through 608 Processing helix chain 'L' and resid 615 through 629 Proline residue: L 620 - end of helix Processing helix chain 'L' and resid 691 through 790 removed outlier: 3.597A pdb=" N ARG L 695 " --> pdb=" O SER L 691 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY L 723 " --> pdb=" O ILE L 719 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR L 724 " --> pdb=" O LEU L 720 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU L 743 " --> pdb=" O TRP L 739 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN L 744 " --> pdb=" O ASP L 740 " (cutoff:3.500A) Proline residue: L 764 - end of helix removed outlier: 3.980A pdb=" N LEU L 767 " --> pdb=" O ILE L 763 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU L 768 " --> pdb=" O PRO L 764 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG L 780 " --> pdb=" O ARG L 776 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN L 785 " --> pdb=" O GLU L 781 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS L 786 " --> pdb=" O LYS L 782 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG L 787 " --> pdb=" O GLU L 783 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR L 788 " --> pdb=" O LEU L 784 " (cutoff:3.500A) Processing helix chain 'L' and resid 790 through 795 removed outlier: 3.702A pdb=" N GLU L 794 " --> pdb=" O ASP L 790 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS L 795 " --> pdb=" O LEU L 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 790 through 795' Processing helix chain 'M' and resid 126 through 142 removed outlier: 3.798A pdb=" N ALA M 130 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN M 131 " --> pdb=" O TYR M 127 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 157 removed outlier: 3.557A pdb=" N TYR M 149 " --> pdb=" O ASP M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 161 removed outlier: 3.801A pdb=" N PHE M 161 " --> pdb=" O GLU M 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 158 through 161' Processing helix chain 'M' and resid 175 through 195 Processing helix chain 'M' and resid 212 through 227 removed outlier: 3.680A pdb=" N ALA M 216 " --> pdb=" O ASN M 212 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS M 217 " --> pdb=" O GLU M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 240 Processing helix chain 'N' and resid 14 through 33 removed outlier: 3.879A pdb=" N ILE N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Proline residue: N 20 - end of helix Processing helix chain 'N' and resid 43 through 45 No H-bonds generated for 'chain 'N' and resid 43 through 45' Processing helix chain 'N' and resid 46 through 65 removed outlier: 3.747A pdb=" N PHE N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 81 Processing helix chain 'N' and resid 85 through 93 Processing helix chain 'N' and resid 103 through 107 removed outlier: 3.734A pdb=" N ILE N 106 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 121 Processing helix chain 'N' and resid 122 through 127 removed outlier: 3.587A pdb=" N LEU N 126 " --> pdb=" O LYS N 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 77 Processing helix chain 'O' and resid 93 through 100 Processing helix chain 'O' and resid 110 through 126 Processing helix chain 'O' and resid 136 through 142 removed outlier: 3.948A pdb=" N SER O 142 " --> pdb=" O GLY O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 150 Processing helix chain 'O' and resid 165 through 170 removed outlier: 3.772A pdb=" N LYS O 170 " --> pdb=" O SER O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 179 removed outlier: 3.655A pdb=" N CYS O 179 " --> pdb=" O GLY O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 195 removed outlier: 3.658A pdb=" N ALA O 194 " --> pdb=" O ASP O 191 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP O 195 " --> pdb=" O PRO O 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 191 through 195' Processing helix chain 'O' and resid 197 through 204 removed outlier: 3.625A pdb=" N GLY O 204 " --> pdb=" O ASP O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 219 Processing helix chain 'O' and resid 244 through 253 removed outlier: 3.709A pdb=" N LEU O 248 " --> pdb=" O THR O 244 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG O 249 " --> pdb=" O GLU O 245 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN O 250 " --> pdb=" O THR O 246 " (cutoff:3.500A) Processing helix chain 'O' and resid 276 through 288 Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 31 through 35 removed outlier: 3.530A pdb=" N LEU P 35 " --> pdb=" O SER P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 56 removed outlier: 4.124A pdb=" N ASN P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 78 removed outlier: 3.951A pdb=" N GLU P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG P 78 " --> pdb=" O LYS P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 209 removed outlier: 3.569A pdb=" N LYS P 208 " --> pdb=" O LYS P 205 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 228 Processing helix chain 'R' and resid 97 through 102 removed outlier: 3.746A pdb=" N ALA R 100 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE R 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 119 Processing helix chain 'R' and resid 136 through 160 removed outlier: 3.677A pdb=" N LYS R 153 " --> pdb=" O VAL R 149 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 245 Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 282 through 317 removed outlier: 4.414A pdb=" N LYS R 286 " --> pdb=" O GLU R 282 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN R 307 " --> pdb=" O GLU R 303 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 46 removed outlier: 3.676A pdb=" N CYS S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 126 removed outlier: 4.254A pdb=" N ASP S 123 " --> pdb=" O THR S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 144 Processing helix chain 'T' and resid 459 through 463 removed outlier: 3.992A pdb=" N SER T 463 " --> pdb=" O ASP T 460 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 106 Processing helix chain 'W' and resid 121 through 135 Processing helix chain 'W' and resid 155 through 162 removed outlier: 3.610A pdb=" N ALA W 159 " --> pdb=" O SER W 155 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU W 160 " --> pdb=" O VAL W 156 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS W 161 " --> pdb=" O GLU W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 211 through 228 removed outlier: 4.059A pdb=" N LYS W 226 " --> pdb=" O LYS W 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY W 227 " --> pdb=" O ARG W 223 " (cutoff:3.500A) Processing helix chain 'W' and resid 518 through 520 No H-bonds generated for 'chain 'W' and resid 518 through 520' Processing helix chain 'U' and resid 598 through 609 Processing helix chain 'U' and resid 614 through 622 removed outlier: 3.759A pdb=" N ARG U 620 " --> pdb=" O LYS U 616 " (cutoff:3.500A) Processing helix chain 'U' and resid 635 through 643 Processing helix chain 'U' and resid 650 through 675 Processing helix chain 'U' and resid 726 through 747 removed outlier: 3.501A pdb=" N GLU U 732 " --> pdb=" O ASP U 728 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS U 742 " --> pdb=" O LYS U 738 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP U 746 " --> pdb=" O LYS U 742 " (cutoff:3.500A) Processing helix chain 'U' and resid 775 through 779 Processing helix chain 'U' and resid 780 through 790 removed outlier: 3.661A pdb=" N TYR U 784 " --> pdb=" O MET U 780 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET U 790 " --> pdb=" O LYS U 786 " (cutoff:3.500A) Processing helix chain 'U' and resid 809 through 813 removed outlier: 3.563A pdb=" N LYS U 812 " --> pdb=" O ASP U 809 " (cutoff:3.500A) Processing helix chain 'U' and resid 845 through 854 removed outlier: 3.825A pdb=" N ILE U 849 " --> pdb=" O PHE U 845 " (cutoff:3.500A) Processing helix chain 'U' and resid 875 through 881 removed outlier: 3.510A pdb=" N GLN U 881 " --> pdb=" O LEU U 877 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 166 Processing helix chain 'I' and resid 174 through 183 Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'I' and resid 205 through 218 Processing helix chain 'I' and resid 223 through 234 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 239 through 250 removed outlier: 4.249A pdb=" N ARG I 250 " --> pdb=" O GLY I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.968A pdb=" N ILE I 267 " --> pdb=" O ALA I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 282 removed outlier: 3.837A pdb=" N LYS I 274 " --> pdb=" O GLY I 270 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA I 282 " --> pdb=" O VAL I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 299 Processing helix chain 'I' and resid 304 through 315 Processing helix chain 'I' and resid 321 through 334 removed outlier: 3.644A pdb=" N VAL I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 350 Processing helix chain 'I' and resid 356 through 367 Processing helix chain 'I' and resid 368 through 383 removed outlier: 3.530A pdb=" N ARG I 372 " --> pdb=" O GLN I 368 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE I 375 " --> pdb=" O PRO I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 398 Proline residue: I 394 - end of helix Processing helix chain 'I' and resid 403 through 418 removed outlier: 3.880A pdb=" N ASP I 407 " --> pdb=" O LYS I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 438 Processing helix chain 'I' and resid 444 through 456 Processing helix chain 'I' and resid 464 through 477 Proline residue: I 475 - end of helix Processing helix chain 'I' and resid 486 through 499 Processing helix chain 'I' and resid 508 through 524 Proline residue: I 518 - end of helix Processing helix chain 'I' and resid 527 through 542 Processing helix chain 'I' and resid 544 through 558 removed outlier: 3.841A pdb=" N PHE I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP I 550 " --> pdb=" O SER I 546 " (cutoff:3.500A) Proline residue: I 551 - end of helix Processing helix chain 'I' and resid 570 through 579 removed outlier: 4.381A pdb=" N ARG I 577 " --> pdb=" O LEU I 573 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP I 578 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 598 Processing helix chain 'I' and resid 601 through 634 removed outlier: 3.522A pdb=" N MET I 613 " --> pdb=" O ALA I 609 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA I 614 " --> pdb=" O ARG I 610 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR I 616 " --> pdb=" O ALA I 612 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLU I 617 " --> pdb=" O MET I 613 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ARG I 618 " --> pdb=" O ALA I 614 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA I 619 " --> pdb=" O VAL I 615 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG I 621 " --> pdb=" O GLU I 617 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA I 622 " --> pdb=" O ARG I 618 " (cutoff:3.500A) Proline residue: I 625 - end of helix Processing helix chain 'I' and resid 643 through 653 removed outlier: 4.281A pdb=" N GLN I 653 " --> pdb=" O ARG I 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 676 removed outlier: 4.047A pdb=" N GLU I 675 " --> pdb=" O PHE I 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 680 through 689 Processing helix chain 'I' and resid 707 through 720 Processing helix chain 'I' and resid 722 through 734 removed outlier: 4.019A pdb=" N ILE I 726 " --> pdb=" O GLU I 722 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG I 727 " --> pdb=" O MET I 723 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL I 730 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN I 731 " --> pdb=" O ARG I 727 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR I 734 " --> pdb=" O VAL I 730 " (cutoff:3.500A) Processing helix chain 'I' and resid 741 through 756 removed outlier: 4.220A pdb=" N SER I 751 " --> pdb=" O LYS I 747 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 773 Processing helix chain 'I' and resid 780 through 792 Proline residue: I 788 - end of helix Processing helix chain 'I' and resid 798 through 818 Proline residue: I 816 - end of helix Processing helix chain 'a' and resid 4 through 13 Processing helix chain 'b' and resid 6 through 11 removed outlier: 4.261A pdb=" N LEU b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 9 removed outlier: 4.035A pdb=" N PHE c 6 " --> pdb=" O LYS c 2 " (cutoff:3.500A) Processing helix chain 'c' and resid 75 through 80 Processing helix chain 'd' and resid 21 through 27 Processing helix chain 'd' and resid 29 through 39 Processing helix chain 'f' and resid 6 through 15 Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'g' and resid 9 through 13 Processing helix chain 'q' and resid 27 through 37 removed outlier: 3.720A pdb=" N LYS q 32 " --> pdb=" O ARG q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 70 through 134 removed outlier: 3.728A pdb=" N LEU q 87 " --> pdb=" O ASP q 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE q 90 " --> pdb=" O MET q 86 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU q 92 " --> pdb=" O HIS q 88 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN q 95 " --> pdb=" O THR q 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR q 98 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN q 101 " --> pdb=" O GLN q 97 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG q 115 " --> pdb=" O ASP q 111 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR q 125 " --> pdb=" O THR q 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR q 133 " --> pdb=" O GLU q 129 " (cutoff:3.500A) Processing helix chain 'r' and resid 27 through 37 Processing helix chain 'r' and resid 69 through 75 Processing helix chain 'r' and resid 75 through 133 removed outlier: 3.603A pdb=" N HIS r 88 " --> pdb=" O ALA r 84 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN r 97 " --> pdb=" O ARG r 93 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR r 98 " --> pdb=" O GLN r 94 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA r 112 " --> pdb=" O TYR r 108 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS r 122 " --> pdb=" O ALA r 118 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR r 125 " --> pdb=" O THR r 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA r 126 " --> pdb=" O LYS r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 71 through 134 removed outlier: 3.640A pdb=" N LEU s 75 " --> pdb=" O ILE s 71 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA s 84 " --> pdb=" O ASP s 80 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR s 91 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN s 95 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU s 102 " --> pdb=" O THR s 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE s 117 " --> pdb=" O ALA s 113 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS s 122 " --> pdb=" O ALA s 118 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU s 129 " --> pdb=" O THR s 125 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 133 removed outlier: 3.705A pdb=" N LYS t 76 " --> pdb=" O PRO t 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU t 87 " --> pdb=" O ASP t 83 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU t 92 " --> pdb=" O HIS t 88 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG t 93 " --> pdb=" O SER t 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN t 95 " --> pdb=" O THR t 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN t 109 " --> pdb=" O HIS t 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS t 114 " --> pdb=" O HIS t 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG t 115 " --> pdb=" O ASP t 111 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA t 118 " --> pdb=" O CYS t 114 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG t 119 " --> pdb=" O ARG t 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 43 Processing helix chain 'K' and resid 65 through 77 removed outlier: 4.179A pdb=" N GLU K 69 " --> pdb=" O ILE K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 135 Processing helix chain 'K' and resid 136 through 199 removed outlier: 3.648A pdb=" N ASN K 141 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS K 148 " --> pdb=" O HIS K 144 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR K 173 " --> pdb=" O ASN K 169 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA K 174 " --> pdb=" O MET K 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR K 193 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 13 Processing helix chain 'i' and resid 6 through 11 removed outlier: 4.263A pdb=" N LEU i 10 " --> pdb=" O SER i 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 9 removed outlier: 4.033A pdb=" N PHE j 6 " --> pdb=" O LYS j 2 " (cutoff:3.500A) Processing helix chain 'j' and resid 75 through 80 Processing helix chain 'k' and resid 21 through 27 Processing helix chain 'k' and resid 29 through 39 Processing helix chain 'm' and resid 6 through 15 Processing helix chain 'l' and resid 16 through 28 Processing helix chain 'n' and resid 9 through 13 Processing helix chain 'o' and resid 5 through 11 removed outlier: 3.512A pdb=" N GLN o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 41 removed outlier: 3.906A pdb=" N ALA o 39 " --> pdb=" O ASN o 36 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 87 removed outlier: 3.573A pdb=" N ALA o 86 " --> pdb=" O GLY o 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 102 through 112 Proline residue: o 108 - end of helix removed outlier: 3.566A pdb=" N SER o 111 " --> pdb=" O PRO o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 128 Processing helix chain 'o' and resid 130 through 139 Processing helix chain 'o' and resid 151 through 161 Processing helix chain 'p' and resid 19 through 33 removed outlier: 4.195A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 69 removed outlier: 3.517A pdb=" N SER p 62 " --> pdb=" O GLU p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 88 through 96 Processing helix chain 'Q' and resid 20 through 31 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.046A pdb=" N ILE Q 46 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 70 Processing helix chain 'Q' and resid 71 through 76 Processing helix chain 'Q' and resid 77 through 81 Processing helix chain 'Q' and resid 87 through 104 Processing helix chain 'Q' and resid 109 through 115 Processing helix chain 'Q' and resid 118 through 132 Processing helix chain 'Q' and resid 139 through 155 Processing helix chain 'Q' and resid 159 through 171 removed outlier: 3.938A pdb=" N GLN Q 165 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLN Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU Q 169 " --> pdb=" O GLN Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 178 Processing helix chain 'Q' and resid 179 through 190 Processing helix chain 'Q' and resid 192 through 206 removed outlier: 4.357A pdb=" N PHE Q 196 " --> pdb=" O LYS Q 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU Q 205 " --> pdb=" O LYS Q 201 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS Q 206 " --> pdb=" O LYS Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 220 Processing helix chain 'Q' and resid 220 through 235 Processing helix chain 'Q' and resid 243 through 262 removed outlier: 3.681A pdb=" N VAL Q 247 " --> pdb=" O THR Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 277 removed outlier: 5.204A pdb=" N TRP Q 269 " --> pdb=" O PRO Q 265 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE Q 270 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR Q 272 " --> pdb=" O ARG Q 268 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE Q 273 " --> pdb=" O TRP Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 285 Processing helix chain 'Q' and resid 286 through 291 removed outlier: 3.620A pdb=" N ARG Q 290 " --> pdb=" O SER Q 286 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 310 Processing helix chain 'Q' and resid 322 through 345 Processing helix chain 'Q' and resid 348 through 354 Processing helix chain 'Q' and resid 355 through 360 removed outlier: 3.587A pdb=" N VAL Q 359 " --> pdb=" O ASN Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 370 Processing helix chain 'Q' and resid 373 through 384 Processing helix chain 'Q' and resid 399 through 412 Processing helix chain 'Q' and resid 416 through 423 Processing helix chain 'Q' and resid 429 through 434 removed outlier: 4.453A pdb=" N TRP Q 434 " --> pdb=" O GLU Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 461 through 492 removed outlier: 3.515A pdb=" N TYR Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU Q 480 " --> pdb=" O GLU Q 476 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 554 Processing helix chain 'Q' and resid 582 through 588 Processing helix chain 'Q' and resid 630 through 645 Processing helix chain 'Q' and resid 648 through 652 Processing helix chain 'Q' and resid 660 through 664 Processing helix chain 'Q' and resid 665 through 679 Processing helix chain 'Q' and resid 684 through 692 removed outlier: 4.793A pdb=" N ASP Q 689 " --> pdb=" O ASP Q 685 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE Q 690 " --> pdb=" O TRP Q 686 " (cutoff:3.500A) Processing helix chain 'Q' and resid 701 through 705 Processing helix chain 'Q' and resid 720 through 728 removed outlier: 3.552A pdb=" N PHE Q 728 " --> pdb=" O LEU Q 724 " (cutoff:3.500A) Processing helix chain 'Q' and resid 790 through 794 Processing helix chain 'Q' and resid 803 through 815 Processing helix chain 'Q' and resid 828 through 844 Processing helix chain 'Q' and resid 855 through 867 removed outlier: 3.578A pdb=" N LEU Q 859 " --> pdb=" O SER Q 855 " (cutoff:3.500A) Processing helix chain 'Q' and resid 872 through 874 No H-bonds generated for 'chain 'Q' and resid 872 through 874' Processing helix chain 'Q' and resid 893 through 919 Processing helix chain 'Q' and resid 928 through 939 Processing helix chain 'Q' and resid 939 through 952 removed outlier: 3.776A pdb=" N ARG Q 943 " --> pdb=" O GLN Q 939 " (cutoff:3.500A) Processing helix chain 'Q' and resid 960 through 967 removed outlier: 3.875A pdb=" N SER Q 965 " --> pdb=" O VAL Q 961 " (cutoff:3.500A) Processing helix chain 'Q' and resid 986 through 1012 Processing helix chain 'Q' and resid 1012 through 1017 Processing helix chain 'Q' and resid 1019 through 1030 Processing helix chain 'Q' and resid 1039 through 1053 removed outlier: 5.524A pdb=" N HIS Q1047 " --> pdb=" O ALA Q1043 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASP Q1048 " --> pdb=" O LEU Q1044 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1063 through 1067 Processing helix chain 'Q' and resid 1068 through 1074 Processing helix chain 'Q' and resid 1075 through 1078 removed outlier: 4.048A pdb=" N LEU Q1078 " --> pdb=" O PRO Q1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1075 through 1078' Processing helix chain 'Q' and resid 1107 through 1114 Processing helix chain 'Q' and resid 1118 through 1127 Processing helix chain 'Q' and resid 1140 through 1149 removed outlier: 4.201A pdb=" N LEU Q1146 " --> pdb=" O SER Q1142 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR Q1147 " --> pdb=" O LEU Q1143 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP Q1149 " --> pdb=" O ASN Q1145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1157 through 1163 Processing helix chain 'Q' and resid 1164 through 1167 Processing helix chain 'Q' and resid 1200 through 1218 Processing helix chain 'Q' and resid 1220 through 1222 No H-bonds generated for 'chain 'Q' and resid 1220 through 1222' Processing helix chain 'Q' and resid 1230 through 1245 Processing helix chain 'Q' and resid 1261 through 1264 removed outlier: 4.096A pdb=" N GLN Q1264 " --> pdb=" O ASP Q1261 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1261 through 1264' Processing helix chain 'Q' and resid 1281 through 1285 removed outlier: 4.118A pdb=" N LEU Q1284 " --> pdb=" O VAL Q1281 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1286 through 1294 Processing helix chain 'Q' and resid 1306 through 1312 removed outlier: 3.753A pdb=" N PHE Q1310 " --> pdb=" O ARG Q1306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1313 through 1315 No H-bonds generated for 'chain 'Q' and resid 1313 through 1315' Processing helix chain 'Q' and resid 1316 through 1324 removed outlier: 4.234A pdb=" N GLN Q1322 " --> pdb=" O PRO Q1318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1357 through 1376 removed outlier: 3.617A pdb=" N GLN Q1374 " --> pdb=" O MET Q1370 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 27 Processing helix chain 'y' and resid 28 through 30 No H-bonds generated for 'chain 'y' and resid 28 through 30' Processing helix chain 'y' and resid 56 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA4, first strand: chain 'A' and resid 905 through 910 Processing sheet with id=AA5, first strand: chain 'A' and resid 1085 through 1091 removed outlier: 5.467A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1087 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1185 through 1188 removed outlier: 3.803A pdb=" N LEU A1185 " --> pdb=" O ILE A1196 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A1223 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1225 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id=AA8, first strand: chain 'A' and resid 1501 through 1503 Processing sheet with id=AA9, first strand: chain 'A' and resid 1553 through 1554 removed outlier: 3.667A pdb=" N VAL A1553 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1629 through 1631 removed outlier: 6.178A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A1702 " --> pdb=" O TYR A1715 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1711 " --> pdb=" O ASP A1706 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1883 through 1886 removed outlier: 6.253A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1787 through 1792 removed outlier: 4.496A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.523A pdb=" N VAL T 199 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU T 196 " --> pdb=" O ARG T 490 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG T 490 " --> pdb=" O LEU T 196 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG T 476 " --> pdb=" O PHE T 470 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE T 470 " --> pdb=" O ARG T 476 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU T 478 " --> pdb=" O CYS T 468 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS T 468 " --> pdb=" O LEU T 478 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA T 480 " --> pdb=" O PHE T 466 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.629A pdb=" N TYR C 198 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL C 225 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS C 256 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU C 227 " --> pdb=" O CYS C 256 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 258 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE C 229 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB7, first strand: chain 'C' and resid 475 through 483 removed outlier: 6.941A pdb=" N MET C 475 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS C 477 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 495 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AB9, first strand: chain 'C' and resid 523 through 526 removed outlier: 3.529A pdb=" N GLN C 523 " --> pdb=" O VAL C 509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 618 through 621 Processing sheet with id=AC2, first strand: chain 'C' and resid 618 through 621 Processing sheet with id=AC3, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.344A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 783 through 784 removed outlier: 3.563A pdb=" N HIS C 903 " --> pdb=" O TYR C 831 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 675 through 676 removed outlier: 3.972A pdb=" N ALA C 676 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 685 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP C 793 " --> pdb=" O THR C 686 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 59 through 62 removed outlier: 4.234A pdb=" N MET E 60 " --> pdb=" O MET E 353 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET E 353 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE E 341 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE E 335 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE E 343 " --> pdb=" O VAL E 333 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL E 333 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA E 345 " --> pdb=" O ASN E 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 71 through 74 removed outlier: 3.551A pdb=" N ALA E 103 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN E 94 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN E 101 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 112 through 117 removed outlier: 4.381A pdb=" N THR E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP E 137 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG E 143 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 154 through 160 removed outlier: 3.678A pdb=" N SER E 156 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU E 166 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL E 176 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR E 189 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU E 178 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 196 through 201 removed outlier: 4.615A pdb=" N GLY E 212 " --> pdb=" O ASP E 216 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASP E 216 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 243 removed outlier: 3.752A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS E 275 " --> pdb=" O VAL E 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 291 through 293 removed outlier: 3.690A pdb=" N TYR E 310 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 54 through 57 removed outlier: 6.749A pdb=" N ILE O 34 " --> pdb=" O ARG R 198 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL R 200 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET O 36 " --> pdb=" O VAL R 200 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR R 176 " --> pdb=" O ALA W 118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 258 through 264 removed outlier: 4.042A pdb=" N THR O 260 " --> pdb=" O GLN O 273 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 292 through 293 Processing sheet with id=AD7, first strand: chain 'S' and resid 55 through 57 removed outlier: 3.803A pdb=" N MET S 61 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE S 97 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET S 100 " --> pdb=" O ILE S 128 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE S 128 " --> pdb=" O MET S 100 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL S 24 " --> pdb=" O CYS S 133 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR S 15 " --> pdb=" O ALA S 162 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA S 162 " --> pdb=" O TYR S 15 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU S 17 " --> pdb=" O ILE S 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 207 through 212 removed outlier: 4.419A pdb=" N THR T 227 " --> pdb=" O SER T 223 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP T 232 " --> pdb=" O LEU T 238 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU T 238 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 249 through 254 removed outlier: 3.856A pdb=" N VAL T 270 " --> pdb=" O TYR T 284 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG T 282 " --> pdb=" O CYS T 272 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP T 274 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL T 280 " --> pdb=" O ASP T 274 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 291 through 296 removed outlier: 3.802A pdb=" N GLY T 293 " --> pdb=" O CYS T 306 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR T 311 " --> pdb=" O SER T 307 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA T 312 " --> pdb=" O THR T 325 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N THR T 325 " --> pdb=" O ALA T 312 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE T 314 " --> pdb=" O VAL T 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 333 through 338 removed outlier: 3.571A pdb=" N GLY T 348 " --> pdb=" O THR T 335 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE T 345 " --> pdb=" O TRP T 357 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE T 354 " --> pdb=" O THR T 367 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR T 367 " --> pdb=" O ILE T 354 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU T 356 " --> pdb=" O ARG T 365 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 377 through 380 removed outlier: 3.711A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN T 407 " --> pdb=" O GLN T 397 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS T 399 " --> pdb=" O PHE T 405 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE T 405 " --> pdb=" O LYS T 399 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 416 through 422 removed outlier: 3.631A pdb=" N THR T 418 " --> pdb=" O GLY T 430 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL T 426 " --> pdb=" O ASN T 422 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP T 440 " --> pdb=" O ASN T 446 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN T 446 " --> pdb=" O ASP T 440 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 291 through 295 removed outlier: 6.506A pdb=" N CYS W 307 " --> pdb=" O SER W 292 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL W 294 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU W 305 " --> pdb=" O VAL W 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 335 through 340 removed outlier: 6.857A pdb=" N ASP W 360 " --> pdb=" O CYS W 366 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS W 366 " --> pdb=" O ASP W 360 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 376 through 381 removed outlier: 4.261A pdb=" N CYS W 378 " --> pdb=" O GLY W 394 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE W 400 " --> pdb=" O GLU W 413 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU W 413 " --> pdb=" O ILE W 400 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN W 402 " --> pdb=" O VAL W 411 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 421 through 428 removed outlier: 6.977A pdb=" N ARG W 432 " --> pdb=" O VAL W 427 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS W 454 " --> pdb=" O VAL W 444 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 466 through 469 removed outlier: 4.303A pdb=" N ALA W 466 " --> pdb=" O GLN W 479 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN W 484 " --> pdb=" O SER W 480 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N ILE W 485 " --> pdb=" O LYS W 499 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N LYS W 499 " --> pdb=" O ILE W 485 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE W 487 " --> pdb=" O ASN W 497 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 514 through 516 removed outlier: 6.133A pdb=" N ASP W 536 " --> pdb=" O LEU W 542 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU W 542 " --> pdb=" O ASP W 536 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 553 through 558 removed outlier: 3.842A pdb=" N GLY W 555 " --> pdb=" O CYS W 569 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 549 through 551 Processing sheet with id=AF4, first strand: chain 'U' and resid 696 through 699 removed outlier: 3.756A pdb=" N LEU U 754 " --> pdb=" O GLU U 769 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE U 825 " --> pdb=" O GLY U 829 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY U 829 " --> pdb=" O PHE U 825 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 17 through 22 removed outlier: 6.817A pdb=" N TYR a 28 " --> pdb=" O VAL a 48 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL a 48 " --> pdb=" O TYR a 28 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY a 30 " --> pdb=" O ILE a 46 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE a 46 " --> pdb=" O GLY a 30 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU a 59 " --> pdb=" O ASN a 45 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR a 47 " --> pdb=" O GLN a 57 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN a 57 " --> pdb=" O THR a 47 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR a 49 " --> pdb=" O VAL a 55 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL a 55 " --> pdb=" O THR a 49 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN a 60 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS g 26 " --> pdb=" O GLU g 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU g 47 " --> pdb=" O HIS g 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN g 28 " --> pdb=" O CYS g 45 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS g 45 " --> pdb=" O GLN g 28 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU g 44 " --> pdb=" O GLY g 58 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY g 58 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL g 46 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN g 56 " --> pdb=" O VAL g 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET g 48 " --> pdb=" O GLN g 54 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN g 54 " --> pdb=" O MET g 48 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET g 59 " --> pdb=" O SER e 89 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER e 89 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP e 34 " --> pdb=" O THR e 85 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU e 87 " --> pdb=" O GLN e 32 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN e 32 " --> pdb=" O LEU e 87 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER e 89 " --> pdb=" O ARG e 30 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG e 30 " --> pdb=" O SER e 89 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N CYS e 46 " --> pdb=" O ASP e 60 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP e 60 " --> pdb=" O CYS e 46 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE e 48 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU e 58 " --> pdb=" O ILE e 48 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE e 50 " --> pdb=" O LEU e 56 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU e 56 " --> pdb=" O PHE e 50 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL e 57 " --> pdb=" O MET e 78 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET e 78 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP e 59 " --> pdb=" O ARG e 76 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG e 76 " --> pdb=" O ASP e 59 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ARG e 76 " --> pdb=" O GLY f 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY f 74 " --> pdb=" O ARG e 76 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR f 32 " --> pdb=" O ASN f 46 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASN f 46 " --> pdb=" O TYR f 32 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL f 34 " --> pdb=" O LEU f 44 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU f 44 " --> pdb=" O VAL f 34 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL f 36 " --> pdb=" O MET f 42 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET f 42 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN f 43 " --> pdb=" O VAL f 62 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL f 62 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA f 45 " --> pdb=" O GLY f 60 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY f 60 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR f 47 " --> pdb=" O HIS f 58 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS f 58 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU f 49 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG d 55 " --> pdb=" O ASN d 69 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASN d 69 " --> pdb=" O ARG d 55 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS d 57 " --> pdb=" O LEU d 67 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU d 67 " --> pdb=" O LYS d 57 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE d 59 " --> pdb=" O MET d 65 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET d 65 " --> pdb=" O PHE d 59 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER d 97 " --> pdb=" O ASN d 69 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS d 71 " --> pdb=" O TYR d 95 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR d 95 " --> pdb=" O LYS d 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET d 73 " --> pdb=" O ASP d 93 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP d 93 " --> pdb=" O MET d 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR d 75 " --> pdb=" O ASN d 91 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN d 91 " --> pdb=" O THR d 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR c 28 " --> pdb=" O ALA c 42 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA c 42 " --> pdb=" O THR c 28 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR c 30 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU c 40 " --> pdb=" O THR c 30 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL c 32 " --> pdb=" O THR c 38 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR c 38 " --> pdb=" O VAL c 32 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU c 56 " --> pdb=" O ALA c 42 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS c 44 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN c 54 " --> pdb=" O LYS c 44 " (cutoff:3.500A) removed outlier: 14.288A pdb=" N LEU c 55 " --> pdb=" O GLY b 84 " (cutoff:3.500A) removed outlier: 12.666A pdb=" N GLY b 84 " --> pdb=" O LEU c 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR c 57 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL b 82 " --> pdb=" O THR c 57 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG b 16 " --> pdb=" O GLU b 83 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE b 26 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU b 47 " --> pdb=" O ILE b 26 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE b 28 " --> pdb=" O CYS b 45 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS b 45 " --> pdb=" O ILE b 28 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE b 41 " --> pdb=" O LYS b 32 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY b 68 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP b 46 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL b 66 " --> pdb=" O ASP b 46 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE b 48 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS b 64 " --> pdb=" O PHE b 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU b 69 " --> pdb=" O LEU a 73 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'q' and resid 24 through 26 Processing sheet with id=AF7, first strand: chain 'r' and resid 24 through 26 Processing sheet with id=AF8, first strand: chain 'h' and resid 17 through 22 removed outlier: 6.816A pdb=" N TYR h 28 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL h 48 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY h 30 " --> pdb=" O ILE h 46 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE h 46 " --> pdb=" O GLY h 30 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU h 59 " --> pdb=" O ASN h 45 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR h 47 " --> pdb=" O GLN h 57 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN h 57 " --> pdb=" O THR h 47 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR h 49 " --> pdb=" O VAL h 55 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL h 55 " --> pdb=" O THR h 49 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLN h 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS n 26 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU n 47 " --> pdb=" O HIS n 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN n 28 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS n 45 " --> pdb=" O GLN n 28 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU n 44 " --> pdb=" O GLY n 58 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLY n 58 " --> pdb=" O GLU n 44 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL n 46 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN n 56 " --> pdb=" O VAL n 46 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N MET n 59 " --> pdb=" O SER l 89 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER l 89 " --> pdb=" O MET n 59 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP l 34 " --> pdb=" O THR l 85 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU l 87 " --> pdb=" O GLN l 32 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN l 32 " --> pdb=" O LEU l 87 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER l 89 " --> pdb=" O ARG l 30 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG l 30 " --> pdb=" O SER l 89 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N CYS l 46 " --> pdb=" O ASP l 60 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP l 60 " --> pdb=" O CYS l 46 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE l 48 " --> pdb=" O LEU l 58 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE l 50 " --> pdb=" O LEU l 56 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU l 56 " --> pdb=" O PHE l 50 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL l 57 " --> pdb=" O MET l 78 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET l 78 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP l 59 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG l 76 " --> pdb=" O ASP l 59 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG l 76 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY m 74 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR m 32 " --> pdb=" O ASN m 46 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASN m 46 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL m 34 " --> pdb=" O LEU m 44 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU m 44 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL m 36 " --> pdb=" O MET m 42 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET m 42 " --> pdb=" O VAL m 36 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN m 43 " --> pdb=" O VAL m 62 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL m 62 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA m 45 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY m 60 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR m 47 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N HIS m 58 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU m 49 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG k 55 " --> pdb=" O ASN k 69 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN k 69 " --> pdb=" O ARG k 55 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS k 57 " --> pdb=" O LEU k 67 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU k 67 " --> pdb=" O LYS k 57 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE k 59 " --> pdb=" O MET k 65 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET k 65 " --> pdb=" O PHE k 59 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER k 97 " --> pdb=" O ASN k 69 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS k 71 " --> pdb=" O TYR k 95 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR k 95 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET k 73 " --> pdb=" O ASP k 93 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP k 93 " --> pdb=" O MET k 73 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR k 75 " --> pdb=" O ASN k 91 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN k 91 " --> pdb=" O THR k 75 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR j 28 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA j 42 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N THR j 30 " --> pdb=" O LEU j 40 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU j 40 " --> pdb=" O THR j 30 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL j 32 " --> pdb=" O THR j 38 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR j 38 " --> pdb=" O VAL j 32 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU j 56 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS j 44 " --> pdb=" O GLN j 54 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN j 54 " --> pdb=" O LYS j 44 " (cutoff:3.500A) removed outlier: 14.289A pdb=" N LEU j 55 " --> pdb=" O GLY i 84 " (cutoff:3.500A) removed outlier: 12.667A pdb=" N GLY i 84 " --> pdb=" O LEU j 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR j 57 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL i 82 " --> pdb=" O THR j 57 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG i 16 " --> pdb=" O GLU i 83 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE i 26 " --> pdb=" O GLU i 47 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU i 47 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE i 28 " --> pdb=" O CYS i 45 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS i 45 " --> pdb=" O ILE i 28 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE i 41 " --> pdb=" O LYS i 32 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY i 68 " --> pdb=" O ASP i 44 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP i 46 " --> pdb=" O VAL i 66 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL i 66 " --> pdb=" O ASP i 46 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE i 48 " --> pdb=" O LYS i 64 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS i 64 " --> pdb=" O PHE i 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU i 69 " --> pdb=" O LEU h 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 14 through 16 removed outlier: 6.181A pdb=" N ARG o 22 " --> pdb=" O ALA o 46 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP o 48 " --> pdb=" O ARG o 22 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU o 24 " --> pdb=" O ASP o 48 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU o 69 " --> pdb=" O ILE o 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'o' and resid 56 through 57 Processing sheet with id=AG2, first strand: chain 'p' and resid 37 through 41 removed outlier: 3.519A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'p' and resid 73 through 74 Processing sheet with id=AG4, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id=AG5, first strand: chain 'Q' and resid 511 through 522 removed outlier: 4.697A pdb=" N ASN Q 542 " --> pdb=" O PRO Q 513 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR Q 540 " --> pdb=" O VAL Q 515 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE Q 517 " --> pdb=" O ASP Q 538 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP Q 538 " --> pdb=" O PHE Q 517 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL Q 519 " --> pdb=" O ARG Q 536 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG Q 536 " --> pdb=" O VAL Q 519 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL Q 535 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE Q 628 " --> pdb=" O ILE Q 597 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE Q 597 " --> pdb=" O PHE Q 628 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 711 through 715 removed outlier: 5.711A pdb=" N PHE Q 747 " --> pdb=" O PHE Q 714 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 876 through 878 removed outlier: 6.777A pdb=" N LEU Q 877 " --> pdb=" O ALA Q1036 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N THR Q1038 " --> pdb=" O LEU Q 877 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE Q1059 " --> pdb=" O ILE Q1092 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE Q1094 " --> pdb=" O ILE Q1059 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N MET Q1061 " --> pdb=" O ILE Q1094 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL Q1131 " --> pdb=" O LEU Q 818 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET Q 820 " --> pdb=" O VAL Q1131 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 1135 through 1136 Processing sheet with id=AG9, first strand: chain 'Q' and resid 1177 through 1181 removed outlier: 6.504A pdb=" N ASP Q1269 " --> pdb=" O GLY Q1300 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR Q1302 " --> pdb=" O ASP Q1269 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE Q1271 " --> pdb=" O TYR Q1302 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE Q1304 " --> pdb=" O ILE Q1271 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU Q1273 " --> pdb=" O PHE Q1304 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR Q1258 " --> pdb=" O ILE Q1224 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE Q1226 " --> pdb=" O THR Q1258 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 1330 through 1332 Processing sheet with id=AH2, first strand: chain 'y' and resid 32 through 36 Processing sheet with id=AH3, first strand: chain 'y' and resid 71 through 72 3749 hydrogen bonds defined for protein. 10768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 171 hydrogen bonds 310 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 169 stacking parallelities Total time for adding SS restraints: 53.05 Time building geometry restraints manager: 17.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 12875 1.31 - 1.44: 22385 1.44 - 1.58: 43536 1.58 - 1.71: 832 1.71 - 1.85: 350 Bond restraints: 79978 Sorted by residual: bond pdb=" C1' C H 77 " pdb=" N1 C H 77 " ideal model delta sigma weight residual 1.480 1.593 -0.113 1.50e-02 4.44e+03 5.68e+01 bond pdb=" CA LYS W 278 " pdb=" C LYS W 278 " ideal model delta sigma weight residual 1.526 1.437 0.089 1.20e-02 6.94e+03 5.46e+01 bond pdb=" CA VAL K 186 " pdb=" CB VAL K 186 " ideal model delta sigma weight residual 1.542 1.435 0.106 1.45e-02 4.76e+03 5.36e+01 bond pdb=" C1' G B 103 " pdb=" N9 G B 103 " ideal model delta sigma weight residual 1.475 1.368 0.107 1.50e-02 4.44e+03 5.11e+01 bond pdb=" C1' U H 74 " pdb=" N1 U H 74 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.07e+01 ... (remaining 79973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 108101 3.67 - 7.34: 2415 7.34 - 11.01: 275 11.01 - 14.68: 90 14.68 - 18.35: 10 Bond angle restraints: 110891 Sorted by residual: angle pdb=" O2' U H 32 " pdb=" C2' U H 32 " pdb=" C1' U H 32 " ideal model delta sigma weight residual 111.80 128.63 -16.83 1.50e+00 4.44e-01 1.26e+02 angle pdb=" O3' C B 104 " pdb=" C3' C B 104 " pdb=" C2' C B 104 " ideal model delta sigma weight residual 109.50 94.44 15.06 1.50e+00 4.44e-01 1.01e+02 angle pdb=" N LEU I 327 " pdb=" CA LEU I 327 " pdb=" C LEU I 327 " ideal model delta sigma weight residual 111.28 100.38 10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" C LYS W 278 " pdb=" CA LYS W 278 " pdb=" CB LYS W 278 " ideal model delta sigma weight residual 111.17 95.78 15.39 1.54e+00 4.22e-01 9.98e+01 angle pdb=" C4' U G 142 " pdb=" C3' U G 142 " pdb=" O3' U G 142 " ideal model delta sigma weight residual 109.40 124.35 -14.95 1.50e+00 4.44e-01 9.93e+01 ... (remaining 110886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 46933 36.00 - 72.00: 1380 72.00 - 108.00: 157 108.00 - 143.99: 24 143.99 - 179.99: 14 Dihedral angle restraints: 48508 sinusoidal: 18282 harmonic: 30226 Sorted by residual: dihedral pdb=" CA GLU T 342 " pdb=" C GLU T 342 " pdb=" N PRO T 343 " pdb=" CA PRO T 343 " ideal model delta harmonic sigma weight residual -180.00 -100.58 -79.42 0 5.00e+00 4.00e-02 2.52e+02 dihedral pdb=" CA LYS N 3 " pdb=" C LYS N 3 " pdb=" N VAL N 4 " pdb=" CA VAL N 4 " ideal model delta harmonic sigma weight residual -180.00 -125.32 -54.68 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" C5' G G 25 " pdb=" C4' G G 25 " pdb=" C3' G G 25 " pdb=" O3' G G 25 " ideal model delta sinusoidal sigma weight residual 82.00 155.81 -73.81 1 8.00e+00 1.56e-02 1.08e+02 ... (remaining 48505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.002: 13340 1.002 - 2.003: 0 2.003 - 3.005: 0 3.005 - 4.006: 0 4.006 - 5.008: 2 Chirality restraints: 13342 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.27e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.59 -4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" CA ALA J 595 " pdb=" N ALA J 595 " pdb=" C ALA J 595 " pdb=" CB ALA J 595 " both_signs ideal model delta sigma weight residual False 2.48 1.59 0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 13339 not shown) Planarity restraints: 13281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 5 " 0.001 2.00e-02 2.50e+03 1.05e-01 3.33e+02 pdb=" N9 G G 5 " 0.129 2.00e-02 2.50e+03 pdb=" C8 G G 5 " 0.012 2.00e-02 2.50e+03 pdb=" N7 G G 5 " -0.173 2.00e-02 2.50e+03 pdb=" C5 G G 5 " -0.109 2.00e-02 2.50e+03 pdb=" C6 G G 5 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G G 5 " 0.086 2.00e-02 2.50e+03 pdb=" N1 G G 5 " 0.041 2.00e-02 2.50e+03 pdb=" C2 G G 5 " -0.041 2.00e-02 2.50e+03 pdb=" N2 G G 5 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G G 5 " -0.158 2.00e-02 2.50e+03 pdb=" C4 G G 5 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A G 6 " -0.175 2.00e-02 2.50e+03 8.74e-02 2.10e+02 pdb=" N9 A G 6 " -0.062 2.00e-02 2.50e+03 pdb=" C8 A G 6 " 0.122 2.00e-02 2.50e+03 pdb=" N7 A G 6 " 0.042 2.00e-02 2.50e+03 pdb=" C5 A G 6 " 0.029 2.00e-02 2.50e+03 pdb=" C6 A G 6 " -0.039 2.00e-02 2.50e+03 pdb=" N6 A G 6 " -0.104 2.00e-02 2.50e+03 pdb=" N1 A G 6 " -0.029 2.00e-02 2.50e+03 pdb=" C2 A G 6 " 0.022 2.00e-02 2.50e+03 pdb=" N3 A G 6 " 0.099 2.00e-02 2.50e+03 pdb=" C4 A G 6 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G G 7 " -0.053 2.00e-02 2.50e+03 7.92e-02 1.88e+02 pdb=" N9 G G 7 " -0.015 2.00e-02 2.50e+03 pdb=" C8 G G 7 " 0.083 2.00e-02 2.50e+03 pdb=" N7 G G 7 " 0.065 2.00e-02 2.50e+03 pdb=" C5 G G 7 " -0.235 2.00e-02 2.50e+03 pdb=" C6 G G 7 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G G 7 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G G 7 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G G 7 " 0.021 2.00e-02 2.50e+03 pdb=" N2 G G 7 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G G 7 " 0.046 2.00e-02 2.50e+03 pdb=" C4 G G 7 " 0.055 2.00e-02 2.50e+03 ... (remaining 13278 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 92 2.27 - 2.92: 32295 2.92 - 3.58: 111340 3.58 - 4.24: 173771 4.24 - 4.90: 282246 Nonbonded interactions: 599744 Sorted by model distance: nonbonded pdb=" P G G 1 " pdb=" O2' A G 144 " model vdw 1.607 3.400 nonbonded pdb=" OG SER A1512 " pdb=" OP2 U G 148 " model vdw 1.675 3.040 nonbonded pdb=" O4 U G 143 " pdb=" N3 U H 34 " model vdw 1.774 3.120 nonbonded pdb=" OG1 THR A 532 " pdb=" C5' A G 3 " model vdw 1.837 3.440 nonbonded pdb=" N2 G F 44 " pdb=" C2 A G 3 " model vdw 1.841 3.420 ... (remaining 599739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 3 through 56 or (resid 57 and (name N or name CA or name C \ or name O )) or resid 58 through 85)) selection = chain 'h' } ncs_group { reference = chain 'b' selection = chain 'i' } ncs_group { reference = chain 'c' selection = chain 'j' } ncs_group { reference = (chain 'd' and (resid 20 through 76 or resid 89 through 116)) selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 5 through 48 or resid 54 through 76)) selection = chain 'n' } ncs_group { reference = (chain 'q' and resid 3 through 133) selection = chain 'r' } ncs_group { reference = (chain 's' and resid 68 through 133) selection = (chain 't' and resid 68 through 133) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.100 Extract box with map and model: 2.220 Check model and map are aligned: 0.450 Set scattering table: 0.550 Process input model: 189.880 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.580 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: 0.030 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 210.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.009 0.178 79978 Z= 0.590 Angle : 1.386 18.351 110891 Z= 0.880 Chirality : 0.097 5.008 13342 Planarity : 0.007 0.105 13281 Dihedral : 16.695 179.993 28798 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.05 % Favored : 91.91 % Rotamer: Outliers : 1.46 % Allowed : 4.94 % Favored : 93.60 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.07), residues: 10189 helix: -1.72 (0.06), residues: 4250 sheet: -0.89 (0.13), residues: 1363 loop : -2.33 (0.08), residues: 4576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP J 336 HIS 0.023 0.003 HIS A 755 PHE 0.051 0.004 PHE J 419 TYR 0.068 0.004 TYR J 349 ARG 0.019 0.002 ARG J 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1353 time to evaluate : 6.379 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: A 923 ASP cc_start: 0.8237 (t70) cc_final: 0.8005 (t70) REVERT: A 1061 MET cc_start: 0.8410 (mtt) cc_final: 0.8020 (mtt) REVERT: A 1070 ASP cc_start: 0.6901 (p0) cc_final: 0.6560 (p0) REVERT: A 1216 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8611 (pp) REVERT: A 1289 VAL cc_start: 0.8913 (t) cc_final: 0.8694 (t) REVERT: A 1474 MET cc_start: 0.8333 (tpp) cc_final: 0.8129 (tpp) REVERT: C 159 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6467 (mmtp) REVERT: C 160 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5114 (ptt180) REVERT: C 461 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4804 (tm) REVERT: E 194 TYR cc_start: 0.5735 (m-80) cc_final: 0.5445 (m-80) REVERT: E 265 ARG cc_start: 0.3246 (mmt90) cc_final: 0.2769 (tmm160) REVERT: L 80 THR cc_start: 0.8346 (p) cc_final: 0.8002 (p) REVERT: L 123 LEU cc_start: 0.2828 (OUTLIER) cc_final: 0.2611 (tp) REVERT: O 115 GLU cc_start: 0.7864 (mp0) cc_final: 0.7564 (mp0) REVERT: S 102 ASN cc_start: 0.6115 (OUTLIER) cc_final: 0.5871 (t0) REVERT: T 195 LYS cc_start: 0.8283 (pttp) cc_final: 0.8055 (ptmm) REVERT: W 93 PHE cc_start: 0.6803 (m-10) cc_final: 0.6446 (m-80) REVERT: U 592 HIS cc_start: 0.7976 (p-80) cc_final: 0.7177 (p-80) REVERT: U 810 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7156 (pp) outliers start: 73 outliers final: 21 residues processed: 1411 average time/residue: 1.6484 time to fit residues: 3070.9540 Evaluate side-chains 774 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 746 time to evaluate : 5.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1518 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain J residue 242 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain S residue 102 ASN Chi-restraints excluded: chain T residue 489 TYR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain U residue 810 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 895 optimal weight: 30.0000 chunk 803 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 chunk 541 optimal weight: 9.9990 chunk 429 optimal weight: 20.0000 chunk 830 optimal weight: 40.0000 chunk 321 optimal weight: 0.7980 chunk 505 optimal weight: 8.9990 chunk 618 optimal weight: 6.9990 chunk 962 optimal weight: 50.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN A 357 ASN A 429 ASN A 457 ASN A 579 GLN A 584 HIS ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN A1096 HIS ** A1124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN A1217 GLN A1227 GLN A1241 HIS A1296 GLN A1466 ASN ** A1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 ASN A1531 ASN A1575 GLN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 GLN A1710 ASN A1737 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1811 ASN A1918 ASN A1995 ASN C 82 GLN C 125 ASN C 140 HIS C 210 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN C 523 GLN C 710 ASN C 786 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS J 188 GLN L 186 GLN M 141 GLN M 165 ASN M 169 HIS M 235 GLN M 236 ASN ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 14 ASN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** O 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 GLN O 289 ASN O 294 ASN P 29 GLN P 212 ASN R 183 GLN R 189 ASN R 242 GLN R 276 GLN ** R 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 ASN S 63 GLN S 87 HIS S 102 ASN S 126 HIS S 140 ASN T 191 HIS ** T 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 412 HIS T 417 ASN T 437 HIS ** T 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 HIS W 119 HIS W 121 ASN W 127 GLN W 145 ASN ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 665 HIS U 702 ASN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 833 HIS U 872 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.143 79978 Z= 0.725 Angle : 0.951 16.636 110891 Z= 0.498 Chirality : 0.057 0.624 13342 Planarity : 0.008 0.156 13281 Dihedral : 17.750 177.861 17158 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.73 % Favored : 92.63 % Rotamer: Outliers : 6.02 % Allowed : 14.67 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.29 % 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: -1.35 (0.08), residues: 10189 helix: -0.01 (0.07), residues: 4343 sheet: -0.66 (0.13), residues: 1361 loop : -1.84 (0.09), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP O 15 HIS 0.025 0.003 HIS T 412 PHE 0.053 0.004 PHE O 20 TYR 0.061 0.004 TYR T 284 ARG 0.018 0.002 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 739 time to evaluate : 6.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8247 (tp) REVERT: A 227 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6360 (mtm180) REVERT: A 587 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: A 699 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: A 1061 MET cc_start: 0.8792 (mtt) cc_final: 0.8534 (mtt) REVERT: A 1185 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8239 (pt) REVERT: A 1192 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.6703 (p90) REVERT: A 1516 LYS cc_start: 0.4114 (OUTLIER) cc_final: 0.3773 (mptt) REVERT: A 1529 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7717 (mm) REVERT: A 1622 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7712 (mpm) REVERT: A 1838 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8224 (mppt) REVERT: C 160 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5361 (ptm-80) REVERT: C 327 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6113 (t80) REVERT: C 461 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5221 (tm) REVERT: C 707 ILE cc_start: 0.3404 (OUTLIER) cc_final: 0.2740 (pp) REVERT: C 934 MET cc_start: 0.5997 (mmm) cc_final: 0.5467 (ttp) REVERT: E 136 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (m100) REVERT: E 165 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5370 (mt0) REVERT: E 177 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7526 (mtmm) REVERT: E 250 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6838 (tp) REVERT: E 265 ARG cc_start: 0.3803 (mmt90) cc_final: 0.2721 (tmm160) REVERT: E 289 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6707 (mm) REVERT: J 212 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (tp40) REVERT: J 343 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7433 (OUTLIER) REVERT: L 111 ASP cc_start: 0.3276 (OUTLIER) cc_final: 0.3031 (m-30) REVERT: L 266 HIS cc_start: 0.5146 (OUTLIER) cc_final: 0.4848 (m90) REVERT: M 156 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6396 (m170) REVERT: N 76 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: R 208 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: S 10 GLN cc_start: 0.6981 (mp-120) cc_final: 0.6770 (mp-120) REVERT: S 61 MET cc_start: 0.8477 (pp-130) cc_final: 0.8249 (pp-130) REVERT: S 125 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6861 (ptpp) REVERT: W 93 PHE cc_start: 0.6841 (m-10) cc_final: 0.6399 (m-80) REVERT: W 111 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8480 (tt) REVERT: U 608 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7547 (mmm) REVERT: U 614 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6331 (mp10) REVERT: U 638 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7585 (p0) REVERT: U 662 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6663 (mp) REVERT: U 686 LYS cc_start: 0.7936 (ttpm) cc_final: 0.7414 (tptt) REVERT: U 755 GLU cc_start: 0.7732 (tt0) cc_final: 0.7247 (tm-30) REVERT: U 810 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7498 (pp) outliers start: 301 outliers final: 124 residues processed: 969 average time/residue: 1.4921 time to fit residues: 1973.3686 Evaluate side-chains 798 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 643 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1388 GLU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1518 LEU Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1622 MET Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1838 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 256 LYS Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 266 HIS Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 197 ASN Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 220 MET Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 137 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 208 GLU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 166 THR Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 538 VAL Chi-restraints excluded: chain U residue 608 MET Chi-restraints excluded: chain U residue 614 GLN Chi-restraints excluded: chain U residue 638 ASP Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 756 THR Chi-restraints excluded: chain U residue 767 VAL Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 810 ILE Chi-restraints excluded: chain U residue 820 TYR Chi-restraints excluded: chain U residue 853 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 534 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 801 optimal weight: 6.9990 chunk 655 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 964 optimal weight: 0.0670 chunk 1041 optimal weight: 0.9990 chunk 858 optimal weight: 50.0000 chunk 956 optimal weight: 50.0000 chunk 328 optimal weight: 8.9990 chunk 773 optimal weight: 30.0000 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN A1124 ASN A1148 ASN A1424 GLN ** A1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 HIS A1580 HIS A1583 GLN A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN C 140 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 HIS C 710 ASN C 856 HIS ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN J 238 ASN J 289 ASN M 131 GLN M 141 GLN M 165 ASN M 235 GLN O 251 HIS R 104 GLN T 283 HIS ** T 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 451 HIS W 71 HIS W 184 ASN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 79978 Z= 0.219 Angle : 0.671 16.550 110891 Z= 0.352 Chirality : 0.044 0.460 13342 Planarity : 0.005 0.086 13281 Dihedral : 17.303 179.181 17136 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.10 % Favored : 93.48 % Rotamer: Outliers : 4.78 % Allowed : 17.15 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.19 % 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: -0.34 (0.08), residues: 10189 helix: 1.13 (0.08), residues: 4348 sheet: -0.27 (0.14), residues: 1282 loop : -1.59 (0.09), residues: 4559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1637 HIS 0.008 0.001 HIS J 294 PHE 0.039 0.002 PHE A 166 TYR 0.026 0.002 TYR A1369 ARG 0.008 0.001 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 746 time to evaluate : 6.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 779 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8807 (mt) REVERT: A 893 GLU cc_start: 0.7695 (pt0) cc_final: 0.7487 (pt0) REVERT: A 923 ASP cc_start: 0.8204 (t70) cc_final: 0.7970 (t70) REVERT: A 1332 HIS cc_start: 0.4778 (OUTLIER) cc_final: 0.4118 (m-70) REVERT: A 1370 ARG cc_start: 0.6540 (tpt170) cc_final: 0.6135 (ttp80) REVERT: A 1427 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7827 (ttp80) REVERT: A 1517 LYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5799 (pptt) REVERT: A 1655 THR cc_start: 0.7383 (p) cc_final: 0.7169 (p) REVERT: C 160 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5113 (ptt180) REVERT: C 175 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: C 327 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6150 (t80) REVERT: C 416 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8804 (tt) REVERT: C 461 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.4832 (mm) REVERT: C 935 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.5876 (mm) REVERT: E 136 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.7535 (m100) REVERT: E 143 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6117 (mmm160) REVERT: E 165 GLN cc_start: 0.5877 (OUTLIER) cc_final: 0.5401 (mt0) REVERT: E 255 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7063 (mtp) REVERT: E 265 ARG cc_start: 0.3798 (mmt90) cc_final: 0.2648 (tmm160) REVERT: J 401 ARG cc_start: 0.7496 (ttp80) cc_final: 0.7266 (mtm110) REVERT: L 59 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8069 (mtmm) REVERT: M 156 HIS cc_start: 0.6514 (OUTLIER) cc_final: 0.6191 (m170) REVERT: N 76 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: O 123 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6683 (ttp80) REVERT: P 73 GLU cc_start: 0.7179 (tp30) cc_final: 0.6782 (tp30) REVERT: P 188 TRP cc_start: 0.6115 (OUTLIER) cc_final: 0.4510 (p-90) REVERT: T 383 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7532 (mtp180) REVERT: W 93 PHE cc_start: 0.6789 (m-10) cc_final: 0.6391 (m-80) REVERT: W 218 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.4088 (tm-30) REVERT: U 662 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6610 (mp) REVERT: U 686 LYS cc_start: 0.7490 (ttpm) cc_final: 0.7125 (tptt) REVERT: U 755 GLU cc_start: 0.7525 (tt0) cc_final: 0.7254 (tm-30) REVERT: U 810 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7290 (pp) outliers start: 239 outliers final: 90 residues processed: 923 average time/residue: 1.4347 time to fit residues: 1833.9670 Evaluate side-chains 763 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 650 time to evaluate : 6.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1143 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1517 LYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 256 LYS Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 234 LYS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 220 MET Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 137 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 760 MET Chi-restraints excluded: chain U residue 767 VAL Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 810 ILE Chi-restraints excluded: chain U residue 818 LEU Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 952 optimal weight: 20.0000 chunk 725 optimal weight: 6.9990 chunk 500 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 460 optimal weight: 5.9990 chunk 647 optimal weight: 5.9990 chunk 967 optimal weight: 10.0000 chunk 1024 optimal weight: 5.9990 chunk 505 optimal weight: 9.9990 chunk 917 optimal weight: 50.0000 chunk 276 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS C 710 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN L 39 HIS M 141 GLN M 165 ASN M 212 ASN M 235 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 251 HIS R 104 GLN ** T 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 163 GLN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 79978 Z= 0.456 Angle : 0.753 17.257 110891 Z= 0.391 Chirality : 0.048 0.471 13342 Planarity : 0.006 0.116 13281 Dihedral : 17.194 178.645 17129 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.96 % Favored : 92.64 % Rotamer: Outliers : 5.84 % Allowed : 17.63 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.08), residues: 10189 helix: 1.30 (0.08), residues: 4364 sheet: -0.26 (0.14), residues: 1312 loop : -1.57 (0.09), residues: 4513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A1412 HIS 0.011 0.002 HIS A 73 PHE 0.050 0.003 PHE O 20 TYR 0.030 0.003 TYR C 167 ARG 0.010 0.001 ARG J 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 669 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (mtm-85) REVERT: A 204 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 498 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: A 941 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6830 (mmmt) REVERT: A 946 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: A 1185 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8164 (pt) REVERT: A 1192 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.6635 (p90) REVERT: A 1249 MET cc_start: 0.7501 (mtt) cc_final: 0.7300 (mtm) REVERT: A 1307 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.5080 (tpp) REVERT: A 1332 HIS cc_start: 0.5411 (OUTLIER) cc_final: 0.5136 (m-70) REVERT: A 1370 ARG cc_start: 0.6705 (tpt170) cc_final: 0.6203 (ttp80) REVERT: A 1427 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7861 (ttp80) REVERT: A 1513 MET cc_start: 0.6239 (tmm) cc_final: 0.5827 (ttt) REVERT: A 2014 MET cc_start: 0.4667 (mmm) cc_final: 0.4382 (mmt) REVERT: C 160 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5042 (ptt180) REVERT: C 175 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: C 327 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6298 (t80) REVERT: C 416 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 461 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5183 (mm) REVERT: C 934 MET cc_start: 0.6172 (mmm) cc_final: 0.5819 (ttp) REVERT: E 136 TRP cc_start: 0.7948 (OUTLIER) cc_final: 0.7714 (m100) REVERT: E 165 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5655 (mt0) REVERT: E 208 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5989 (mp) REVERT: E 250 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7038 (tp) REVERT: E 255 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6918 (mtp) REVERT: E 265 ARG cc_start: 0.3789 (mmt90) cc_final: 0.2382 (tmm160) REVERT: J 212 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6448 (tp40) REVERT: L 59 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8234 (mtmm) REVERT: L 251 LEU cc_start: 0.7698 (pp) cc_final: 0.7420 (pt) REVERT: M 156 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.6250 (m170) REVERT: O 123 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6713 (ttp80) REVERT: O 254 GLN cc_start: 0.5682 (mm-40) cc_final: 0.5479 (mm-40) REVERT: P 188 TRP cc_start: 0.6306 (OUTLIER) cc_final: 0.4681 (p-90) REVERT: R 202 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8062 (ttp) REVERT: S 20 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6786 (mmt) REVERT: S 25 LEU cc_start: 0.8212 (mt) cc_final: 0.7955 (mt) REVERT: S 61 MET cc_start: 0.8468 (pp-130) cc_final: 0.8194 (pp-130) REVERT: T 383 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7456 (mtp180) REVERT: T 400 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7896 (t80) REVERT: W 93 PHE cc_start: 0.6919 (m-10) cc_final: 0.6438 (m-80) REVERT: U 662 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6866 (mp) REVERT: U 686 LYS cc_start: 0.7828 (ttpm) cc_final: 0.7291 (tptt) REVERT: U 755 GLU cc_start: 0.7647 (tt0) cc_final: 0.7302 (tm-30) REVERT: U 810 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7370 (pp) outliers start: 292 outliers final: 152 residues processed: 892 average time/residue: 1.3925 time to fit residues: 1714.7044 Evaluate side-chains 820 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 638 time to evaluate : 6.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1143 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 256 LYS Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 197 ASN Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 220 MET Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 60 ARG Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 137 GLU Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain S residue 20 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 230 ILE Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 538 VAL Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 614 GLN Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 718 HIS Chi-restraints excluded: chain U residue 756 THR Chi-restraints excluded: chain U residue 760 MET Chi-restraints excluded: chain U residue 767 VAL Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain U residue 810 ILE Chi-restraints excluded: chain U residue 844 TYR Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 853 optimal weight: 2.9990 chunk 581 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 762 optimal weight: 8.9990 chunk 422 optimal weight: 8.9990 chunk 874 optimal weight: 8.9990 chunk 708 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 523 optimal weight: 0.8980 chunk 919 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 GLN A1583 GLN A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1890 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN J 373 HIS M 141 GLN M 165 ASN O 251 HIS R 104 GLN S 38 ASN ** T 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 451 HIS ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 79978 Z= 0.223 Angle : 0.640 17.195 110891 Z= 0.333 Chirality : 0.043 0.326 13342 Planarity : 0.005 0.080 13281 Dihedral : 16.960 179.984 17129 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.04 % Favored : 93.63 % Rotamer: Outliers : 4.90 % Allowed : 19.19 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.13 % 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: 0.17 (0.09), residues: 10189 helix: 1.70 (0.08), residues: 4361 sheet: -0.09 (0.14), residues: 1294 loop : -1.48 (0.09), residues: 4534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1637 HIS 0.007 0.001 HIS A 884 PHE 0.042 0.002 PHE A 166 TYR 0.026 0.002 TYR A1369 ARG 0.011 0.001 ARG L 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 706 time to evaluate : 6.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7989 (tp) REVERT: A 341 LYS cc_start: 0.7191 (mppt) cc_final: 0.6900 (ptpp) REVERT: A 498 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7583 (ttp-170) REVERT: A 779 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8808 (mt) REVERT: A 1185 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8094 (pt) REVERT: A 1249 MET cc_start: 0.7345 (mtt) cc_final: 0.7099 (mtm) REVERT: A 1332 HIS cc_start: 0.5532 (OUTLIER) cc_final: 0.5224 (m-70) REVERT: A 1370 ARG cc_start: 0.6349 (tpt170) cc_final: 0.5984 (ttp80) REVERT: A 1408 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 1427 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7751 (ttp80) REVERT: A 1822 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7505 (mt) REVERT: A 2014 MET cc_start: 0.4547 (mmm) cc_final: 0.4308 (mmt) REVERT: C 160 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.4922 (ptt180) REVERT: C 175 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: C 327 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6335 (t80) REVERT: C 416 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8792 (tt) REVERT: C 461 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.5068 (mm) REVERT: C 934 MET cc_start: 0.6271 (mmm) cc_final: 0.5960 (ttp) REVERT: E 165 GLN cc_start: 0.5992 (OUTLIER) cc_final: 0.5546 (mt0) REVERT: E 250 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7154 (tp) REVERT: E 265 ARG cc_start: 0.3756 (mmt90) cc_final: 0.2362 (tmm160) REVERT: L 59 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8067 (mtmm) REVERT: M 146 MET cc_start: 0.7743 (mmm) cc_final: 0.7490 (mmm) REVERT: M 156 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.6360 (m170) REVERT: N 5 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8557 (mmtm) REVERT: O 123 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6660 (ttp80) REVERT: P 73 GLU cc_start: 0.7058 (tp30) cc_final: 0.6692 (tp30) REVERT: P 188 TRP cc_start: 0.6220 (OUTLIER) cc_final: 0.4735 (p-90) REVERT: S 25 LEU cc_start: 0.8325 (mt) cc_final: 0.8043 (mt) REVERT: S 61 MET cc_start: 0.8316 (pp-130) cc_final: 0.7872 (pp-130) REVERT: W 93 PHE cc_start: 0.6676 (m-10) cc_final: 0.6272 (m-80) REVERT: W 158 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.5746 (mp0) REVERT: W 218 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.4205 (tm-30) REVERT: U 662 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6728 (mp) REVERT: U 820 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7581 (p90) outliers start: 245 outliers final: 104 residues processed: 880 average time/residue: 1.4494 time to fit residues: 1775.1862 Evaluate side-chains 788 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 660 time to evaluate : 5.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1143 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1822 ILE Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 137 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 158 GLU Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 586 GLU Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 767 VAL Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain U residue 818 LEU Chi-restraints excluded: chain U residue 820 TYR Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 344 optimal weight: 0.5980 chunk 922 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 601 optimal weight: 50.0000 chunk 252 optimal weight: 10.0000 chunk 1025 optimal weight: 30.0000 chunk 851 optimal weight: 0.0370 chunk 474 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 538 optimal weight: 10.0000 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN A1710 ASN A1784 ASN A1913 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 902 HIS E 116 HIS E 215 ASN M 141 GLN M 165 ASN M 235 GLN O 251 HIS O 289 ASN R 104 GLN ** T 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 451 HIS W 163 GLN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 79978 Z= 0.191 Angle : 0.619 15.805 110891 Z= 0.321 Chirality : 0.042 0.266 13342 Planarity : 0.004 0.099 13281 Dihedral : 16.744 179.460 17125 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.31 % Favored : 93.38 % Rotamer: Outliers : 4.56 % Allowed : 20.07 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.11 % 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: 0.40 (0.09), residues: 10189 helix: 1.96 (0.08), residues: 4358 sheet: -0.09 (0.14), residues: 1337 loop : -1.40 (0.09), residues: 4494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1637 HIS 0.007 0.001 HIS J 294 PHE 0.037 0.001 PHE A 166 TYR 0.024 0.001 TYR A1369 ARG 0.012 0.000 ARG L 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 695 time to evaluate : 5.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.3882 (m-30) REVERT: A 204 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 227 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6812 (mtm180) REVERT: A 341 LYS cc_start: 0.7065 (mppt) cc_final: 0.6792 (ptpp) REVERT: A 498 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7460 (ttp-170) REVERT: A 1192 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7198 (p90) REVERT: A 1249 MET cc_start: 0.7355 (mtt) cc_final: 0.7087 (mtm) REVERT: A 1408 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 1498 TRP cc_start: 0.7449 (p90) cc_final: 0.7211 (p90) REVERT: A 2014 MET cc_start: 0.4529 (mmm) cc_final: 0.4307 (mmt) REVERT: C 160 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5108 (ptm160) REVERT: C 291 MET cc_start: 0.6456 (tmt) cc_final: 0.6185 (ppp) REVERT: C 327 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6356 (t80) REVERT: C 461 LEU cc_start: 0.5433 (OUTLIER) cc_final: 0.5128 (tm) REVERT: C 934 MET cc_start: 0.6032 (mmm) cc_final: 0.5722 (ttp) REVERT: E 165 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5566 (mt0) REVERT: E 250 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7146 (tp) REVERT: E 265 ARG cc_start: 0.3594 (mmt90) cc_final: 0.2234 (tmm160) REVERT: J 212 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6747 (tp40) REVERT: J 343 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6930 (mp0) REVERT: L 59 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8144 (mtmm) REVERT: L 258 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7486 (mtm-85) REVERT: M 156 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6325 (m170) REVERT: N 5 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8625 (mmtm) REVERT: O 123 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6551 (ttp80) REVERT: P 188 TRP cc_start: 0.6453 (OUTLIER) cc_final: 0.4938 (p-90) REVERT: S 55 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.5980 (ttp80) REVERT: S 61 MET cc_start: 0.8275 (pp-130) cc_final: 0.7866 (pp-130) REVERT: W 93 PHE cc_start: 0.6400 (m-10) cc_final: 0.6000 (m-80) REVERT: W 218 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.4002 (tm-30) REVERT: U 662 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6612 (mp) REVERT: U 686 LYS cc_start: 0.7572 (ttpm) cc_final: 0.7194 (tptp) outliers start: 228 outliers final: 110 residues processed: 863 average time/residue: 1.3689 time to fit residues: 1637.5371 Evaluate side-chains 780 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 649 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1693 SER Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 537 TYR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 586 GLU Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 988 optimal weight: 0.0070 chunk 115 optimal weight: 0.6980 chunk 584 optimal weight: 5.9990 chunk 748 optimal weight: 40.0000 chunk 580 optimal weight: 2.9990 chunk 863 optimal weight: 40.0000 chunk 572 optimal weight: 0.5980 chunk 1021 optimal weight: 50.0000 chunk 639 optimal weight: 50.0000 chunk 622 optimal weight: 30.0000 chunk 471 optimal weight: 0.8980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 HIS A1460 HIS A1710 ASN A1913 GLN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN M 141 GLN M 165 ASN M 235 GLN R 104 GLN T 216 ASN ** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 79978 Z= 0.196 Angle : 0.615 14.307 110891 Z= 0.319 Chirality : 0.042 0.265 13342 Planarity : 0.004 0.077 13281 Dihedral : 16.616 178.464 17124 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.13 % Favored : 93.57 % Rotamer: Outliers : 4.08 % Allowed : 21.17 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 10189 helix: 2.08 (0.08), residues: 4358 sheet: -0.05 (0.14), residues: 1342 loop : -1.36 (0.09), residues: 4489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 179 HIS 0.007 0.001 HIS C 538 PHE 0.037 0.001 PHE A 166 TYR 0.042 0.001 TYR C 537 ARG 0.020 0.000 ARG U 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 682 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7771 (mtm-85) REVERT: A 180 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.3826 (m-30) REVERT: A 204 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7859 (tp) REVERT: A 498 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7478 (ttp-170) REVERT: A 868 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: A 1249 MET cc_start: 0.7317 (mtt) cc_final: 0.7061 (mtm) REVERT: A 1332 HIS cc_start: 0.5228 (OUTLIER) cc_final: 0.4998 (m-70) REVERT: A 1408 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 1498 TRP cc_start: 0.7431 (p90) cc_final: 0.7201 (p90) REVERT: C 137 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7864 (t-90) REVERT: C 160 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5097 (ptm160) REVERT: C 291 MET cc_start: 0.6430 (tmt) cc_final: 0.6229 (ppp) REVERT: C 327 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6741 (t80) REVERT: C 416 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8722 (tt) REVERT: C 461 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.5152 (tm) REVERT: C 934 MET cc_start: 0.5963 (mmm) cc_final: 0.5604 (mtp) REVERT: E 90 ILE cc_start: 0.7509 (mm) cc_final: 0.7304 (mp) REVERT: E 165 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.5546 (mt0) REVERT: E 208 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5519 (mp) REVERT: E 265 ARG cc_start: 0.3833 (mmt90) cc_final: 0.2359 (tmm160) REVERT: J 212 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6879 (tp40) REVERT: L 258 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7506 (mtm-85) REVERT: M 146 MET cc_start: 0.7863 (mmm) cc_final: 0.7492 (mmm) REVERT: M 156 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.6355 (m170) REVERT: N 5 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8661 (mmtm) REVERT: N 76 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: O 72 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: O 123 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6544 (ttp80) REVERT: O 160 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7677 (m-40) REVERT: P 72 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6604 (ptp-110) REVERT: P 73 GLU cc_start: 0.7072 (tp30) cc_final: 0.6684 (tp30) REVERT: P 188 TRP cc_start: 0.6523 (OUTLIER) cc_final: 0.4998 (p-90) REVERT: R 202 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8186 (ttp) REVERT: S 55 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.5990 (ttp80) REVERT: S 61 MET cc_start: 0.8278 (pp-130) cc_final: 0.7818 (pp-130) REVERT: W 93 PHE cc_start: 0.6455 (m-10) cc_final: 0.6016 (m-80) REVERT: W 218 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.3995 (tm-30) REVERT: U 662 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6711 (mp) REVERT: U 686 LYS cc_start: 0.7456 (ttpm) cc_final: 0.7180 (tptp) outliers start: 204 outliers final: 108 residues processed: 844 average time/residue: 1.3725 time to fit residues: 1605.1322 Evaluate side-chains 778 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 642 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1693 SER Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 72 GLN Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 632 optimal weight: 20.0000 chunk 407 optimal weight: 3.9990 chunk 610 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 649 optimal weight: 6.9990 chunk 696 optimal weight: 6.9990 chunk 505 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 803 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN ** A1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 905 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN M 165 ASN M 235 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 GLN R 104 GLN T 446 ASN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 79978 Z= 0.536 Angle : 0.778 15.184 110891 Z= 0.401 Chirality : 0.050 0.439 13342 Planarity : 0.006 0.165 13281 Dihedral : 16.743 179.862 17124 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.04 % Favored : 92.63 % Rotamer: Outliers : 4.76 % Allowed : 21.07 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.12 % 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: 0.14 (0.09), residues: 10189 helix: 1.73 (0.08), residues: 4367 sheet: -0.22 (0.14), residues: 1424 loop : -1.55 (0.09), residues: 4398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 179 HIS 0.012 0.002 HIS A 73 PHE 0.048 0.003 PHE O 20 TYR 0.051 0.003 TYR U 590 ARG 0.016 0.001 ARG L 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 637 time to evaluate : 6.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7916 (mtm-85) REVERT: A 204 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 498 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7624 (ttp-170) REVERT: A 779 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8846 (mp) REVERT: A 1332 HIS cc_start: 0.5759 (OUTLIER) cc_final: 0.5331 (m-70) REVERT: A 1408 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 1865 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7851 (mmm-85) REVERT: C 160 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5194 (ptm160) REVERT: C 327 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6421 (t80) REVERT: C 416 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8892 (tt) REVERT: C 461 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4621 (tm) REVERT: C 935 ILE cc_start: 0.6553 (mm) cc_final: 0.6316 (mm) REVERT: E 165 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5607 (mt0) REVERT: E 208 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5691 (mp) REVERT: J 212 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6822 (tp40) REVERT: J 343 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7077 (mp0) REVERT: J 410 HIS cc_start: 0.4558 (OUTLIER) cc_final: 0.3273 (m90) REVERT: L 59 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8346 (mtmm) REVERT: L 258 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7534 (mtm-85) REVERT: M 146 MET cc_start: 0.8142 (mmm) cc_final: 0.7757 (mmm) REVERT: M 156 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6447 (m170) REVERT: O 123 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6617 (ttp80) REVERT: P 72 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6581 (ptp-110) REVERT: P 188 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.5588 (p-90) REVERT: R 163 MET cc_start: 0.6550 (pmm) cc_final: 0.6332 (ptp) REVERT: R 202 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8037 (ttp) REVERT: S 55 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.5883 (ttp80) REVERT: S 61 MET cc_start: 0.8361 (pp-130) cc_final: 0.7905 (pp-130) REVERT: S 125 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7097 (ptpp) REVERT: W 93 PHE cc_start: 0.6628 (m-10) cc_final: 0.6061 (m-10) REVERT: U 662 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6837 (mp) outliers start: 238 outliers final: 123 residues processed: 825 average time/residue: 1.3929 time to fit residues: 1587.4153 Evaluate side-chains 769 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 622 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1568 THR Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1693 SER Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain J residue 410 HIS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 137 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 929 optimal weight: 30.0000 chunk 978 optimal weight: 50.0000 chunk 893 optimal weight: 50.0000 chunk 952 optimal weight: 10.0000 chunk 573 optimal weight: 0.9990 chunk 414 optimal weight: 0.9990 chunk 747 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 860 optimal weight: 20.0000 chunk 900 optimal weight: 50.0000 chunk 948 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 426 GLN M 141 GLN M 165 ASN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN ** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 79978 Z= 0.329 Angle : 0.677 15.195 110891 Z= 0.350 Chirality : 0.045 0.333 13342 Planarity : 0.005 0.083 13281 Dihedral : 16.626 179.470 17124 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.29 % Favored : 93.41 % Rotamer: Outliers : 3.62 % Allowed : 22.41 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.13 % 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: 0.30 (0.09), residues: 10189 helix: 1.89 (0.08), residues: 4365 sheet: -0.13 (0.14), residues: 1375 loop : -1.48 (0.09), residues: 4449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 179 HIS 0.007 0.001 HIS A1024 PHE 0.046 0.002 PHE A 166 TYR 0.036 0.002 TYR U 590 ARG 0.015 0.001 ARG L 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 645 time to evaluate : 6.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7832 (mtm-85) REVERT: A 204 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 498 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7603 (ttp-170) REVERT: A 1332 HIS cc_start: 0.5917 (OUTLIER) cc_final: 0.5410 (m-70) REVERT: A 1865 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7839 (mmm-85) REVERT: C 94 ILE cc_start: 0.7216 (pt) cc_final: 0.6737 (pt) REVERT: C 160 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5143 (ptm160) REVERT: C 327 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.6427 (t80) REVERT: C 397 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6894 (p0) REVERT: C 416 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8828 (tt) REVERT: C 461 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4746 (tm) REVERT: C 820 PHE cc_start: 0.2739 (t80) cc_final: 0.2428 (t80) REVERT: E 165 GLN cc_start: 0.5998 (OUTLIER) cc_final: 0.5561 (mt0) REVERT: E 208 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5571 (mp) REVERT: E 250 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7223 (tp) REVERT: J 212 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6834 (tp40) REVERT: J 343 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7029 (mp0) REVERT: J 410 HIS cc_start: 0.4444 (OUTLIER) cc_final: 0.3197 (m90) REVERT: L 59 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8260 (mtmm) REVERT: L 100 TYR cc_start: 0.8648 (t80) cc_final: 0.8428 (t80) REVERT: M 146 MET cc_start: 0.8056 (mmm) cc_final: 0.7693 (mmm) REVERT: M 156 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.6428 (m170) REVERT: O 123 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6593 (ttp80) REVERT: P 72 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6669 (ptp-110) REVERT: P 73 GLU cc_start: 0.7088 (tp30) cc_final: 0.6775 (tp30) REVERT: P 188 TRP cc_start: 0.6819 (OUTLIER) cc_final: 0.5741 (p-90) REVERT: R 202 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8193 (ttp) REVERT: S 55 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.5849 (ttp80) REVERT: S 61 MET cc_start: 0.8396 (pp-130) cc_final: 0.7814 (pp-130) REVERT: W 93 PHE cc_start: 0.6520 (m-10) cc_final: 0.6012 (m-10) REVERT: W 218 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.4164 (tm-30) REVERT: U 662 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6672 (mp) REVERT: U 791 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7316 (mm-30) outliers start: 181 outliers final: 115 residues processed: 789 average time/residue: 1.3535 time to fit residues: 1487.5199 Evaluate side-chains 758 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 620 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1143 MET Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1693 SER Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain J residue 410 HIS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 137 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 673 GLU Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 625 optimal weight: 30.0000 chunk 1006 optimal weight: 7.9990 chunk 614 optimal weight: 40.0000 chunk 477 optimal weight: 0.8980 chunk 699 optimal weight: 8.9990 chunk 1056 optimal weight: 50.0000 chunk 971 optimal weight: 50.0000 chunk 840 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 649 optimal weight: 0.7980 chunk 515 optimal weight: 2.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN M 165 ASN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 216 ASN ** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 79978 Z= 0.351 Angle : 0.697 18.548 110891 Z= 0.359 Chirality : 0.046 0.368 13342 Planarity : 0.005 0.090 13281 Dihedral : 16.575 179.982 17124 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.72 % Favored : 92.97 % Rotamer: Outliers : 3.26 % Allowed : 22.89 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.11 % 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 (0.09), residues: 10189 helix: 1.89 (0.08), residues: 4373 sheet: -0.13 (0.14), residues: 1384 loop : -1.48 (0.09), residues: 4432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 179 HIS 0.009 0.001 HIS A 73 PHE 0.044 0.002 PHE O 20 TYR 0.029 0.002 TYR A1369 ARG 0.012 0.001 ARG S 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20378 Ramachandran restraints generated. 10189 Oldfield, 0 Emsley, 10189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 629 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7872 (mtm-85) REVERT: A 204 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 498 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7604 (ttp-170) REVERT: A 1332 HIS cc_start: 0.5942 (OUTLIER) cc_final: 0.5391 (m-70) REVERT: A 1513 MET cc_start: 0.6037 (tmm) cc_final: 0.5798 (ttt) REVERT: A 1865 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7942 (mmm-85) REVERT: C 94 ILE cc_start: 0.7240 (pt) cc_final: 0.6766 (pt) REVERT: C 160 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5210 (ptm160) REVERT: C 327 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6371 (t80) REVERT: C 397 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6854 (p0) REVERT: C 416 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8833 (tt) REVERT: E 165 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.5581 (mt0) REVERT: E 208 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5581 (mp) REVERT: E 250 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7267 (tp) REVERT: J 212 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6873 (tp40) REVERT: J 410 HIS cc_start: 0.4125 (OUTLIER) cc_final: 0.2989 (m90) REVERT: L 59 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: L 240 ARG cc_start: 0.7276 (mmm160) cc_final: 0.7021 (mtp180) REVERT: M 146 MET cc_start: 0.8102 (mmm) cc_final: 0.7548 (mmm) REVERT: M 156 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.6296 (m170) REVERT: O 123 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6583 (ttp80) REVERT: O 147 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6737 (pp) REVERT: P 72 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6704 (ptp-110) REVERT: P 188 TRP cc_start: 0.6829 (OUTLIER) cc_final: 0.5938 (p-90) REVERT: R 202 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: S 55 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.5855 (ttp80) REVERT: W 93 PHE cc_start: 0.6476 (m-10) cc_final: 0.6003 (m-10) REVERT: W 218 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.4275 (tm-30) REVERT: U 662 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6767 (mp) outliers start: 163 outliers final: 122 residues processed: 757 average time/residue: 1.3957 time to fit residues: 1469.9574 Evaluate side-chains 763 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 618 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1693 SER Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 161 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 387 GLU Chi-restraints excluded: chain J residue 410 HIS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 165 ASN Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 123 ARG Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain T residue 310 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 81 TYR Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 626 MET Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 673 GLU Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain I residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 667 optimal weight: 4.9990 chunk 895 optimal weight: 50.0000 chunk 257 optimal weight: 8.9990 chunk 775 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 842 optimal weight: 10.0000 chunk 352 optimal weight: 0.7980 chunk 864 optimal weight: 50.0000 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN M 235 GLN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.216941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.177668 restraints weight = 139772.965| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.62 r_work: 0.3462 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 79978 Z= 0.357 Angle : 0.783 59.195 110891 Z= 0.433 Chirality : 0.046 0.776 13342 Planarity : 0.005 0.192 13281 Dihedral : 16.576 179.981 17122 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.73 % Favored : 92.96 % Rotamer: Outliers : 3.50 % Allowed : 23.01 % Favored : 73.49 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.11 % 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: 0.32 (0.09), residues: 10189 helix: 1.90 (0.08), residues: 4373 sheet: -0.13 (0.14), residues: 1384 loop : -1.48 (0.09), residues: 4432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 179 HIS 0.008 0.001 HIS A 73 PHE 0.043 0.002 PHE O 20 TYR 0.177 0.002 TYR W 81 ARG 0.010 0.001 ARG U 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27588.46 seconds wall clock time: 472 minutes 16.97 seconds (28336.97 seconds total)