Starting phenix.real_space_refine on Sun Mar 17 07:00:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/03_2024/6id0_9646_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/03_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_9646/03_2024/6id0_9646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/03_2024/6id0_9646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/03_2024/6id0_9646_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id0_9646/03_2024/6id0_9646_updated.pdb" } 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 Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 861": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1195": "NH1" <-> "NH2" Residue "A ARG 1201": "NH1" <-> "NH2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "A ARG 1341": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1402": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1437": "NH1" <-> "NH2" Residue "A ARG 1439": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A ARG 1544": "NH1" <-> "NH2" Residue "A ARG 1681": "NH1" <-> "NH2" Residue "A ARG 1744": "NH1" <-> "NH2" Residue "A ARG 1746": "NH1" <-> "NH2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A TYR 1930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 273": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "T PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 550": "NH1" <-> "NH2" Residue "U ARG 556": "NH1" <-> "NH2" Residue "U ARG 585": "NH1" <-> "NH2" Residue "U TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 649": "NH1" <-> "NH2" Residue "U ARG 704": "NH1" <-> "NH2" Residue "U TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 862": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 34.53, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.11 Conformation dependent library (CDL) restraints added in 12.1 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... running ksdssp... Secondary structure from input PDB file: 362 helices and 89 sheets defined 40.0% alpha, 12.5% beta 70 base pairs and 169 stacking pairs defined. Time for finding SS restraints: 26.19 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 5.374A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 63 through 72 removed outlier: 3.861A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 105 removed outlier: 3.704A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Proline residue: A 96 - end of helix removed outlier: 3.846A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 542 through 565 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 596 through 616 removed outlier: 4.286A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 612 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 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 677 through 696 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) Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 796 removed outlier: 3.673A pdb=" N ARG A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 819 Processing helix chain 'A' and resid 835 through 847 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 913 through 932 Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 990 through 1000 Processing helix chain 'A' and resid 1003 through 1013 removed outlier: 3.642A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1053 Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1123 through 1125 No H-bonds generated for 'chain 'A' and resid 1123 through 1125' Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.702A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1248 Processing helix chain 'A' and resid 1258 through 1273 Processing helix chain 'A' and resid 1282 through 1302 Processing helix chain 'A' and resid 1314 through 1317 No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1368 through 1371 Processing helix chain 'A' and resid 1375 through 1398 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 1405 through 1411 removed outlier: 4.098A pdb=" N SER A1411 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1436 through 1445 removed outlier: 5.174A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1478 Processing helix chain 'A' and resid 1480 through 1484 Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1520 through 1524 removed outlier: 3.571A pdb=" N SER A1524 " --> pdb=" O ALA A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1537 removed outlier: 3.701A pdb=" N ARG A1532 " --> pdb=" O ILE A1529 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A1533 " --> pdb=" O PRO A1530 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1534 " --> pdb=" O ASN A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1569 through 1576 Processing helix chain 'A' and resid 1581 through 1597 Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1723 through 1735 removed outlier: 3.827A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.573A pdb=" N PHE A1772 " --> pdb=" O GLY A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1826 No H-bonds generated for 'chain 'A' and resid 1824 through 1826' Processing helix chain 'A' and resid 1837 through 1851 Processing helix chain 'A' and resid 1866 through 1875 removed outlier: 4.013A pdb=" N ASP A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1895 through 1898 Processing helix chain 'A' and resid 1900 through 1907 Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1949 through 1954 Processing helix chain 'A' and resid 1973 through 1995 removed outlier: 3.607A pdb=" N ASP A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2011 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 174 through 177 No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.677A pdb=" N SER C 212 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 214 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.196A pdb=" N LEU C 265 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 292 removed outlier: 3.696A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 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 368 through 385 Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 435 Processing helix chain 'C' and resid 443 through 452 removed outlier: 3.725A pdb=" N LYS C 446 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Proline residue: C 447 - end of helix removed outlier: 3.506A pdb=" N GLU C 450 " --> pdb=" O PRO C 447 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 452 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 467 Processing helix chain 'C' and resid 597 through 613 removed outlier: 4.168A pdb=" N LEU C 600 " --> pdb=" O PRO C 597 " (cutoff:3.500A) Proline residue: C 601 - end of helix Processing helix chain 'C' and resid 634 through 647 Processing helix chain 'C' and resid 694 through 700 Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 729 No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 756 through 776 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) Processing helix chain 'C' and resid 804 through 821 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 840 through 853 removed outlier: 3.753A pdb=" N SER C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 853 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 926 through 940 removed outlier: 3.856A pdb=" N LEU C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 937 " --> pdb=" O MET C 934 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 201 removed outlier: 3.584A pdb=" N ARG J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 238 Processing helix chain 'J' and resid 243 through 254 Processing helix chain 'J' and resid 258 through 271 Processing helix chain 'J' and resid 276 through 288 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 310 through 322 Processing helix chain 'J' and resid 326 through 339 removed outlier: 4.264A pdb=" N TRP J 339 " --> pdb=" O ARG J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 356 Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 376 through 388 Processing helix chain 'J' and resid 392 through 406 removed outlier: 3.605A pdb=" N GLU J 404 " --> pdb=" O GLU J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 430 through 439 Processing helix chain 'J' and resid 452 through 466 Processing helix chain 'J' and resid 478 through 490 Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 497 through 512 Processing helix chain 'J' and resid 521 through 533 Processing helix chain 'J' and resid 541 through 554 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 568 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 594 through 596 No H-bonds generated for 'chain 'J' and resid 594 through 596' Processing helix chain 'J' and resid 610 through 623 removed outlier: 3.503A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 642 Processing helix chain 'J' and resid 649 through 659 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) Processing helix chain 'J' and resid 666 through 678 Proline residue: J 670 - end of helix Proline residue: J 675 - end of helix Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 700 through 707 Processing helix chain 'J' and resid 719 through 729 Processing helix chain 'J' and resid 742 through 754 Processing helix chain 'J' and resid 765 through 774 Processing helix chain 'J' and resid 782 through 799 Processing helix chain 'L' and resid 13 through 26 Processing helix chain 'L' and resid 31 through 34 No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 43 through 53 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 82 through 89 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 93 through 111 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) Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 146 through 160 Processing helix chain 'L' and resid 165 through 194 Processing helix chain 'L' and resid 209 through 212 No H-bonds generated for 'chain 'L' and resid 209 through 212' Processing helix chain 'L' and resid 244 through 248 removed outlier: 3.612A pdb=" N ASP L 248 " --> pdb=" O GLN L 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 244 through 248' Processing helix chain 'L' and resid 252 through 268 Processing helix chain 'L' and resid 508 through 525 removed outlier: 3.799A pdb=" N ILE L 525 " --> pdb=" O ARG L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 533 Processing helix chain 'L' and resid 544 through 551 Proline residue: L 548 - end of helix Processing helix chain 'L' and resid 557 through 570 Proline residue: L 563 - end of helix Processing helix chain 'L' and resid 594 through 607 Processing helix chain 'L' and resid 615 through 628 Proline residue: L 620 - end of helix Processing helix chain 'L' and resid 691 through 794 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) removed outlier: 4.083A pdb=" N LEU L 792 " --> pdb=" O TYR L 788 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU L 793 " --> pdb=" O ALA L 789 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU L 794 " --> pdb=" O ASP L 790 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 141 removed outlier: 3.516A pdb=" N GLN M 131 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 160 removed outlier: 6.977A pdb=" N GLU M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU M 159 " --> pdb=" O LYS M 155 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE M 160 " --> pdb=" O HIS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 194 Processing helix chain 'M' and resid 213 through 226 removed outlier: 3.689A pdb=" N LYS M 217 " --> pdb=" O GLU M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 239 Processing helix chain 'N' and resid 13 through 34 removed outlier: 4.329A pdb=" N GLU N 16 " --> pdb=" O ASP N 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU N 17 " --> pdb=" O GLY N 14 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU N 19 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Proline residue: N 20 - end of helix removed outlier: 3.572A pdb=" N ASP N 26 " --> pdb=" O ASP N 23 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU N 33 " --> pdb=" O ARG N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 64 Proline residue: N 48 - end of helix removed outlier: 3.552A pdb=" N ILE N 52 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS N 53 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS N 56 " --> pdb=" O HIS N 53 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR N 57 " --> pdb=" O HIS N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 80 Processing helix chain 'N' and resid 86 through 92 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 123 through 125 No H-bonds generated for 'chain 'N' and resid 123 through 125' Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 94 through 99 Processing helix chain 'O' and resid 111 through 127 Processing helix chain 'O' and resid 137 through 141 Processing helix chain 'O' and resid 146 through 150 Processing helix chain 'O' and resid 166 through 169 No H-bonds generated for 'chain 'O' and resid 166 through 169' Processing helix chain 'O' and resid 176 through 178 No H-bonds generated for 'chain 'O' and resid 176 through 178' Processing helix chain 'O' and resid 192 through 194 No H-bonds generated for 'chain 'O' and resid 192 through 194' Processing helix chain 'O' and resid 198 through 203 Processing helix chain 'O' and resid 208 through 218 Processing helix chain 'O' and resid 245 through 252 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 277 through 287 Processing helix chain 'P' and resid 23 through 26 No H-bonds generated for 'chain 'P' and resid 23 through 26' Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 51 through 55 Processing helix chain 'P' and resid 59 through 77 Processing helix chain 'P' and resid 206 through 208 No H-bonds generated for 'chain 'P' and resid 206 through 208' Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'R' and resid 98 through 101 removed outlier: 3.602A pdb=" N ILE R 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 101' Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing helix chain 'R' and resid 137 through 161 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) removed outlier: 4.647A pdb=" N ALA R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 244 Processing helix chain 'R' and resid 264 through 267 No H-bonds generated for 'chain 'R' and resid 264 through 267' Processing helix chain 'R' and resid 283 through 316 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) Processing helix chain 'S' and resid 33 through 45 Processing helix chain 'S' and resid 120 through 125 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'W' and resid 102 through 105 No H-bonds generated for 'chain 'W' and resid 102 through 105' Processing helix chain 'W' and resid 122 through 134 Processing helix chain 'W' and resid 156 through 161 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) No H-bonds generated for 'chain 'W' and resid 156 through 161' Processing helix chain 'W' and resid 212 through 227 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 599 through 608 Processing helix chain 'U' and resid 615 through 621 removed outlier: 3.759A pdb=" N ARG U 620 " --> pdb=" O LYS U 616 " (cutoff:3.500A) Processing helix chain 'U' and resid 636 through 642 Processing helix chain 'U' and resid 651 through 674 Processing helix chain 'U' and resid 727 through 746 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 790 removed outlier: 4.958A pdb=" N MET U 780 " --> pdb=" O GLU U 776 " (cutoff:3.500A) Proline residue: U 782 - end of helix removed outlier: 3.819A pdb=" N MET U 790 " --> pdb=" O LYS U 786 " (cutoff:3.500A) Processing helix chain 'U' and resid 810 through 812 No H-bonds generated for 'chain 'U' and resid 810 through 812' Processing helix chain 'U' and resid 846 through 853 Processing helix chain 'U' and resid 858 through 861 No H-bonds generated for 'chain 'U' and resid 858 through 861' Processing helix chain 'U' and resid 876 through 882 removed outlier: 3.510A pdb=" N GLN U 881 " --> pdb=" O LEU U 877 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP U 882 " --> pdb=" O GLN U 878 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 165 Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 173 through 182 Proline residue: I 177 - end of helix Processing helix chain 'I' and resid 187 through 200 Processing helix chain 'I' and resid 205 through 217 Processing helix chain 'I' and resid 223 through 233 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 240 through 249 Processing helix chain 'I' and resid 255 through 268 removed outlier: 3.755A pdb=" N ILE I 267 " --> pdb=" O ASP I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.837A pdb=" N LYS I 274 " --> pdb=" O GLY I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 Processing helix chain 'I' and resid 304 through 314 Processing helix chain 'I' and resid 322 through 333 Processing helix chain 'I' and resid 338 through 349 Proline residue: I 342 - end of helix Processing helix chain 'I' and resid 357 through 366 Processing helix chain 'I' and resid 369 through 381 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 399 Proline residue: I 394 - end of helix removed outlier: 3.843A pdb=" N VAL I 399 " --> pdb=" O HIS I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 417 Processing helix chain 'I' and resid 425 through 437 Processing helix chain 'I' and resid 444 through 457 removed outlier: 4.637A pdb=" N ARG I 457 " --> pdb=" O LEU I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 476 Proline residue: I 475 - end of helix Processing helix chain 'I' and resid 487 through 498 Processing helix chain 'I' and resid 508 through 523 Proline residue: I 518 - end of helix Processing helix chain 'I' and resid 528 through 541 Processing helix chain 'I' and resid 545 through 557 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 578 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 597 Processing helix chain 'I' and resid 602 through 633 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 652 Processing helix chain 'I' and resid 664 through 675 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 688 Processing helix chain 'I' and resid 707 through 719 Processing helix chain 'I' and resid 723 through 733 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) Processing helix chain 'I' and resid 741 through 755 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 772 Processing helix chain 'I' and resid 780 through 791 Proline residue: I 788 - end of helix Processing helix chain 'I' and resid 799 through 817 Proline residue: I 816 - end of helix Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 65 through 67 No H-bonds generated for 'chain 'a' and resid 65 through 67' Processing helix chain 'b' and resid 7 through 10 No H-bonds generated for 'chain 'b' and resid 7 through 10' Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.960A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 64 No H-bonds generated for 'chain 'c' and resid 62 through 64' Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN d 34 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL d 36 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 38 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 105 No H-bonds generated for 'chain 'd' and resid 103 through 105' Processing helix chain 'f' and resid 7 through 14 Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'e' and resid 17 through 27 Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'q' and resid 27 through 36 removed outlier: 3.720A pdb=" N LYS q 32 " --> pdb=" O ARG q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 133 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 36 Processing helix chain 'r' and resid 70 through 74 Processing helix chain 'r' and resid 76 through 132 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 72 through 133 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 71 through 132 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 42 Processing helix chain 'K' and resid 66 through 77 Processing helix chain 'K' and resid 106 through 134 Processing helix chain 'K' and resid 137 through 198 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 5 through 13 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'i' and resid 7 through 12 removed outlier: 4.672A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.960A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.636A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'o' and resid 6 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 37 through 40 Processing helix chain 'o' and resid 83 through 86 No H-bonds generated for 'chain 'o' and resid 83 through 86' Processing helix chain 'o' and resid 103 through 111 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 124 through 127 Processing helix chain 'o' and resid 131 through 138 Processing helix chain 'o' and resid 152 through 160 Processing helix chain 'p' and resid 20 through 34 removed outlier: 4.195A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE p 34 " --> pdb=" O LEU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 68 Processing helix chain 'p' and resid 89 through 95 Processing helix chain 'Q' and resid 20 through 30 Processing helix chain 'Q' and resid 43 through 52 Processing helix chain 'Q' and resid 61 through 69 Processing helix chain 'Q' and resid 72 through 75 No H-bonds generated for 'chain 'Q' and resid 72 through 75' Processing helix chain 'Q' and resid 88 through 103 Processing helix chain 'Q' and resid 110 through 114 Processing helix chain 'Q' and resid 116 through 131 Proline residue: Q 120 - end of helix removed outlier: 3.609A pdb=" N LYS Q 128 " --> pdb=" O HIS Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 156 Processing helix chain 'Q' and resid 160 through 170 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 177 Processing helix chain 'Q' and resid 180 through 189 Processing helix chain 'Q' and resid 191 through 205 removed outlier: 3.997A pdb=" N LYS Q 195 " --> pdb=" O LYS Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 219 Processing helix chain 'Q' and resid 221 through 235 Processing helix chain 'Q' and resid 244 through 261 Processing helix chain 'Q' and resid 264 through 276 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 279 through 284 Processing helix chain 'Q' and resid 287 through 290 No H-bonds generated for 'chain 'Q' and resid 287 through 290' Processing helix chain 'Q' and resid 296 through 309 Processing helix chain 'Q' and resid 323 through 344 Processing helix chain 'Q' and resid 346 through 353 removed outlier: 5.090A pdb=" N ASP Q 350 " --> pdb=" O GLU Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 359 No H-bonds generated for 'chain 'Q' and resid 356 through 359' Processing helix chain 'Q' and resid 362 through 369 Processing helix chain 'Q' and resid 374 through 384 Processing helix chain 'Q' and resid 400 through 411 Processing helix chain 'Q' and resid 417 through 423 Processing helix chain 'Q' and resid 462 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 547 through 553 Processing helix chain 'Q' and resid 583 through 587 Processing helix chain 'Q' and resid 631 through 644 Processing helix chain 'Q' and resid 649 through 651 No H-bonds generated for 'chain 'Q' and resid 649 through 651' Processing helix chain 'Q' and resid 661 through 663 No H-bonds generated for 'chain 'Q' and resid 661 through 663' Processing helix chain 'Q' and resid 666 through 678 Processing helix chain 'Q' and resid 685 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 702 through 704 No H-bonds generated for 'chain 'Q' and resid 702 through 704' Processing helix chain 'Q' and resid 721 through 727 Processing helix chain 'Q' and resid 791 through 793 No H-bonds generated for 'chain 'Q' and resid 791 through 793' Processing helix chain 'Q' and resid 804 through 814 Processing helix chain 'Q' and resid 829 through 843 Processing helix chain 'Q' and resid 856 through 868 removed outlier: 3.809A pdb=" N ALA Q 868 " --> pdb=" O GLU Q 864 " (cutoff:3.500A) Processing helix chain 'Q' and resid 873 through 875 No H-bonds generated for 'chain 'Q' and resid 873 through 875' Processing helix chain 'Q' and resid 894 through 918 Processing helix chain 'Q' and resid 929 through 938 Processing helix chain 'Q' and resid 940 through 951 Processing helix chain 'Q' and resid 961 through 966 removed outlier: 3.875A pdb=" N SER Q 965 " --> pdb=" O VAL Q 961 " (cutoff:3.500A) Processing helix chain 'Q' and resid 987 through 1016 removed outlier: 4.838A pdb=" N ALA Q1013 " --> pdb=" O GLU Q1009 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER Q1014 " --> pdb=" O GLU Q1010 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU Q1015 " --> pdb=" O PHE Q1011 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1020 through 1029 Processing helix chain 'Q' and resid 1039 through 1052 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 1064 through 1066 No H-bonds generated for 'chain 'Q' and resid 1064 through 1066' Processing helix chain 'Q' and resid 1069 through 1077 Proline residue: Q1075 - end of helix Processing helix chain 'Q' and resid 1108 through 1113 Processing helix chain 'Q' and resid 1119 through 1126 Processing helix chain 'Q' and resid 1141 through 1150 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) removed outlier: 6.677A pdb=" N ARG Q1150 " --> pdb=" O LEU Q1146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1158 through 1162 Processing helix chain 'Q' and resid 1164 through 1166 No H-bonds generated for 'chain 'Q' and resid 1164 through 1166' Processing helix chain 'Q' and resid 1201 through 1217 Processing helix chain 'Q' and resid 1221 through 1223 No H-bonds generated for 'chain 'Q' and resid 1221 through 1223' Processing helix chain 'Q' and resid 1231 through 1244 Processing helix chain 'Q' and resid 1260 through 1262 No H-bonds generated for 'chain 'Q' and resid 1260 through 1262' Processing helix chain 'Q' and resid 1282 through 1285 Processing helix chain 'Q' and resid 1287 through 1295 Processing helix chain 'Q' and resid 1307 through 1311 Processing helix chain 'Q' and resid 1314 through 1325 Proline residue: Q1318 - end of helix removed outlier: 4.548A pdb=" N SER Q1321 " --> pdb=" O PRO Q1318 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR Q1324 " --> pdb=" O SER Q1321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1358 through 1375 removed outlier: 3.617A pdb=" N GLN Q1374 " --> pdb=" O MET Q1370 " (cutoff:3.500A) Processing helix chain 'y' and resid 19 through 29 Proline residue: y 28 - end of helix Processing helix chain 'y' and resid 57 through 67 Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= B, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= C, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= D, first strand: chain 'A' and resid 895 through 900 Processing sheet with id= E, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 3.523A pdb=" N LEU A1087 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= G, 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= H, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id= I, first strand: chain 'A' and resid 1629 through 1631 removed outlier: 6.770A pdb=" N VAL A1701 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN A1665 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A1703 " --> pdb=" O GLN A1665 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG A1667 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A1705 " --> pdb=" O ARG A1667 " (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= J, first strand: chain 'A' and resid 1914 through 1918 removed outlier: 6.697A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'C' and resid 308 through 310 removed outlier: 3.547A pdb=" N CYS C 308 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 225 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 198 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= N, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= O, 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= P, first strand: chain 'C' and resid 653 through 655 Processing sheet with id= Q, first strand: chain 'C' and resid 663 through 666 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= R, first strand: chain 'C' and resid 743 through 747 removed outlier: 6.894A pdb=" N VAL C 787 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL C 746 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE C 789 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 831 through 838 Processing sheet with id= T, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.723A pdb=" N SER C 498 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N HIS C 477 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 496 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id= U, 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= V, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.546A pdb=" N ALA E 127 " --> pdb=" O MET E 113 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU E 115 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE E 125 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR E 117 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N MET E 123 " --> pdb=" O TYR E 117 " (cutoff:3.500A) 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= W, first strand: chain 'E' and resid 189 through 191 removed outlier: 3.951A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU E 166 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 156 " --> pdb=" O GLY E 170 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.649A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 209 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE E 201 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) 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= Y, first strand: chain 'E' and resid 275 through 277 removed outlier: 3.770A pdb=" N LYS E 275 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing sheet with id= Z, 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= AA, first strand: chain 'E' and resid 351 through 355 Processing sheet with id= AB, first strand: chain 'O' and resid 36 through 39 Processing sheet with id= AC, first strand: chain 'O' and resid 299 through 302 Processing sheet with id= AD, first strand: chain 'R' and resid 175 through 180 Processing sheet with id= AE, 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) Processing sheet with id= AF, first strand: chain 'S' and resid 15 through 18 Processing sheet with id= AG, first strand: chain 'S' and resid 24 through 27 removed outlier: 5.083A pdb=" N GLU S 26 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL S 132 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 207 through 212 removed outlier: 6.617A pdb=" N GLY T 222 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE T 210 " --> pdb=" O VAL T 220 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL T 212 " --> pdb=" O TRP T 218 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TRP T 218 " --> pdb=" O VAL T 212 " (cutoff:3.500A) 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= AI, first strand: chain 'T' and resid 249 through 254 removed outlier: 6.652A pdb=" N CYS T 264 " --> pdb=" O ARG T 250 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL T 252 " --> pdb=" O PHE T 262 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE T 262 " --> pdb=" O VAL T 252 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL T 254 " --> pdb=" O TYR T 260 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR T 260 " --> pdb=" O VAL T 254 " (cutoff:3.500A) 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= AJ, first strand: chain 'T' and resid 291 through 296 removed outlier: 6.609A pdb=" N CYS T 306 " --> pdb=" O TYR T 292 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU T 294 " --> pdb=" O VAL T 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL T 304 " --> pdb=" O LEU T 294 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU T 296 " --> pdb=" O VAL T 302 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL T 302 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR T 311 " --> pdb=" O SER T 307 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP T 316 " --> pdb=" O SER T 322 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER T 322 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'T' and resid 345 through 348 removed outlier: 4.368A pdb=" N ILE T 345 " --> pdb=" O TRP T 357 " (cutoff:3.500A) Processing sheet with id= AL, 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) Processing sheet with id= AM, first strand: chain 'T' and resid 416 through 422 removed outlier: 7.167A pdb=" N GLY T 430 " --> pdb=" O ASN T 417 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU T 419 " --> pdb=" O VAL T 428 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL T 428 " --> pdb=" O LEU T 419 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL T 421 " --> pdb=" O VAL T 426 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL T 426 " --> pdb=" O VAL T 421 " (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= AN, first strand: chain 'T' and resid 194 through 201 removed outlier: 6.805A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL T 199 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE T 486 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA T 467 " --> pdb=" O ALA T 480 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 312 through 316 removed outlier: 3.673A pdb=" N ALA W 293 " --> pdb=" O CYS W 307 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'W' and resid 335 through 340 removed outlier: 6.795A pdb=" N ALA W 350 " --> pdb=" O ARG W 336 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE W 338 " --> pdb=" O LEU W 348 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU W 348 " --> pdb=" O ILE W 338 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE W 340 " --> pdb=" O GLN W 346 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN W 346 " --> pdb=" O PHE W 340 " (cutoff:3.500A) 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= AQ, first strand: chain 'W' and resid 379 through 381 removed outlier: 5.955A pdb=" N ASP W 404 " --> pdb=" O ILE W 410 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE W 410 " --> pdb=" O ASP W 404 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'W' and resid 421 through 425 removed outlier: 6.777A pdb=" N THR W 436 " --> pdb=" O ASN W 422 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE W 424 " --> pdb=" O VAL W 434 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL W 434 " --> pdb=" O ILE W 424 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS W 454 " --> pdb=" O VAL W 444 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU W 446 " --> pdb=" O ASP W 452 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP W 452 " --> pdb=" O GLU W 446 " (cutoff:3.500A) Processing sheet with id= AS, 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) Processing sheet with id= AT, 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= AU, first strand: chain 'W' and resid 556 through 558 Processing sheet with id= AV, first strand: chain 'U' and resid 549 through 551 Processing sheet with id= AW, first strand: chain 'U' and resid 696 through 699 Processing sheet with id= AX, first strand: chain 'U' and resid 771 through 774 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= AY, first strand: chain 'a' and resid 55 through 58 Processing sheet with id= AZ, first strand: chain 'a' and resid 60 through 63 removed outlier: 6.828A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.213A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG b 18 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL b 82 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE b 20 " --> pdb=" O MET b 80 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET b 80 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'b' and resid 70 through 72 removed outlier: 3.686A pdb=" N ALA b 33 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS b 43 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE b 31 " --> pdb=" O CYS b 43 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'c' and resid 53 through 55 Processing sheet with id= BD, first strand: chain 'c' and resid 57 through 60 removed outlier: 6.029A pdb=" N LYS c 41 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE c 29 " --> pdb=" O LYS c 41 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'd' and resid 89 through 96 Processing sheet with id= BF, first strand: chain 'd' and resid 98 through 101 removed outlier: 6.581A pdb=" N GLU d 68 " --> pdb=" O VAL d 56 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL d 56 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.570A pdb=" N GLY f 57 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.671A pdb=" N SER f 35 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA f 45 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU f 33 " --> pdb=" O ALA f 45 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.722A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY e 49 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP e 59 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE e 47 " --> pdb=" O ASP e 59 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.923A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'g' and resid 45 through 48 removed outlier: 6.474A pdb=" N GLU g 47 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASN g 56 " --> pdb=" O GLU g 47 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'q' and resid 15 through 17 Processing sheet with id= BN, first strand: chain 'r' and resid 15 through 17 Processing sheet with id= BO, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BP, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.828A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.216A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG i 18 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.686A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= BT, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.031A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= BV, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.582A pdb=" N GLU k 68 " --> pdb=" O VAL k 56 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL k 56 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.571A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.672A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.724A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.791A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.922A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.476A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'o' and resid 14 through 16 removed outlier: 7.108A pdb=" N ALA o 46 " --> pdb=" O LEU o 24 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR o 68 " --> pdb=" O ILE o 47 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU o 92 " --> pdb=" O LEU o 69 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR o 117 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'p' and resid 80 through 83 removed outlier: 3.519A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id= CF, first strand: chain 'Q' and resid 511 through 513 removed outlier: 6.825A pdb=" N ARG Q 626 " --> pdb=" O GLN Q 598 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N MET Q 600 " --> pdb=" O THR Q 624 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR Q 624 " --> pdb=" O MET Q 600 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL Q 535 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN Q 542 " --> pdb=" O ILE Q 514 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE Q 514 " --> pdb=" O ASN Q 542 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'Q' and resid 732 through 735 removed outlier: 3.609A pdb=" N PHE Q 747 " --> pdb=" O ASN Q 715 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN Q 715 " --> pdb=" O PHE Q 747 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Q 749 " --> pdb=" O ASP Q 713 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASP Q 713 " --> pdb=" O ILE Q 749 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'Q' and resid 1131 through 1133 Processing sheet with id= CI, first strand: chain 'Q' and resid 1177 through 1181 removed outlier: 6.781A pdb=" N LEU Q1301 " --> pdb=" O GLN Q1178 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE Q1180 " --> pdb=" O LEU Q1301 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE Q1303 " --> pdb=" O ILE Q1180 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'Q' and resid 1330 through 1332 Processing sheet with id= CK, first strand: chain 'y' and resid 78 through 81 3251 hydrogen bonds defined for protein. 9049 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: 40.17 Time building geometry restraints manager: 28.57 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: 91.00 - 100.78: 229 100.78 - 110.56: 26190 110.56 - 120.33: 49991 120.33 - 130.11: 33857 130.11 - 139.89: 624 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: 93 2.27 - 2.92: 32483 2.92 - 3.58: 111717 3.58 - 4.24: 174878 4.24 - 4.90: 282505 Nonbonded interactions: 601676 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 2.440 nonbonded pdb=" O4 U G 143 " pdb=" N3 U H 34 " model vdw 1.774 2.520 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 601671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 16.380 Check model and map are aligned: 0.830 Set scattering table: 0.530 Process input model: 199.270 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.530 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: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 235.030 ------------------------------------------------------------------------------- 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= 0.588 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 : 6.080 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: 1.5886 time to fit residues: 2953.8686 Evaluate side-chains 774 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 746 time to evaluate : 5.992 ------------------------------------------------------------------------------- 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: 6.9990 chunk 803 optimal weight: 9.9990 chunk 445 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 541 optimal weight: 8.9990 chunk 429 optimal weight: 8.9990 chunk 830 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 505 optimal weight: 7.9990 chunk 618 optimal weight: 10.0000 chunk 962 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 210 HIS A 333 HIS A 357 ASN A 429 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 579 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN A1014 ASN A1096 HIS A1215 ASN A1217 GLN A1227 GLN A1241 HIS A1296 GLN A1466 ASN ** A1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1531 ASN A1575 GLN ** A1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 513 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN M 165 ASN M 169 HIS ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 GLN M 236 ASN ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 14 ASN O 79 ASN O 95 GLN 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 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** W 163 GLN W 184 ASN U 665 HIS U 702 ASN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 872 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.148 79978 Z= 0.635 Angle : 0.893 16.539 110891 Z= 0.469 Chirality : 0.054 0.527 13342 Planarity : 0.007 0.140 13281 Dihedral : 17.728 176.170 17158 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.76 % Favored : 92.60 % Rotamer: Outliers : 6.24 % Allowed : 14.61 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.26 % 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: -1.41 (0.08), residues: 10189 helix: -0.12 (0.07), residues: 4266 sheet: -0.65 (0.13), residues: 1391 loop : -1.79 (0.09), residues: 4532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP O 15 HIS 0.026 0.003 HIS T 412 PHE 0.051 0.003 PHE O 20 TYR 0.066 0.004 TYR T 284 ARG 0.019 0.001 ARG T 282 *********************** 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 1045 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 733 time to evaluate : 6.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8531 (mtm-85) REVERT: A 204 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8169 (tp) REVERT: A 227 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6288 (mtm180) REVERT: A 587 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: A 699 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 893 GLU cc_start: 0.7767 (pt0) cc_final: 0.7561 (pt0) REVERT: A 1061 MET cc_start: 0.8714 (mtt) cc_final: 0.8507 (mtt) REVERT: A 1185 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8193 (pt) REVERT: A 1516 LYS cc_start: 0.3564 (OUTLIER) cc_final: 0.3267 (mptt) REVERT: A 1529 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7676 (mm) REVERT: A 1622 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7580 (mpm) REVERT: A 1822 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 1838 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8246 (mppt) REVERT: C 85 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7949 (p0) REVERT: C 160 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5124 (ptt180) REVERT: C 327 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6119 (t80) REVERT: C 630 LEU cc_start: 0.7334 (mm) cc_final: 0.6793 (tp) REVERT: C 707 ILE cc_start: 0.3357 (OUTLIER) cc_final: 0.2699 (pp) REVERT: C 938 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.3805 (mmm160) REVERT: E 124 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7186 (tp) REVERT: E 143 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6243 (mmm160) REVERT: E 165 GLN cc_start: 0.6035 (OUTLIER) cc_final: 0.5441 (mt0) REVERT: E 177 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7511 (mtmm) REVERT: E 250 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6660 (tp) REVERT: E 255 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7040 (mtp) REVERT: E 265 ARG cc_start: 0.3895 (mmt90) cc_final: 0.2789 (tmm160) REVERT: E 289 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6716 (mm) REVERT: J 212 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7544 (tp40) REVERT: J 343 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7460 (mp0) REVERT: L 209 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.4900 (p0) REVERT: M 156 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.6360 (m170) REVERT: N 23 ASP cc_start: 0.7909 (m-30) cc_final: 0.7646 (m-30) REVERT: N 76 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: R 208 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: S 61 MET cc_start: 0.8491 (pp-130) cc_final: 0.8259 (pp-130) REVERT: S 125 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6772 (ptpp) REVERT: T 276 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: T 376 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.7886 (mtp180) REVERT: W 93 PHE cc_start: 0.6891 (m-10) cc_final: 0.6403 (m-80) REVERT: W 111 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8505 (tt) REVERT: W 147 GLN cc_start: 0.4245 (mt0) cc_final: 0.3982 (mp10) REVERT: W 158 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: U 596 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: U 608 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7487 (mmm) REVERT: U 638 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7760 (p0) REVERT: U 652 GLU cc_start: 0.6704 (tm-30) cc_final: 0.5964 (pm20) REVERT: U 662 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6722 (mp) REVERT: U 686 LYS cc_start: 0.7928 (ttpm) cc_final: 0.7379 (tptt) REVERT: U 810 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7407 (pp) outliers start: 312 outliers final: 133 residues processed: 971 average time/residue: 1.4633 time to fit residues: 1931.3706 Evaluate side-chains 819 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 648 time to evaluate : 5.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 337 VAL 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 704 ASN 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 789 GLU 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 1066 GLN 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 1216 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1351 THR 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 1822 ILE Chi-restraints excluded: chain A residue 1838 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 149 LEU 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 221 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 488 VAL 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 808 ILE Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain C residue 938 ARG 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 124 LEU Chi-restraints excluded: chain E residue 143 ARG 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 250 LEU Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain E residue 280 ASN 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 376 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 209 ASP 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 M residue 165 ASN Chi-restraints excluded: chain M residue 166 SER 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 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 109 LYS 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 P residue 209 ARG 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 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 68 THR 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 376 ARG Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 413 ASN Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 158 GLU 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 193 LEU Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 538 VAL Chi-restraints excluded: chain U residue 596 ASN Chi-restraints excluded: chain U residue 608 MET 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 726 ASP Chi-restraints excluded: chain U residue 767 VAL Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 779 ASP Chi-restraints excluded: chain U residue 810 ILE Chi-restraints excluded: chain U residue 820 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1060 random chunks: chunk 534 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 801 optimal weight: 6.9990 chunk 655 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 964 optimal weight: 8.9990 chunk 1041 optimal weight: 40.0000 chunk 858 optimal weight: 30.0000 chunk 956 optimal weight: 50.0000 chunk 328 optimal weight: 9.9990 chunk 773 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 429 ASN A 457 ASN A 573 GLN A 584 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 GLN A1450 GLN A1487 HIS ** A1527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 366 GLN C 437 HIS C 477 HIS C 523 GLN C 710 ASN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 238 ASN J 373 HIS L 39 HIS M 131 GLN 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** R 104 GLN S 120 GLN T 283 HIS T 324 HIS T 437 HIS ** T 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 HIS W 82 ASN W 184 ASN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 833 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.145 79978 Z= 0.720 Angle : 0.898 17.833 110891 Z= 0.469 Chirality : 0.055 0.681 13342 Planarity : 0.007 0.146 13281 Dihedral : 17.623 177.315 17138 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.80 % Favored : 91.62 % Rotamer: Outliers : 8.24 % Allowed : 15.97 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.24 % 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: -1.05 (0.08), residues: 10189 helix: 0.38 (0.08), residues: 4233 sheet: -0.52 (0.14), residues: 1361 loop : -1.78 (0.09), residues: 4595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP O 15 HIS 0.017 0.003 HIS A 73 PHE 0.062 0.004 PHE O 20 TYR 0.055 0.004 TYR U 784 ARG 0.015 0.001 ARG J 260 *********************** 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 1104 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 692 time to evaluate : 6.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7533 (ttm-80) REVERT: A 82 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7373 (ptm160) REVERT: A 189 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7474 (pp20) REVERT: A 204 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 227 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6827 (mtm180) REVERT: A 498 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7620 (ttp-170) REVERT: A 699 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: A 1061 MET cc_start: 0.8789 (mtt) cc_final: 0.8389 (mtt) REVERT: A 1185 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8123 (pt) REVERT: A 1370 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6462 (tpm-80) REVERT: A 1427 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7701 (ttp80) REVERT: A 1598 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7387 (t0) REVERT: A 1622 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: A 1710 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8121 (m-40) REVERT: A 1838 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8352 (mppt) REVERT: C 160 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.5050 (ptt180) REVERT: C 327 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6306 (t80) REVERT: C 416 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8880 (tt) REVERT: C 832 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5095 (m-10) REVERT: C 938 ARG cc_start: 0.4585 (OUTLIER) cc_final: 0.3604 (mmm160) REVERT: E 60 MET cc_start: 0.6665 (mmm) cc_final: 0.6451 (tpt) REVERT: E 124 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7478 (mt) REVERT: E 136 TRP cc_start: 0.7987 (OUTLIER) cc_final: 0.7653 (m100) REVERT: E 143 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6990 (mmm-85) REVERT: E 165 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5684 (mt0) REVERT: E 250 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7030 (tp) REVERT: E 265 ARG cc_start: 0.4422 (mmt90) cc_final: 0.2821 (tmm160) REVERT: E 289 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6771 (mm) REVERT: J 200 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: J 212 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: J 343 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7550 (OUTLIER) REVERT: J 410 HIS cc_start: 0.5213 (OUTLIER) cc_final: 0.4067 (m90) REVERT: L 59 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8304 (mtmm) REVERT: L 209 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.5147 (p0) REVERT: M 156 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6557 (m170) REVERT: M 234 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8138 (tttt) REVERT: N 8 ARG cc_start: 0.7313 (mmt180) cc_final: 0.7085 (mmt90) REVERT: N 23 ASP cc_start: 0.7849 (m-30) cc_final: 0.7637 (m-30) REVERT: O 77 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8486 (tp) REVERT: P 72 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7071 (ptp-110) REVERT: P 188 TRP cc_start: 0.6646 (OUTLIER) cc_final: 0.5020 (p-90) REVERT: R 163 MET cc_start: 0.7151 (pmm) cc_final: 0.6710 (pmm) REVERT: R 208 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: R 235 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.7495 (mpt90) REVERT: S 61 MET cc_start: 0.8487 (pp-130) cc_final: 0.8171 (pp-130) REVERT: T 376 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: T 383 ARG cc_start: 0.7629 (mtm110) cc_final: 0.7390 (mtp180) REVERT: T 400 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7751 (t80) REVERT: T 497 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.2635 (pm20) REVERT: W 93 PHE cc_start: 0.7059 (m-10) cc_final: 0.6531 (m-80) REVERT: W 100 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6683 (mtp85) REVERT: W 129 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: W 158 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: W 211 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: U 596 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: U 638 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7905 (p0) REVERT: U 662 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6829 (mp) REVERT: U 686 LYS cc_start: 0.7756 (ttpm) cc_final: 0.7290 (tptt) REVERT: U 810 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7626 (pp) outliers start: 412 outliers final: 190 residues processed: 1015 average time/residue: 1.4238 time to fit residues: 1962.5851 Evaluate side-chains 866 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 630 time to evaluate : 6.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 623 LYS 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 704 ASN 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 780 THR Chi-restraints excluded: chain A residue 789 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 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 1255 THR Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1353 PHE Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1388 GLU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1437 ARG Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1459 ARG Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1568 THR Chi-restraints excluded: chain A residue 1598 ASP 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 1710 ASN Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1838 LYS Chi-restraints excluded: chain A residue 1849 ILE Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 139 HIS Chi-restraints excluded: chain C residue 149 LEU 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 243 ILE Chi-restraints excluded: chain C residue 253 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 488 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 652 ASP 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 832 TYR Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 938 ARG 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 89 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 296 ASP 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 200 GLU Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 220 LEU 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 277 THR Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 292 VAL 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 J residue 411 MET Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 165 ASN Chi-restraints excluded: chain M residue 166 SER 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 70 ILE Chi-restraints excluded: chain N residue 89 ILE 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 36 MET Chi-restraints excluded: chain O residue 62 ARG Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 109 LYS 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 26 LEU Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 60 ARG Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 209 ARG Chi-restraints excluded: chain P residue 214 THR 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 152 GLU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR 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 R residue 308 VAL Chi-restraints excluded: chain S residue 9 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 107 THR 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 261 LEU Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 376 ARG Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 413 ASN Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain T residue 497 GLU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 100 ARG Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 129 ARG 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 174 LYS Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 205 VAL Chi-restraints excluded: chain W residue 211 GLU Chi-restraints excluded: chain W residue 218 GLU Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 596 ASN 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 718 HIS 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 779 ASP Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain U residue 810 ILE Chi-restraints excluded: chain U residue 820 TYR Chi-restraints excluded: chain U residue 855 ASP 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: 8.9990 chunk 500 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 460 optimal weight: 0.9980 chunk 647 optimal weight: 5.9990 chunk 967 optimal weight: 5.9990 chunk 1024 optimal weight: 20.0000 chunk 505 optimal weight: 10.0000 chunk 917 optimal weight: 50.0000 chunk 276 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 361 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** A1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1816 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 HIS C 710 ASN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 ASN M 141 GLN M 165 ASN M 189 GLN 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 283 HIS ** T 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 HIS ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 79978 Z= 0.389 Angle : 0.707 17.161 110891 Z= 0.369 Chirality : 0.047 0.461 13342 Planarity : 0.005 0.087 13281 Dihedral : 17.314 179.797 17136 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.74 % Favored : 92.86 % Rotamer: Outliers : 6.86 % Allowed : 18.79 % Favored : 74.35 % 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: -0.56 (0.08), residues: 10189 helix: 0.92 (0.08), residues: 4255 sheet: -0.35 (0.14), residues: 1327 loop : -1.65 (0.09), residues: 4607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 179 HIS 0.010 0.002 HIS A 884 PHE 0.054 0.002 PHE A 166 TYR 0.026 0.002 TYR U 590 ARG 0.013 0.001 ARG L 240 *********************** 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 1029 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 686 time to evaluate : 6.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 227 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6327 (mtm180) REVERT: A 459 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 498 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7591 (ttp-170) REVERT: A 519 ASP cc_start: 0.7750 (p0) cc_final: 0.7419 (p0) REVERT: A 699 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: A 779 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8744 (mt) REVERT: A 844 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 1061 MET cc_start: 0.8730 (mtt) cc_final: 0.8437 (mtt) REVERT: A 1192 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.6620 (p90) REVERT: A 1370 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6298 (tpm-80) REVERT: A 1437 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7523 (mtt90) REVERT: A 1518 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6416 (mp) REVERT: A 1595 GLN cc_start: 0.7978 (mt0) cc_final: 0.7558 (mt0) REVERT: A 1598 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7259 (t0) REVERT: A 1622 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7711 (mpp) REVERT: A 1792 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (ttmt) REVERT: A 2014 MET cc_start: 0.4646 (mmm) cc_final: 0.4367 (mmt) REVERT: C 160 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.4837 (ptt180) REVERT: C 327 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6186 (t80) REVERT: C 416 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8872 (tt) REVERT: C 832 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.4710 (m-10) REVERT: C 841 ASP cc_start: 0.4257 (OUTLIER) cc_final: 0.3833 (p0) REVERT: C 934 MET cc_start: 0.6314 (tpt) cc_final: 0.5875 (ttp) REVERT: C 938 ARG cc_start: 0.4631 (OUTLIER) cc_final: 0.3639 (mmm160) REVERT: E 136 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.7585 (m100) REVERT: E 165 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5651 (mt0) REVERT: E 250 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6919 (tp) REVERT: E 265 ARG cc_start: 0.4218 (mmt90) cc_final: 0.2685 (tmm160) REVERT: J 212 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: J 301 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8310 (mtp-110) REVERT: L 59 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: L 251 LEU cc_start: 0.7728 (pp) cc_final: 0.7395 (pt) REVERT: M 156 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6430 (m170) REVERT: N 5 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (mmtm) REVERT: N 8 ARG cc_start: 0.7245 (mmt180) cc_final: 0.7037 (mmt90) REVERT: N 23 ASP cc_start: 0.7770 (m-30) cc_final: 0.7504 (m-30) REVERT: O 216 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6491 (mmp-170) REVERT: P 188 TRP cc_start: 0.6688 (OUTLIER) cc_final: 0.5079 (p-90) REVERT: R 163 MET cc_start: 0.7004 (pmm) cc_final: 0.6662 (pmm) REVERT: R 195 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8466 (ptp-170) REVERT: S 35 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.7026 (m) REVERT: S 61 MET cc_start: 0.8438 (pp-130) cc_final: 0.8043 (pp-130) REVERT: T 230 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8787 (mm) REVERT: T 383 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7307 (mtp180) REVERT: W 93 PHE cc_start: 0.6918 (m-10) cc_final: 0.6492 (m-80) REVERT: W 218 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.4284 (tm-30) REVERT: W 222 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5655 (ttmm) REVERT: U 596 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7799 (m-40) REVERT: U 638 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7758 (p0) REVERT: U 662 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6753 (mp) REVERT: U 686 LYS cc_start: 0.7637 (ttpm) cc_final: 0.7340 (tptt) REVERT: U 810 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7545 (pp) REVERT: U 873 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6765 (mtt90) outliers start: 343 outliers final: 155 residues processed: 942 average time/residue: 1.4151 time to fit residues: 1834.2437 Evaluate side-chains 832 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 638 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 ARG 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 413 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 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 693 ILE Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 704 ASN 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 1070 ASP 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 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1353 PHE Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1437 ARG 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 1553 VAL Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1610 GLN 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 1655 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1759 THR Chi-restraints excluded: chain A residue 1792 LYS Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 97 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 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain E residue 55 LEU 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 144 VAL Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 214 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 200 GLU Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 256 LYS Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 301 ARG Chi-restraints excluded: chain J residue 343 GLU 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 145 ASP Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 255 LYS Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 243 VAL 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 70 ILE Chi-restraints excluded: chain N residue 118 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 102 SER 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 198 ILE Chi-restraints excluded: chain O residue 216 ARG 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 188 TRP Chi-restraints excluded: chain P residue 191 ASP Chi-restraints excluded: chain P residue 209 ARG Chi-restraints excluded: chain P residue 214 THR 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 165 VAL Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 195 ARG 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 9 TRP Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 195 LYS 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 261 LEU Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 294 LEU 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 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 W residue 222 LYS Chi-restraints excluded: chain U residue 586 GLU Chi-restraints excluded: chain U residue 588 VAL Chi-restraints excluded: chain U residue 596 ASN Chi-restraints excluded: chain U residue 599 LEU 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 718 HIS Chi-restraints excluded: chain U residue 726 ASP 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 855 ASP Chi-restraints excluded: chain U residue 873 ARG 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: 50.0000 chunk 581 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 762 optimal weight: 8.9990 chunk 422 optimal weight: 40.0000 chunk 874 optimal weight: 50.0000 chunk 708 optimal weight: 30.0000 chunk 1 optimal weight: 0.9990 chunk 523 optimal weight: 2.9990 chunk 919 optimal weight: 0.0010 chunk 258 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1580 HIS A1583 GLN A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN C 710 ASN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN R 242 GLN ** T 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 79978 Z= 0.315 Angle : 0.660 17.536 110891 Z= 0.344 Chirality : 0.045 0.397 13342 Planarity : 0.005 0.083 13281 Dihedral : 17.116 179.616 17132 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.10 % Favored : 92.54 % Rotamer: Outliers : 6.74 % Allowed : 19.57 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.15 % 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: -0.27 (0.08), residues: 10189 helix: 1.26 (0.08), residues: 4257 sheet: -0.31 (0.14), residues: 1370 loop : -1.57 (0.09), residues: 4562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 15 HIS 0.008 0.001 HIS A 73 PHE 0.049 0.002 PHE A 166 TYR 0.026 0.002 TYR U 590 ARG 0.010 0.001 ARG A 603 *********************** 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 1007 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 670 time to evaluate : 6.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 227 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6302 (mtm180) REVERT: A 459 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8316 (tp) REVERT: A 519 ASP cc_start: 0.7727 (p0) cc_final: 0.7362 (p0) REVERT: A 699 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: A 779 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8736 (mt) REVERT: A 946 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: A 1185 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8068 (pt) REVERT: A 1192 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6593 (p90) REVERT: A 1307 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4551 (tpp) REVERT: A 1370 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6354 (ttp80) REVERT: A 1427 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7743 (ttp80) REVERT: A 1437 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7400 (mtt90) REVERT: A 1513 MET cc_start: 0.6240 (tmm) cc_final: 0.5766 (ttt) REVERT: A 1622 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7982 (mpm) REVERT: A 1792 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7387 (ttmt) REVERT: A 1865 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8061 (mmm-85) REVERT: A 2014 MET cc_start: 0.4622 (mmm) cc_final: 0.4344 (mmt) REVERT: C 160 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.4872 (ptt180) REVERT: C 327 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6180 (t80) REVERT: C 832 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.4996 (m-10) REVERT: C 841 ASP cc_start: 0.4093 (OUTLIER) cc_final: 0.3795 (OUTLIER) REVERT: C 934 MET cc_start: 0.6328 (tpt) cc_final: 0.6097 (tpt) REVERT: C 938 ARG cc_start: 0.4545 (OUTLIER) cc_final: 0.3566 (mmm160) REVERT: E 136 TRP cc_start: 0.8007 (OUTLIER) cc_final: 0.7604 (m100) REVERT: E 165 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5642 (mt0) REVERT: E 177 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7469 (mtmm) REVERT: E 188 GLN cc_start: 0.5838 (tm-30) cc_final: 0.5454 (tm-30) REVERT: E 265 ARG cc_start: 0.4254 (mmt90) cc_final: 0.2708 (tmm160) REVERT: E 289 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6606 (mm) REVERT: J 338 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7787 (mt-10) REVERT: J 410 HIS cc_start: 0.4392 (OUTLIER) cc_final: 0.3158 (m90) REVERT: L 59 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: L 209 ASP cc_start: 0.5647 (OUTLIER) cc_final: 0.5287 (p0) REVERT: M 156 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6361 (m170) REVERT: N 23 ASP cc_start: 0.7768 (m-30) cc_final: 0.7494 (m-30) REVERT: P 188 TRP cc_start: 0.6688 (OUTLIER) cc_final: 0.5266 (p-90) REVERT: R 163 MET cc_start: 0.7020 (pmm) cc_final: 0.6670 (pmm) REVERT: R 195 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8462 (ptp-170) REVERT: S 55 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.5956 (ttp80) REVERT: S 61 MET cc_start: 0.8396 (pp-130) cc_final: 0.8017 (pp-130) REVERT: S 125 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6630 (ptpp) REVERT: T 230 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8665 (mm) REVERT: T 383 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7400 (mtp180) REVERT: W 93 PHE cc_start: 0.6871 (m-10) cc_final: 0.6437 (m-80) REVERT: W 158 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: W 218 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.4294 (tm-30) REVERT: U 596 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7720 (m-40) REVERT: U 662 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6653 (mp) REVERT: U 673 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.5302 (tm-30) REVERT: U 686 LYS cc_start: 0.7643 (ttpm) cc_final: 0.7374 (tptt) REVERT: U 704 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7841 (mtp85) REVERT: U 761 LYS cc_start: 0.6779 (pptt) cc_final: 0.6502 (pptt) outliers start: 337 outliers final: 158 residues processed: 921 average time/residue: 1.3875 time to fit residues: 1748.5937 Evaluate side-chains 834 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 638 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 97 HIS 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 215 ASP Chi-restraints excluded: chain A residue 227 ARG 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 427 VAL Chi-restraints excluded: chain A residue 459 LEU 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 699 GLU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 946 GLU 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 1070 ASP 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 1306 LYS Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1388 GLU Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1437 ARG Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1459 ARG 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 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 1759 THR Chi-restraints excluded: chain A residue 1792 LYS Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1865 ARG 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 162 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 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 457 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain E residue 55 LEU 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 144 VAL Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 237 LYS 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 372 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 77 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain L residue 231 ASN 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 186 LEU 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 89 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 109 LYS 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 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 188 TRP 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 165 VAL Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 195 ARG 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 9 TRP Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain T residue 195 LYS Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 230 ILE Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 294 LEU 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 T residue 449 ARG Chi-restraints excluded: chain W residue 122 ASP 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 538 VAL Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 561 ASN Chi-restraints excluded: chain U residue 596 ASN 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 673 GLU Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 704 ARG Chi-restraints excluded: chain U residue 706 LEU Chi-restraints excluded: chain U residue 718 HIS 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 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: 0.8980 chunk 922 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 601 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 1025 optimal weight: 8.9990 chunk 851 optimal weight: 0.2980 chunk 474 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 538 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 HIS A1583 GLN ** A1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN C 710 ASN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN M 165 ASN M 235 GLN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN T 384 HIS ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 79978 Z= 0.172 Angle : 0.588 17.211 110891 Z= 0.306 Chirality : 0.042 0.289 13342 Planarity : 0.004 0.078 13281 Dihedral : 16.838 178.611 17127 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.78 % Rotamer: Outliers : 4.98 % Allowed : 21.63 % Favored : 73.39 % 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: 0.13 (0.09), residues: 10189 helix: 1.68 (0.08), residues: 4245 sheet: -0.17 (0.14), residues: 1344 loop : -1.41 (0.09), residues: 4600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 750 HIS 0.004 0.001 HIS A1024 PHE 0.045 0.001 PHE A 166 TYR 0.023 0.001 TYR U 820 ARG 0.009 0.000 ARG A 603 *********************** 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 967 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 718 time to evaluate : 6.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7819 (tp) REVERT: A 331 TRP cc_start: 0.8033 (t-100) cc_final: 0.7600 (t-100) REVERT: A 498 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7528 (ttp-170) REVERT: A 519 ASP cc_start: 0.7895 (p0) cc_final: 0.7623 (p0) REVERT: A 1192 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6407 (p90) REVERT: A 1332 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4786 (m90) REVERT: A 1427 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: A 2014 MET cc_start: 0.4758 (mmm) cc_final: 0.4493 (mmt) REVERT: C 160 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5016 (ptm160) REVERT: C 162 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6557 (m-30) REVERT: C 327 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.5738 (t80) REVERT: C 416 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8790 (tt) REVERT: C 832 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: C 938 ARG cc_start: 0.4505 (OUTLIER) cc_final: 0.3488 (mmm160) REVERT: E 136 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7704 (m100) REVERT: E 188 GLN cc_start: 0.5831 (tm-30) cc_final: 0.5604 (tm-30) REVERT: J 212 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: J 338 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7796 (mt-10) REVERT: L 59 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8105 (mtmm) REVERT: L 209 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5368 (p0) REVERT: M 156 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.6223 (m170) REVERT: N 23 ASP cc_start: 0.7728 (m-30) cc_final: 0.7424 (m-30) REVERT: P 188 TRP cc_start: 0.6626 (OUTLIER) cc_final: 0.5270 (p-90) REVERT: R 163 MET cc_start: 0.6579 (pmm) cc_final: 0.6222 (pmm) REVERT: S 55 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.5900 (ttp80) REVERT: S 61 MET cc_start: 0.8339 (pp-130) cc_final: 0.7878 (pp-130) REVERT: T 383 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7484 (mtp180) REVERT: W 93 PHE cc_start: 0.6707 (m-10) cc_final: 0.6353 (m-80) REVERT: W 100 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6121 (mtp85) REVERT: W 218 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.4059 (tm-30) REVERT: U 662 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6692 (mp) REVERT: U 686 LYS cc_start: 0.7448 (ttpm) cc_final: 0.7234 (tptt) REVERT: U 760 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.6004 (mtp) REVERT: U 791 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7267 (mm-30) outliers start: 249 outliers final: 104 residues processed: 901 average time/residue: 1.3823 time to fit residues: 1708.2931 Evaluate side-chains 788 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 662 time to evaluate : 5.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 215 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 763 ARG Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1070 ASP 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 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1332 HIS Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1459 ARG 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 1826 VAL Chi-restraints excluded: chain C residue 62 ASP 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 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 247 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 CYS 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 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 209 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain M residue 146 MET 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 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 44 GLU 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 223 LEU Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain P residue 188 TRP Chi-restraints excluded: chain P residue 191 ASP Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain R residue 99 ASP 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 186 VAL Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain S residue 9 TRP 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 294 LEU 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 W residue 100 ARG Chi-restraints excluded: chain W residue 120 ILE 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 586 GLU Chi-restraints excluded: chain U residue 588 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 760 MET Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 818 LEU 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: 50.0000 chunk 115 optimal weight: 0.5980 chunk 584 optimal weight: 5.9990 chunk 748 optimal weight: 30.0000 chunk 580 optimal weight: 4.9990 chunk 863 optimal weight: 50.0000 chunk 572 optimal weight: 2.9990 chunk 1021 optimal weight: 10.0000 chunk 639 optimal weight: 50.0000 chunk 622 optimal weight: 30.0000 chunk 471 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1024 HIS A1188 ASN ** A1599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 786 ASN ** C 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** 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 119 GLN R 104 GLN S 10 GLN U 605 ASN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 79978 Z= 0.452 Angle : 0.709 14.360 110891 Z= 0.366 Chirality : 0.047 0.394 13342 Planarity : 0.006 0.128 13281 Dihedral : 16.843 178.403 17124 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.24 % Favored : 92.42 % Rotamer: Outliers : 5.88 % Allowed : 21.67 % Favored : 72.45 % 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: -0.05 (0.09), residues: 10189 helix: 1.51 (0.08), residues: 4252 sheet: -0.20 (0.14), residues: 1379 loop : -1.52 (0.09), residues: 4558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 220 HIS 0.011 0.002 HIS A 73 PHE 0.053 0.002 PHE O 20 TYR 0.029 0.002 TYR J 356 ARG 0.015 0.001 ARG R 220 *********************** 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 946 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 652 time to evaluate : 6.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7573 (mtm-85) REVERT: A 204 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 498 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7582 (ttp-170) REVERT: A 519 ASP cc_start: 0.7778 (p0) cc_final: 0.7464 (p0) REVERT: A 1192 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6608 (p90) REVERT: A 1370 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6445 (tpm-80) REVERT: A 1427 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7726 (ttp80) REVERT: A 1678 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7509 (ttp80) REVERT: A 1865 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8081 (mmm-85) REVERT: A 2014 MET cc_start: 0.4777 (mmm) cc_final: 0.4533 (mmt) REVERT: C 160 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5039 (ptm160) REVERT: C 327 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6280 (t80) REVERT: C 334 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6138 (pp) REVERT: C 416 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8845 (tt) REVERT: C 536 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6750 (ptt180) REVERT: C 832 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5339 (m-10) REVERT: C 841 ASP cc_start: 0.4442 (OUTLIER) cc_final: 0.4067 (OUTLIER) REVERT: C 938 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.4061 (mmm160) REVERT: E 106 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7858 (mtpt) REVERT: E 136 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.7680 (m100) REVERT: E 165 GLN cc_start: 0.5860 (OUTLIER) cc_final: 0.5297 (mt0) REVERT: E 177 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7762 (mtmm) REVERT: E 250 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7233 (tp) REVERT: J 212 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: J 225 LEU cc_start: 0.8976 (tp) cc_final: 0.8769 (tp) REVERT: J 321 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: J 338 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7816 (mt-10) REVERT: J 343 GLU cc_start: 0.7320 (mp0) cc_final: 0.7012 (mp0) REVERT: J 410 HIS cc_start: 0.4705 (OUTLIER) cc_final: 0.3360 (m90) REVERT: L 59 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8252 (mtmm) REVERT: L 209 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.5401 (p0) REVERT: M 156 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.6296 (m170) REVERT: M 209 ASP cc_start: 0.7950 (p0) cc_final: 0.7741 (p0) REVERT: M 234 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8063 (tttt) REVERT: N 23 ASP cc_start: 0.7798 (m-30) cc_final: 0.7557 (m-30) REVERT: P 188 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5717 (p-90) REVERT: R 106 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7831 (mm-40) REVERT: S 55 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.5912 (ttp80) REVERT: S 61 MET cc_start: 0.8439 (pp-130) cc_final: 0.7986 (pp-130) REVERT: T 376 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7856 (mtp85) REVERT: T 383 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7377 (mtp180) REVERT: T 400 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: T 481 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: W 93 PHE cc_start: 0.6678 (m-10) cc_final: 0.6230 (m-10) REVERT: W 100 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6177 (mtp85) REVERT: W 218 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.4581 (tm-30) REVERT: W 222 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5677 (ttmm) REVERT: U 636 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8805 (tt) REVERT: U 662 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6724 (mp) REVERT: U 686 LYS cc_start: 0.7856 (ttpm) cc_final: 0.7443 (tptt) REVERT: U 704 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7817 (mtp85) outliers start: 294 outliers final: 156 residues processed: 887 average time/residue: 1.4247 time to fit residues: 1732.1766 Evaluate side-chains 835 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 640 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 57 GLN 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 215 ASP 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 337 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 443 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 546 LEU 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 766 THR Chi-restraints excluded: chain A residue 934 ARG 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 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1388 GLU Chi-restraints excluded: chain A residue 1413 ASP 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 1459 ARG Chi-restraints excluded: chain A residue 1467 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 1635 TYR Chi-restraints excluded: chain A residue 1636 LYS Chi-restraints excluded: chain A residue 1678 ARG Chi-restraints excluded: chain A residue 1693 SER Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1849 ILE Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1997 VAL Chi-restraints excluded: chain C residue 78 GLU 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 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 330 THR 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 536 ARG Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain C residue 938 ARG 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 106 LYS Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 CYS 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 321 GLU 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 410 HIS Chi-restraints excluded: chain J residue 411 MET Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain M residue 148 THR 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 M residue 208 ILE Chi-restraints excluded: chain M residue 234 LYS Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 118 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 44 GLU 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 242 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 41 ILE 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 99 ASP Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 106 GLN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR 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 35 THR Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 195 LYS Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain T residue 364 THR Chi-restraints excluded: chain T residue 376 ARG Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain T residue 481 GLU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 100 ARG Chi-restraints excluded: chain W residue 120 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 W residue 222 LYS Chi-restraints excluded: chain U residue 546 VAL Chi-restraints excluded: chain U residue 588 VAL Chi-restraints excluded: chain U residue 599 LEU Chi-restraints excluded: chain U residue 614 GLN Chi-restraints excluded: chain U residue 626 MET Chi-restraints excluded: chain U residue 636 LEU Chi-restraints excluded: chain U residue 662 ILE Chi-restraints excluded: chain U residue 703 VAL Chi-restraints excluded: chain U residue 704 ARG 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: 0.9990 chunk 610 optimal weight: 40.0000 chunk 307 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 649 optimal weight: 0.0270 chunk 696 optimal weight: 9.9990 chunk 505 optimal weight: 0.0010 chunk 95 optimal weight: 0.6980 chunk 803 optimal weight: 30.0000 overall best weight: 0.7448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN C 710 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN M 141 GLN ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 GLN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 GLN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 833 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 79978 Z= 0.175 Angle : 0.599 18.555 110891 Z= 0.309 Chirality : 0.042 0.269 13342 Planarity : 0.004 0.087 13281 Dihedral : 16.682 178.895 17124 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.85 % Favored : 93.86 % Rotamer: Outliers : 4.12 % Allowed : 23.35 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.10 % 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: 0.25 (0.09), residues: 10189 helix: 1.78 (0.08), residues: 4270 sheet: -0.09 (0.14), residues: 1398 loop : -1.39 (0.09), residues: 4521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 750 HIS 0.005 0.001 HIS A1024 PHE 0.048 0.001 PHE A 166 TYR 0.023 0.001 TYR A1369 ARG 0.013 0.001 ARG R 220 *********************** 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 893 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 687 time to evaluate : 6.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8695 (mmm) cc_final: 0.8411 (mmp) REVERT: A 204 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7904 (tp) REVERT: A 331 TRP cc_start: 0.8093 (t-100) cc_final: 0.7820 (t-100) REVERT: A 498 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7578 (ttp-170) REVERT: A 519 ASP cc_start: 0.7909 (p0) cc_final: 0.7612 (p0) REVERT: A 1192 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6431 (p90) REVERT: A 1332 HIS cc_start: 0.6313 (m90) cc_final: 0.6065 (m-70) REVERT: A 1370 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6511 (ttp80) REVERT: A 1427 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7713 (ttp80) REVERT: A 2014 MET cc_start: 0.4825 (mmm) cc_final: 0.4557 (mmt) REVERT: C 160 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5045 (ptm160) REVERT: C 162 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: C 327 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6168 (t80) REVERT: C 334 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6393 (pp) REVERT: C 416 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8799 (tt) REVERT: C 822 MET cc_start: 0.2915 (pmt) cc_final: 0.2588 (pmt) REVERT: C 832 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5429 (m-10) REVERT: C 938 ARG cc_start: 0.4287 (OUTLIER) cc_final: 0.3907 (mmm160) REVERT: E 136 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7794 (m100) REVERT: E 143 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6147 (mmm160) REVERT: J 225 LEU cc_start: 0.8880 (tp) cc_final: 0.8655 (tp) REVERT: J 321 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: J 343 GLU cc_start: 0.7288 (mp0) cc_final: 0.6862 (mp0) REVERT: J 396 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7083 (ttm-80) REVERT: L 59 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8106 (mtmm) REVERT: M 156 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.6247 (m170) REVERT: N 1 MET cc_start: 0.3174 (ppp) cc_final: 0.2943 (ppp) REVERT: N 23 ASP cc_start: 0.7750 (m-30) cc_final: 0.7481 (m-30) REVERT: P 73 GLU cc_start: 0.7099 (tp30) cc_final: 0.6859 (tp30) REVERT: P 188 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.5679 (p-90) REVERT: S 55 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.5904 (ttp80) REVERT: S 61 MET cc_start: 0.8326 (pp-130) cc_final: 0.7871 (pp-130) REVERT: T 383 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7338 (mtp180) REVERT: W 77 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.4700 (mmpt) REVERT: W 93 PHE cc_start: 0.6450 (m-10) cc_final: 0.5972 (m-80) REVERT: W 100 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6024 (mtp85) REVERT: W 218 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.3989 (tm-30) REVERT: U 662 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6667 (mp) outliers start: 206 outliers final: 115 residues processed: 845 average time/residue: 1.4456 time to fit residues: 1696.8950 Evaluate side-chains 788 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 650 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 215 ASP 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 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1370 ARG 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 1459 ARG 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 1636 LYS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 78 GLU 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 179 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR 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 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 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 294 LEU Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 77 LYS Chi-restraints excluded: chain W residue 100 ARG Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 190 ASP 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 614 GLN Chi-restraints excluded: chain U residue 626 MET 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 818 LEU 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: 8.9990 chunk 978 optimal weight: 6.9990 chunk 893 optimal weight: 9.9990 chunk 952 optimal weight: 10.0000 chunk 573 optimal weight: 0.6980 chunk 414 optimal weight: 0.8980 chunk 747 optimal weight: 50.0000 chunk 292 optimal weight: 5.9990 chunk 860 optimal weight: 0.0970 chunk 900 optimal weight: 0.0170 chunk 948 optimal weight: 40.0000 overall best weight: 1.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1188 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 289 ASN M 141 GLN M 165 ASN M 235 GLN R 104 GLN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 79978 Z= 0.242 Angle : 0.627 17.769 110891 Z= 0.322 Chirality : 0.043 0.283 13342 Planarity : 0.005 0.080 13281 Dihedral : 16.592 179.979 17124 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.25 % Rotamer: Outliers : 4.00 % Allowed : 23.71 % Favored : 72.29 % 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: 0.29 (0.09), residues: 10189 helix: 1.81 (0.08), residues: 4286 sheet: -0.07 (0.14), residues: 1377 loop : -1.38 (0.09), residues: 4526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 220 HIS 0.006 0.001 HIS A 73 PHE 0.043 0.002 PHE A 166 TYR 0.027 0.002 TYR E 158 ARG 0.014 0.001 ARG R 220 *********************** 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 843 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 643 time to evaluate : 6.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7301 (ttt90) REVERT: A 204 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7880 (tp) REVERT: A 227 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6860 (mtm180) REVERT: A 498 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7536 (ttp-170) REVERT: A 519 ASP cc_start: 0.7936 (p0) cc_final: 0.7651 (p0) REVERT: A 1192 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6472 (p90) REVERT: A 1332 HIS cc_start: 0.6312 (m90) cc_final: 0.5963 (m-70) REVERT: A 1370 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6422 (tpm-80) REVERT: A 1427 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7728 (ttp80) REVERT: A 2014 MET cc_start: 0.4924 (mmm) cc_final: 0.4643 (mmt) REVERT: C 160 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5068 (ptm-80) REVERT: C 162 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6626 (m-30) REVERT: C 327 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6369 (t80) REVERT: C 334 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6405 (pp) REVERT: C 416 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8823 (tt) REVERT: C 608 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7736 (ptt90) REVERT: C 832 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.5462 (m-10) REVERT: C 841 ASP cc_start: 0.4260 (OUTLIER) cc_final: 0.4036 (OUTLIER) REVERT: C 938 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.4158 (mmm160) REVERT: E 136 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7797 (m100) REVERT: E 143 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6189 (mmm160) REVERT: J 321 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: L 59 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8144 (mtmm) REVERT: L 209 ASP cc_start: 0.5407 (OUTLIER) cc_final: 0.5047 (p0) REVERT: M 156 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.6366 (m170) REVERT: N 23 ASP cc_start: 0.7773 (m-30) cc_final: 0.7502 (m-30) REVERT: P 188 TRP cc_start: 0.6726 (OUTLIER) cc_final: 0.5722 (p-90) REVERT: R 199 MET cc_start: 0.8332 (tpp) cc_final: 0.8121 (tpp) REVERT: S 55 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.5960 (ttp80) REVERT: S 61 MET cc_start: 0.8366 (pp-130) cc_final: 0.7932 (pp-130) REVERT: T 383 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7487 (mtp180) REVERT: T 481 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: W 77 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5637 (mmpt) REVERT: W 93 PHE cc_start: 0.6244 (m-10) cc_final: 0.5824 (m-80) REVERT: W 100 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6281 (mtp85) REVERT: W 218 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.4122 (tm-30) REVERT: U 662 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6468 (mp) REVERT: U 820 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7511 (p90) outliers start: 200 outliers final: 126 residues processed: 801 average time/residue: 1.4024 time to fit residues: 1548.2596 Evaluate side-chains 792 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 637 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG 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 215 ASP Chi-restraints excluded: chain A residue 227 ARG 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 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 668 VAL 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 1015 VAL 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 1125 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1413 ASP 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 1459 ARG 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 1636 LYS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 87 GLN 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 221 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 209 ASP 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 186 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 134 CYS Chi-restraints excluded: chain N residue 137 CYS Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 242 THR 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 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 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 195 LYS Chi-restraints excluded: chain T residue 220 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain T residue 481 GLU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 77 LYS Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 100 ARG Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 167 VAL Chi-restraints excluded: chain W residue 190 ASP 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 614 GLN Chi-restraints excluded: chain U residue 626 MET 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 726 ASP Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain U residue 793 ASP Chi-restraints excluded: chain U residue 798 MET 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=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: 5.9990 chunk 477 optimal weight: 2.9990 chunk 699 optimal weight: 30.0000 chunk 1056 optimal weight: 50.0000 chunk 971 optimal weight: 9.9990 chunk 840 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 649 optimal weight: 5.9990 chunk 515 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1188 ASN A1282 GLN A1424 GLN ** A1784 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 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN M 141 GLN M 165 ASN M 235 GLN O 119 GLN R 104 GLN R 242 GLN ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 384 HIS W 172 GLN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 79978 Z= 0.591 Angle : 0.797 17.112 110891 Z= 0.408 Chirality : 0.051 0.503 13342 Planarity : 0.006 0.136 13281 Dihedral : 16.781 179.593 17124 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.78 % Favored : 91.89 % Rotamer: Outliers : 4.22 % Allowed : 23.85 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.10 % 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 (0.08), residues: 10189 helix: 1.40 (0.08), residues: 4265 sheet: -0.33 (0.14), residues: 1379 loop : -1.56 (0.09), residues: 4545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 220 HIS 0.012 0.002 HIS A 73 PHE 0.046 0.003 PHE O 20 TYR 0.036 0.003 TYR J 356 ARG 0.020 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 836 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 625 time to evaluate : 6.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7569 (mtm-85) REVERT: A 79 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7487 (ttt90) REVERT: A 204 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8214 (tp) REVERT: A 498 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: A 519 ASP cc_start: 0.7833 (p0) cc_final: 0.7525 (p0) REVERT: A 1192 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.6647 (p90) REVERT: A 1370 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6475 (tpm-80) REVERT: A 1427 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7724 (ttp80) REVERT: A 2014 MET cc_start: 0.4881 (mmm) cc_final: 0.4678 (mmt) REVERT: C 160 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5049 (ptm160) REVERT: C 327 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6394 (t80) REVERT: C 334 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6317 (pp) REVERT: C 416 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8877 (tt) REVERT: C 832 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5749 (m-10) REVERT: C 841 ASP cc_start: 0.4476 (OUTLIER) cc_final: 0.4251 (p0) REVERT: C 938 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.3851 (mmm160) REVERT: E 136 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7726 (m100) REVERT: E 165 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.5271 (mt0) REVERT: E 250 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7247 (tp) REVERT: J 321 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: J 343 GLU cc_start: 0.7698 (mp0) cc_final: 0.7387 (mp0) REVERT: L 59 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8325 (mtmm) REVERT: L 209 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.5242 (p0) REVERT: M 156 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6492 (m170) REVERT: P 188 TRP cc_start: 0.6868 (OUTLIER) cc_final: 0.6235 (p-90) REVERT: S 55 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.5929 (ttp80) REVERT: S 80 LYS cc_start: 0.7617 (tppt) cc_final: 0.7076 (mmtt) REVERT: T 400 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.8050 (t80) REVERT: W 93 PHE cc_start: 0.6674 (m-10) cc_final: 0.6118 (m-10) REVERT: W 100 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6219 (mtp85) REVERT: U 662 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6813 (mp) REVERT: U 673 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.5366 (tm-30) REVERT: U 810 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7331 (pp) outliers start: 211 outliers final: 130 residues processed: 796 average time/residue: 1.4228 time to fit residues: 1586.1993 Evaluate side-chains 765 residues out of total 9241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 607 time to evaluate : 6.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 79 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 215 ASP 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 498 ARG Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 617 ASN 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 1015 VAL 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 1190 CYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1413 ASP 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 1459 ARG Chi-restraints excluded: chain A residue 1481 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 C residue 78 GLU 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 203 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 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 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 832 TYR Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 903 HIS Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 136 TRP Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain J residue 366 TYR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 148 THR 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 21 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 118 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 44 GLU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 107 MET 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 111 VAL Chi-restraints excluded: chain R residue 157 GLN Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 180 THR 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 294 LEU Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 398 TRP Chi-restraints excluded: chain T residue 400 PHE Chi-restraints excluded: chain T residue 416 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 77 LYS Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 100 ARG Chi-restraints excluded: chain W residue 120 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 614 GLN 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 726 ASP 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 820 TYR 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: 0.9980 chunk 895 optimal weight: 40.0000 chunk 257 optimal weight: 5.9990 chunk 775 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 842 optimal weight: 10.0000 chunk 352 optimal weight: 0.7980 chunk 864 optimal weight: 50.0000 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN ** A1784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 426 GLN M 141 GLN M 165 ASN O 119 GLN R 104 GLN W 163 GLN ** U 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.217869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186365 restraints weight = 140255.360| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 1.93 r_work: 0.3799 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5100 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= 0.194 Angle : 0.627 17.510 110891 Z= 0.322 Chirality : 0.042 0.249 13342 Planarity : 0.004 0.081 13281 Dihedral : 16.575 178.101 17124 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.02 % Favored : 93.66 % Rotamer: Outliers : 3.50 % Allowed : 24.65 % Favored : 71.85 % 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: 0.25 (0.09), residues: 10189 helix: 1.80 (0.08), residues: 4274 sheet: -0.12 (0.14), residues: 1356 loop : -1.38 (0.09), residues: 4559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1839 HIS 0.005 0.001 HIS A 884 PHE 0.051 0.002 PHE A 166 TYR 0.025 0.001 TYR A1369 ARG 0.014 0.001 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27162.83 seconds wall clock time: 470 minutes 58.81 seconds (28258.81 seconds total)