Starting phenix.real_space_refine on Sun Mar 17 19:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exn_3979/03_2024/6exn_3979_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exn_3979/03_2024/6exn_3979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exn_3979/03_2024/6exn_3979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exn_3979/03_2024/6exn_3979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exn_3979/03_2024/6exn_3979_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6exn_3979/03_2024/6exn_3979_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 488 5.49 5 Mg 1 5.21 5 S 253 5.16 5 C 49139 2.51 5 N 14269 2.21 5 O 16520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 623": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A ARG 1315": "NH1" <-> "NH2" Residue "A ARG 1317": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1426": "NH1" <-> "NH2" Residue "A ARG 1456": "NH1" <-> "NH2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1543": "NH1" <-> "NH2" Residue "A TYR 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "A ARG 1753": "NH1" <-> "NH2" Residue "A PHE 1791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1904": "NH1" <-> "NH2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "A ARG 2056": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 495": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 752": "NH1" <-> "NH2" Residue "C ARG 883": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C ARG 973": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "H ARG 350": "NH1" <-> "NH2" Residue "H ARG 478": "NH1" <-> "NH2" Residue "H ARG 480": "NH1" <-> "NH2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "J ARG 193": "NH1" <-> "NH2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J ARG 254": "NH1" <-> "NH2" Residue "J ARG 256": "NH1" <-> "NH2" Residue "J ARG 400": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 216": "NH1" <-> "NH2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L ARG 134": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M ARG 237": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 285": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 174": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "O ARG 246": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 135": "NH1" <-> "NH2" Residue "S ARG 20": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S ARG 124": "NH1" <-> "NH2" Residue "S ARG 131": "NH1" <-> "NH2" Residue "S ARG 207": "NH1" <-> "NH2" Residue "V GLU 550": "OE1" <-> "OE2" Residue "V GLU 604": "OE1" <-> "OE2" Residue "V GLU 628": "OE1" <-> "OE2" Residue "V GLU 645": "OE1" <-> "OE2" Residue "V GLU 663": "OE1" <-> "OE2" Residue "V GLU 702": "OE1" <-> "OE2" Residue "V GLU 737": "OE1" <-> "OE2" Residue "V GLU 832": "OE1" <-> "OE2" Residue "V GLU 897": "OE1" <-> "OE2" Residue "V TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 116": "NH1" <-> "NH2" Residue "W ARG 141": "NH1" <-> "NH2" Residue "W ARG 146": "NH1" <-> "NH2" Residue "Y PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 215": "NH1" <-> "NH2" Residue "b ARG 11": "NH1" <-> "NH2" Residue "c ARG 161": "NH1" <-> "NH2" Residue "c ARG 170": "NH1" <-> "NH2" Residue "c ARG 173": "NH1" <-> "NH2" Residue "c TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 289": "NH1" <-> "NH2" Residue "f TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 82": "NH1" <-> "NH2" Residue "g ARG 30": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j ARG 97": "NH1" <-> "NH2" Residue "l ARG 51": "NH1" <-> "NH2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m GLU 74": "OE1" <-> "OE2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 213": "NH1" <-> "NH2" Residue "o ARG 228": "NH1" <-> "NH2" Residue "o ARG 318": "NH1" <-> "NH2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 181": "NH1" <-> "NH2" Residue "y PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 209": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80677 Number of models: 1 Model: "" Number of chains: 53 Chain: "2" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2868 Classifications: {'RNA': 136} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 13, 'rna3p_pur': 55, 'rna3p_pyr': 65} Link IDs: {'rna2p': 16, 'rna3p': 119} Chain breaks: 7 Chain: "5" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3626 Classifications: {'RNA': 171} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 70, 'rna3p_pyr': 74} Link IDs: {'rna2p': 27, 'rna3p': 143} Chain breaks: 2 Chain: "6" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2170 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 45, 'rna3p_pyr': 33} Link IDs: {'rna2p': 24, 'rna3p': 77} Chain: "A" Number of atoms: 16046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1945, 16046 Classifications: {'peptide': 1945} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 99, 'TRANS': 1841} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 6999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6999 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 48, 'TRANS': 831} Chain breaks: 5 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 579 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 5, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 130 Chain: "E" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 586 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 10, 'rna3p': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {' C%rna3p_pyr:plan2': 5, ' C%rna3p_pyr:plan': 5, ' U%rna3p_pyr:plan': 3, ' A%rna3p_pur:plan2': 3, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 2689 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 6, 'TRANS': 404} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 708 Unresolved non-hydrogen angles: 903 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 9, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 356 Chain: "I" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 804 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 17} Link IDs: {'rna2p': 10, 'rna3p': 28} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2691 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 329} Chain: "K" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1355 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain breaks: 3 Chain: "L" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1283 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "M" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2048 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "N" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1917 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Chain: "O" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2350 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 173 Chain: "P" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 600 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 2 Chain: "R" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 423 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "S" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3189 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 7, 'TRANS': 464} Chain breaks: 17 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 794 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 18, 'ASN:plan1': 3, 'TRP:plan': 8, 'ASP:plan': 12, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 545 Chain: "T" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 2957 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 548} Link IDs: {'PTRANS': 8, 'TRANS': 585} Chain breaks: 38 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 2177 Unresolved non-hydrogen angles: 2792 Unresolved non-hydrogen dihedrals: 1876 Unresolved non-hydrogen chiralities: 169 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 6, 'TYR:plan': 33, 'ASN:plan1': 24, 'TRP:plan': 19, 'ASP:plan': 28, 'PHE:plan': 31, 'GLU:plan': 64, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 1278 Chain: "V" Number of atoms: 5059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5059 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 27, 'TRANS': 610} Chain breaks: 3 Chain: "W" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1211 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain breaks: 2 Chain: "X" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 475 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'TRANS': 94} Chain breaks: 5 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'UNK:plan-1': 95} Unresolved non-hydrogen planarities: 95 Chain: "Y" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 704 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "a" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1372 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain breaks: 1 Chain: "b" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "c" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1709 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain breaks: 8 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "j" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "k" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 563 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Chain: "l" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 2 Chain: "m" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 752 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 632 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Chain: "o" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2599 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain breaks: 4 Chain: "p" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 602 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "q" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 585 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "r" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 577 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "s" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 548 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 237 Chain: "t" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 583 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 159 Chain: "u" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 578 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 588 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "w" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 568 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 151 Chain: "y" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 719 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain breaks: 2 Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" 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 41293 SG CYS L 104 177.070 182.174 104.883 1.00 59.56 S ATOM 41299 SG CYS L 105 173.819 181.836 106.765 1.00 60.56 S ATOM 41324 SG CYS L 108 176.183 178.923 106.501 1.00 59.72 S ATOM 41638 SG CYS L 148 174.305 180.136 103.459 1.00 58.31 S ATOM 41293 SG CYS L 104 177.070 182.174 104.883 1.00 59.56 S ATOM 41427 SG CYS L 122 179.167 179.105 104.244 1.00 64.23 S ATOM 41648 SG CYS L 150 177.213 180.623 101.418 1.00 60.68 S ATOM 41669 SG CYS L 153 180.199 182.407 102.844 1.00 60.56 S ATOM 41324 SG CYS L 108 176.183 178.923 106.501 1.00 59.72 S ATOM 41413 SG CYS L 120 178.779 176.200 106.574 1.00 63.08 S ATOM 41427 SG CYS L 122 179.167 179.105 104.244 1.00 64.23 S ATOM 41615 SG CYS L 145 176.486 176.526 103.648 1.00 59.95 S ATOM 42263 SG CYS M 73 170.294 158.730 91.232 1.00 62.29 S ATOM 42325 SG CYS M 81 168.012 160.793 90.094 1.00 68.11 S ATOM 42365 SG CYS M 87 170.988 161.993 92.339 1.00 66.32 S ATOM 43954 SG CYS N 34 173.216 143.211 115.957 1.00 55.28 S ATOM 43977 SG CYS N 37 171.948 141.512 119.024 1.00 56.98 S ATOM 44176 SG CYS N 61 175.140 143.543 119.177 1.00 64.50 S ATOM 44200 SG CYS N 64 175.085 140.260 117.390 1.00 65.80 S ATOM 43796 SG CYS N 13 188.463 146.148 109.169 1.00 72.77 S ATOM 43820 SG CYS N 16 185.797 148.591 108.167 1.00 71.50 S ATOM 44254 SG CYS N 71 184.934 145.707 110.412 1.00 68.07 S ATOM 44275 SG CYS N 74 185.713 145.116 106.808 1.00 71.66 S ATOM 65020 SG CYS c 122 133.435 211.856 138.777 1.00 84.21 S ATOM 65045 SG CYS c 125 131.610 213.262 135.747 1.00 79.04 S ATOM 65118 SG CYS c 135 134.088 210.402 135.403 1.00 64.53 S Time building chain proxies: 31.56, per 1000 atoms: 0.39 Number of scatterers: 80677 At special positions: 0 Unit cell: (276.64, 281.12, 246.4, 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 253 16.00 P 488 15.00 Mg 1 11.99 O 16520 8.00 N 14269 7.00 C 49139 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: 26.84 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 104 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 148 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 105 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 153 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 122 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 150 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 104 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 145 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 120 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 108 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 122 " pdb=" ZN M1000 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 73 " pdb="ZN ZN M1000 " - pdb=" NE2 HIS M 91 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 81 " pdb="ZN ZN M1000 " - pdb=" SG CYS M 87 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 64 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 34 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 61 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 74 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 16 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 71 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 13 " pdb=" ZN c 400 " pdb="ZN ZN c 400 " - pdb=" NE2 HIS c 130 " pdb="ZN ZN c 400 " - pdb=" SG CYS c 122 " pdb="ZN ZN c 400 " - pdb=" SG CYS c 125 " pdb="ZN ZN c 400 " - pdb=" SG CYS c 135 " Number of angles added : 36 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 342 helices and 84 sheets defined 44.1% alpha, 9.8% beta 139 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 27.61 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 152 through 177 removed outlier: 4.536A pdb=" N THR A 156 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 165 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 166 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 4.376A pdb=" N GLU A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 229 Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.645A pdb=" N SER A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.841A pdb=" N PHE A 506 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 533 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 564 through 586 removed outlier: 3.632A pdb=" N LYS A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 611 No H-bonds generated for 'chain 'A' and resid 608 through 611' Processing helix chain 'A' and resid 617 through 640 Processing helix chain 'A' and resid 646 through 656 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 671 through 689 removed outlier: 4.517A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 806 through 834 Processing helix chain 'A' and resid 842 through 869 removed outlier: 3.870A pdb=" N ILE A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 892 Processing helix chain 'A' and resid 908 through 920 removed outlier: 3.637A pdb=" N LEU A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 986 through 1005 removed outlier: 4.356A pdb=" N ILE A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1063 through 1072 removed outlier: 3.975A pdb=" N LEU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1108 through 1125 removed outlier: 4.230A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1113 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR A1117 " --> pdb=" O PHE A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1135 Processing helix chain 'A' and resid 1150 through 1153 No H-bonds generated for 'chain 'A' and resid 1150 through 1153' Processing helix chain 'A' and resid 1176 through 1189 removed outlier: 3.767A pdb=" N GLU A1180 " --> pdb=" O GLU A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1233 removed outlier: 3.538A pdb=" N ARG A1233 " --> pdb=" O GLU A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1328 through 1343 Processing helix chain 'A' and resid 1354 through 1373 Processing helix chain 'A' and resid 1385 through 1387 No H-bonds generated for 'chain 'A' and resid 1385 through 1387' Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1447 through 1470 removed outlier: 4.118A pdb=" N ASP A1453 " --> pdb=" O ASN A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1493 No H-bonds generated for 'chain 'A' and resid 1491 through 1493' Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 4.500A pdb=" N TYR A1504 " --> pdb=" O HIS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1517 removed outlier: 3.603A pdb=" N LYS A1515 " --> pdb=" O ARG A1511 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1549 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 3.659A pdb=" N ILE A1556 " --> pdb=" O GLY A1552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1573 No H-bonds generated for 'chain 'A' and resid 1571 through 1573' Processing helix chain 'A' and resid 1595 through 1609 Proline residue: A1602 - end of helix removed outlier: 3.695A pdb=" N ARG A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1653 through 1671 removed outlier: 4.084A pdb=" N SER A1660 " --> pdb=" O LYS A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1676 No H-bonds generated for 'chain 'A' and resid 1673 through 1676' Processing helix chain 'A' and resid 1748 through 1759 Processing helix chain 'A' and resid 1794 through 1808 Processing helix chain 'A' and resid 1810 through 1822 Processing helix chain 'A' and resid 1840 through 1842 No H-bonds generated for 'chain 'A' and resid 1840 through 1842' Processing helix chain 'A' and resid 1896 through 1898 No H-bonds generated for 'chain 'A' and resid 1896 through 1898' Processing helix chain 'A' and resid 1905 through 1923 Processing helix chain 'A' and resid 1939 through 1950 removed outlier: 3.714A pdb=" N ASP A1942 " --> pdb=" O ALA A1939 " (cutoff:3.500A) Proline residue: A1943 - end of helix removed outlier: 4.460A pdb=" N MET A1948 " --> pdb=" O GLU A1945 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A1950 " --> pdb=" O HIS A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1966 through 1970 removed outlier: 4.172A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1979 Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2019 through 2026 Processing helix chain 'A' and resid 2045 through 2067 Processing helix chain 'A' and resid 2075 through 2082 Processing helix chain 'A' and resid 2092 through 2103 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.575A pdb=" N LEU C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 219 through 230 removed outlier: 3.714A pdb=" N MET C 222 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASP C 223 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.901A pdb=" N ARG C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 removed outlier: 4.933A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.578A pdb=" N LYS C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 445 through 455 removed outlier: 4.197A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 515 removed outlier: 4.489A pdb=" N GLU C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 509 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG C 510 " --> pdb=" O SER C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 628 removed outlier: 3.545A pdb=" N LEU C 615 " --> pdb=" O PRO C 612 " (cutoff:3.500A) Proline residue: C 616 - end of helix Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 744 through 754 Processing helix chain 'C' and resid 759 through 763 Processing helix chain 'C' and resid 785 through 804 removed outlier: 4.211A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 839 through 852 Processing helix chain 'C' and resid 870 through 882 Proline residue: C 874 - end of helix removed outlier: 4.081A pdb=" N LYS C 882 " --> pdb=" O LEU C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 959 through 974 removed outlier: 5.721A pdb=" N SER C 963 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C 964 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 967 " --> pdb=" O ARG C 964 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS C 969 " --> pdb=" O PHE C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 991 No H-bonds generated for 'chain 'C' and resid 988 through 991' Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'D' and resid 129 through 151 Processing helix chain 'D' and resid 155 through 176 Processing helix chain 'D' and resid 185 through 222 Processing helix chain 'H' and resid 12 through 31 Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 37 through 46 Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 73 through 86 Processing helix chain 'H' and resid 88 through 108 Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 148 through 157 removed outlier: 4.334A pdb=" N ALA H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 165 Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 188 through 203 Processing helix chain 'H' and resid 248 through 261 Processing helix chain 'H' and resid 291 through 301 Processing helix chain 'H' and resid 306 through 314 Processing helix chain 'H' and resid 323 through 334 Processing helix chain 'H' and resid 342 through 354 Processing helix chain 'H' and resid 356 through 375 removed outlier: 4.894A pdb=" N ILE H 374 " --> pdb=" O TYR H 370 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLU H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 394 Processing helix chain 'H' and resid 400 through 402 No H-bonds generated for 'chain 'H' and resid 400 through 402' Processing helix chain 'H' and resid 415 through 432 Processing helix chain 'H' and resid 435 through 441 Processing helix chain 'H' and resid 458 through 469 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'J' and resid 111 through 120 Processing helix chain 'J' and resid 397 through 400 removed outlier: 3.612A pdb=" N ARG J 400 " --> pdb=" O GLU J 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 397 through 400' Processing helix chain 'K' and resid 40 through 43 No H-bonds generated for 'chain 'K' and resid 40 through 43' Processing helix chain 'K' and resid 60 through 83 Processing helix chain 'K' and resid 88 through 91 Processing helix chain 'K' and resid 182 through 185 No H-bonds generated for 'chain 'K' and resid 182 through 185' Processing helix chain 'K' and resid 199 through 222 removed outlier: 4.140A pdb=" N SER K 205 " --> pdb=" O MET K 202 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU K 206 " --> pdb=" O LYS K 203 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE K 219 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG K 220 " --> pdb=" O GLN K 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 34 Proline residue: L 21 - end of helix Processing helix chain 'L' and resid 47 through 67 removed outlier: 4.177A pdb=" N ILE L 52 " --> pdb=" O GLN L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 83 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 106 through 109 removed outlier: 3.621A pdb=" N ILE L 109 " --> pdb=" O LEU L 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 106 through 109' Processing helix chain 'L' and resid 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 126 through 136 Processing helix chain 'M' and resid 55 through 58 No H-bonds generated for 'chain 'M' and resid 55 through 58' Processing helix chain 'M' and resid 63 through 66 No H-bonds generated for 'chain 'M' and resid 63 through 66' Processing helix chain 'M' and resid 74 through 77 No H-bonds generated for 'chain 'M' and resid 74 through 77' Processing helix chain 'M' and resid 96 through 101 Processing helix chain 'M' and resid 142 through 145 No H-bonds generated for 'chain 'M' and resid 142 through 145' Processing helix chain 'M' and resid 153 through 164 Processing helix chain 'M' and resid 189 through 198 Processing helix chain 'M' and resid 210 through 212 No H-bonds generated for 'chain 'M' and resid 210 through 212' Processing helix chain 'M' and resid 232 through 256 Processing helix chain 'N' and resid 14 through 17 No H-bonds generated for 'chain 'N' and resid 14 through 17' Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.583A pdb=" N ARG N 68 " --> pdb=" O CYS N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 95 Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 129 through 144 Processing helix chain 'N' and resid 216 through 226 removed outlier: 3.595A pdb=" N VAL N 223 " --> pdb=" O ILE N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 264 removed outlier: 3.587A pdb=" N GLU N 260 " --> pdb=" O SER N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 323 removed outlier: 3.508A pdb=" N ILE N 310 " --> pdb=" O THR N 306 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS N 311 " --> pdb=" O ALA N 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 25 Processing helix chain 'O' and resid 33 through 37 Processing helix chain 'O' and resid 46 through 54 Processing helix chain 'O' and resid 67 through 79 removed outlier: 3.724A pdb=" N ASP O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 91 Processing helix chain 'O' and resid 95 through 106 Processing helix chain 'O' and resid 146 through 158 Processing helix chain 'O' and resid 165 through 194 Processing helix chain 'O' and resid 231 through 250 removed outlier: 3.978A pdb=" N GLN O 236 " --> pdb=" O THR O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 507 through 551 removed outlier: 6.186A pdb=" N HIS O 529 " --> pdb=" O ARG O 525 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL O 530 " --> pdb=" O LYS O 526 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN O 531 " --> pdb=" O LEU O 527 " (cutoff:3.500A) Proline residue: O 532 - end of helix removed outlier: 3.967A pdb=" N THR O 543 " --> pdb=" O GLU O 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU O 544 " --> pdb=" O MET O 540 " (cutoff:3.500A) Proline residue: O 550 - end of helix Processing helix chain 'O' and resid 556 through 589 removed outlier: 3.643A pdb=" N TYR O 560 " --> pdb=" O GLN O 556 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA O 561 " --> pdb=" O ARG O 557 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP O 562 " --> pdb=" O LYS O 558 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU O 569 " --> pdb=" O ALA O 565 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE O 570 " --> pdb=" O TYR O 566 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG O 571 " --> pdb=" O ARG O 567 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER O 572 " --> pdb=" O GLN O 568 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU O 574 " --> pdb=" O ILE O 570 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY O 575 " --> pdb=" O ARG O 571 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 164 through 172 Processing helix chain 'R' and resid 3 through 5 No H-bonds generated for 'chain 'R' and resid 3 through 5' Processing helix chain 'R' and resid 65 through 86 Processing helix chain 'R' and resid 92 through 109 Processing helix chain 'S' and resid 15 through 25 Processing helix chain 'S' and resid 40 through 59 Processing helix chain 'S' and resid 65 through 77 Processing helix chain 'S' and resid 81 through 94 Processing helix chain 'S' and resid 99 through 111 Processing helix chain 'S' and resid 115 through 128 Processing helix chain 'S' and resid 133 through 145 Processing helix chain 'S' and resid 149 through 162 removed outlier: 3.661A pdb=" N SER S 161 " --> pdb=" O THR S 157 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU S 162 " --> pdb=" O LYS S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 182 through 195 removed outlier: 3.868A pdb=" N ARG S 186 " --> pdb=" O TRP S 182 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU S 187 " --> pdb=" O ASN S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 211 Processing helix chain 'S' and resid 215 through 231 Processing helix chain 'S' and resid 240 through 254 Processing helix chain 'S' and resid 261 through 271 Processing helix chain 'S' and resid 279 through 290 Processing helix chain 'S' and resid 297 through 313 removed outlier: 3.989A pdb=" N GLU S 308 " --> pdb=" O LYS S 304 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR S 309 " --> pdb=" O ARG S 305 " (cutoff:3.500A) Processing helix chain 'S' and resid 322 through 331 Processing helix chain 'S' and resid 336 through 348 Processing helix chain 'S' and resid 357 through 376 Processing helix chain 'S' and resid 382 through 394 Processing helix chain 'S' and resid 404 through 415 Processing helix chain 'S' and resid 420 through 431 Processing helix chain 'S' and resid 440 through 449 Processing helix chain 'S' and resid 453 through 466 Processing helix chain 'S' and resid 471 through 482 Processing helix chain 'S' and resid 486 through 499 Processing helix chain 'S' and resid 508 through 520 Processing helix chain 'S' and resid 531 through 540 Processing helix chain 'S' and resid 546 through 555 Processing helix chain 'T' and resid 22 through 31 Processing helix chain 'T' and resid 38 through 47 removed outlier: 3.935A pdb=" N TYR T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP T 47 " --> pdb=" O TYR T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 66 Processing helix chain 'T' and resid 73 through 82 Processing helix chain 'T' and resid 90 through 101 Processing helix chain 'T' and resid 108 through 120 removed outlier: 3.577A pdb=" N SER T 114 " --> pdb=" O ARG T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 129 through 138 Processing helix chain 'T' and resid 146 through 158 Proline residue: T 150 - end of helix removed outlier: 3.609A pdb=" N VAL T 155 " --> pdb=" O VAL T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 175 through 190 Processing helix chain 'T' and resid 210 through 217 Processing helix chain 'T' and resid 225 through 237 Processing helix chain 'T' and resid 241 through 250 Processing helix chain 'T' and resid 271 through 281 Processing helix chain 'T' and resid 285 through 295 Processing helix chain 'T' and resid 301 through 313 Processing helix chain 'T' and resid 318 through 331 Processing helix chain 'T' and resid 340 through 364 Processing helix chain 'T' and resid 374 through 402 removed outlier: 3.507A pdb=" N ILE T 389 " --> pdb=" O PHE T 385 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP T 393 " --> pdb=" O ILE T 389 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE T 394 " --> pdb=" O ASN T 390 " (cutoff:3.500A) Processing helix chain 'T' and resid 408 through 416 Processing helix chain 'T' and resid 422 through 434 removed outlier: 3.513A pdb=" N TYR T 428 " --> pdb=" O LYS T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 460 Processing helix chain 'T' and resid 464 through 474 Processing helix chain 'T' and resid 482 through 497 removed outlier: 3.500A pdb=" N ARG T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU T 496 " --> pdb=" O ALA T 492 " (cutoff:3.500A) Processing helix chain 'T' and resid 501 through 511 Processing helix chain 'T' and resid 519 through 526 Processing helix chain 'T' and resid 542 through 555 Processing helix chain 'T' and resid 567 through 579 Processing helix chain 'T' and resid 586 through 597 Processing helix chain 'T' and resid 601 through 614 Proline residue: T 613 - end of helix Processing helix chain 'T' and resid 618 through 632 Processing helix chain 'T' and resid 642 through 654 Processing helix chain 'T' and resid 663 through 674 Processing helix chain 'T' and resid 682 through 692 Processing helix chain 'T' and resid 703 through 717 Processing helix chain 'T' and resid 725 through 735 Processing helix chain 'T' and resid 744 through 752 Processing helix chain 'T' and resid 761 through 770 Processing helix chain 'T' and resid 778 through 789 Processing helix chain 'T' and resid 794 through 806 Processing helix chain 'V' and resid 295 through 305 Processing helix chain 'V' and resid 477 through 482 Processing helix chain 'V' and resid 484 through 498 removed outlier: 3.717A pdb=" N MET V 488 " --> pdb=" O PRO V 484 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER V 490 " --> pdb=" O TYR V 486 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU V 491 " --> pdb=" O ALA V 487 " (cutoff:3.500A) Processing helix chain 'V' and resid 512 through 523 removed outlier: 4.513A pdb=" N THR V 517 " --> pdb=" O THR V 513 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN V 518 " --> pdb=" O THR V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 538 through 552 Processing helix chain 'V' and resid 581 through 590 Processing helix chain 'V' and resid 605 through 607 No H-bonds generated for 'chain 'V' and resid 605 through 607' Processing helix chain 'V' and resid 610 through 625 removed outlier: 3.613A pdb=" N ILE V 624 " --> pdb=" O LYS V 620 " (cutoff:3.500A) Processing helix chain 'V' and resid 640 through 646 removed outlier: 3.779A pdb=" N GLU V 645 " --> pdb=" O LYS V 642 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR V 646 " --> pdb=" O PHE V 643 " (cutoff:3.500A) Processing helix chain 'V' and resid 674 through 688 Processing helix chain 'V' and resid 701 through 720 removed outlier: 4.020A pdb=" N ASP V 720 " --> pdb=" O LYS V 716 " (cutoff:3.500A) Processing helix chain 'V' and resid 736 through 743 removed outlier: 3.612A pdb=" N ILE V 742 " --> pdb=" O ILE V 738 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE V 743 " --> pdb=" O GLN V 739 " (cutoff:3.500A) Processing helix chain 'V' and resid 758 through 762 removed outlier: 3.787A pdb=" N THR V 762 " --> pdb=" O ILE V 759 " (cutoff:3.500A) Processing helix chain 'V' and resid 799 through 808 Processing helix chain 'V' and resid 823 through 828 Processing helix chain 'V' and resid 844 through 852 Processing helix chain 'V' and resid 858 through 860 No H-bonds generated for 'chain 'V' and resid 858 through 860' Processing helix chain 'V' and resid 869 through 881 Processing helix chain 'V' and resid 893 through 900 Processing helix chain 'V' and resid 905 through 917 removed outlier: 4.280A pdb=" N VAL V 915 " --> pdb=" O LEU V 911 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP V 916 " --> pdb=" O LEU V 912 " (cutoff:3.500A) Processing helix chain 'V' and resid 920 through 931 Processing helix chain 'V' and resid 943 through 953 removed outlier: 3.841A pdb=" N PHE V 953 " --> pdb=" O LYS V 949 " (cutoff:3.500A) Processing helix chain 'V' and resid 959 through 970 Processing helix chain 'V' and resid 977 through 983 Processing helix chain 'V' and resid 987 through 1006 Processing helix chain 'V' and resid 1018 through 1029 Processing helix chain 'V' and resid 1088 through 1094 Processing helix chain 'W' and resid 111 through 117 removed outlier: 3.954A pdb=" N GLN W 115 " --> pdb=" O GLU W 112 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG W 116 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 145 Processing helix chain 'W' and resid 163 through 165 No H-bonds generated for 'chain 'W' and resid 163 through 165' Processing helix chain 'X' and resid 2 through 27 Processing helix chain 'X' and resid 61 through 69 Processing helix chain 'X' and resid 101 through 116 Processing helix chain 'X' and resid 131 through 141 Processing helix chain 'X' and resid 151 through 155 Processing helix chain 'X' and resid 201 through 216 Processing helix chain 'Y' and resid 41 through 47 removed outlier: 3.575A pdb=" N VAL Y 46 " --> pdb=" O GLN Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 55 Processing helix chain 'Y' and resid 79 through 89 removed outlier: 3.794A pdb=" N SER Y 83 " --> pdb=" O ILE Y 79 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU Y 84 " --> pdb=" O ASP Y 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN Y 86 " --> pdb=" O ALA Y 82 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 88 Processing helix chain 'a' and resid 97 through 101 removed outlier: 4.426A pdb=" N GLY a 101 " --> pdb=" O PRO a 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 97 through 101' Processing helix chain 'a' and resid 106 through 126 removed outlier: 3.529A pdb=" N ILE a 117 " --> pdb=" O CYS a 113 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA a 126 " --> pdb=" O SER a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 130 No H-bonds generated for 'chain 'a' and resid 128 through 130' Processing helix chain 'a' and resid 136 through 151 removed outlier: 3.562A pdb=" N PHE a 144 " --> pdb=" O LYS a 140 " (cutoff:3.500A) Proline residue: a 145 - end of helix removed outlier: 3.806A pdb=" N ARG a 151 " --> pdb=" O LEU a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 169 Processing helix chain 'a' and resid 176 through 187 Processing helix chain 'a' and resid 207 through 209 No H-bonds generated for 'chain 'a' and resid 207 through 209' Processing helix chain 'a' and resid 224 through 245 removed outlier: 3.616A pdb=" N TRP a 229 " --> pdb=" O ARG a 225 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS a 234 " --> pdb=" O ILE a 230 " (cutoff:3.500A) Processing helix chain 'b' and resid 89 through 91 No H-bonds generated for 'chain 'b' and resid 89 through 91' Processing helix chain 'c' and resid 35 through 38 No H-bonds generated for 'chain 'c' and resid 35 through 38' Processing helix chain 'c' and resid 132 through 134 No H-bonds generated for 'chain 'c' and resid 132 through 134' Processing helix chain 'c' and resid 168 through 171 No H-bonds generated for 'chain 'c' and resid 168 through 171' Processing helix chain 'c' and resid 180 through 194 Processing helix chain 'c' and resid 218 through 221 No H-bonds generated for 'chain 'c' and resid 218 through 221' Processing helix chain 'c' and resid 295 through 312 Processing helix chain 'c' and resid 333 through 344 removed outlier: 3.687A pdb=" N GLU c 344 " --> pdb=" O LYS c 340 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 13 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'd' and resid 76 through 79 removed outlier: 3.577A pdb=" N LYS d 79 " --> pdb=" O ASP d 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 76 through 79' Processing helix chain 'e' and resid 13 through 23 Processing helix chain 'f' and resid 15 through 18 No H-bonds generated for 'chain 'f' and resid 15 through 18' Processing helix chain 'g' and resid 65 through 67 No H-bonds generated for 'chain 'g' and resid 65 through 67' Processing helix chain 'h' and resid 3 through 9 removed outlier: 3.863A pdb=" N LYS h 9 " --> pdb=" O ASN h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 89 through 91 No H-bonds generated for 'chain 'h' and resid 89 through 91' Processing helix chain 'j' and resid 19 through 27 Processing helix chain 'j' and resid 32 through 35 No H-bonds generated for 'chain 'j' and resid 32 through 35' Processing helix chain 'j' and resid 37 through 40 No H-bonds generated for 'chain 'j' and resid 37 through 40' Processing helix chain 'l' and resid 3 through 9 removed outlier: 3.516A pdb=" N LEU l 7 " --> pdb=" O LEU l 3 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 61 through 67 Processing helix chain 'l' and resid 89 through 91 No H-bonds generated for 'chain 'l' and resid 89 through 91' Processing helix chain 'm' and resid 18 through 25 removed outlier: 3.785A pdb=" N GLU m 25 " --> pdb=" O LEU m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 40 removed outlier: 4.327A pdb=" N LEU m 33 " --> pdb=" O PRO m 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE m 34 " --> pdb=" O MET m 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP m 36 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA m 37 " --> pdb=" O ILE m 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET m 38 " --> pdb=" O ASN m 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR m 40 " --> pdb=" O ALA m 37 " (cutoff:3.500A) Processing helix chain 'm' and resid 98 through 100 No H-bonds generated for 'chain 'm' and resid 98 through 100' Processing helix chain 'n' and resid 6 through 13 Processing helix chain 'n' and resid 66 through 68 No H-bonds generated for 'chain 'n' and resid 66 through 68' Processing helix chain 'n' and resid 76 through 80 removed outlier: 3.772A pdb=" N LYS n 79 " --> pdb=" O ASP n 76 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN n 80 " --> pdb=" O LEU n 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 76 through 80' Processing helix chain 'o' and resid 53 through 60 Processing helix chain 'p' and resid 13 through 23 removed outlier: 3.781A pdb=" N ILE p 17 " --> pdb=" O ILE p 14 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE p 18 " --> pdb=" O ASN p 15 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN p 19 " --> pdb=" O CYS p 16 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN p 22 " --> pdb=" O ASN p 19 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN p 23 " --> pdb=" O PHE p 20 " (cutoff:3.500A) Processing helix chain 'p' and resid 84 through 86 No H-bonds generated for 'chain 'p' and resid 84 through 86' Processing helix chain 'q' and resid 15 through 20 Processing helix chain 'q' and resid 75 through 77 No H-bonds generated for 'chain 'q' and resid 75 through 77' Processing helix chain 'r' and resid 8 through 10 No H-bonds generated for 'chain 'r' and resid 8 through 10' Processing helix chain 'r' and resid 65 through 67 No H-bonds generated for 'chain 'r' and resid 65 through 67' Processing helix chain 's' and resid 16 through 30 Processing helix chain 's' and resid 86 through 93 removed outlier: 4.091A pdb=" N ARG s 93 " --> pdb=" O GLU s 89 " (cutoff:3.500A) Processing helix chain 's' and resid 114 through 117 No H-bonds generated for 'chain 's' and resid 114 through 117' Processing helix chain 's' and resid 121 through 130 Processing helix chain 's' and resid 138 through 173 removed outlier: 3.689A pdb=" N ASN s 143 " --> pdb=" O GLN s 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR s 146 " --> pdb=" O ILE s 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE s 153 " --> pdb=" O GLN s 149 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL s 154 " --> pdb=" O THR s 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU s 155 " --> pdb=" O CYS s 151 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 34 Processing helix chain 't' and resid 79 through 142 removed outlier: 3.563A pdb=" N ALA t 90 " --> pdb=" O ASN t 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS t 108 " --> pdb=" O SER t 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL t 122 " --> pdb=" O ALA t 118 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) Proline residue: t 138 - end of helix Processing helix chain 'u' and resid 25 through 34 Processing helix chain 'u' and resid 77 through 138 removed outlier: 3.709A pdb=" N THR u 82 " --> pdb=" O PRO u 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU u 93 " --> pdb=" O ASP u 89 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU u 98 " --> pdb=" O GLU u 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR u 101 " --> pdb=" O LYS u 97 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU u 102 " --> pdb=" O LEU u 98 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR u 106 " --> pdb=" O LEU u 102 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS u 107 " --> pdb=" O ASP u 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL u 112 " --> pdb=" O LYS u 108 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU u 121 " --> pdb=" O ASP u 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA u 124 " --> pdb=" O LYS u 120 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) Proline residue: u 138 - end of helix Processing helix chain 'v' and resid 25 through 34 removed outlier: 3.578A pdb=" N LYS v 33 " --> pdb=" O GLU v 29 " (cutoff:3.500A) Processing helix chain 'v' and resid 77 through 80 No H-bonds generated for 'chain 'v' and resid 77 through 80' Processing helix chain 'v' and resid 82 through 140 removed outlier: 3.502A pdb=" N LEU v 105 " --> pdb=" O THR v 101 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER v 110 " --> pdb=" O THR v 106 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR v 111 " --> pdb=" O LYS v 107 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN v 131 " --> pdb=" O LEU v 127 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU v 132 " --> pdb=" O MET v 128 " (cutoff:3.500A) Proline residue: v 138 - end of helix Processing helix chain 'w' and resid 25 through 34 removed outlier: 3.562A pdb=" N GLN w 30 " --> pdb=" O SER w 26 " (cutoff:3.500A) Processing helix chain 'w' and resid 78 through 105 removed outlier: 3.816A pdb=" N LEU w 93 " --> pdb=" O ASP w 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU w 98 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR w 101 " --> pdb=" O LYS w 97 " (cutoff:3.500A) Processing helix chain 'w' and resid 107 through 136 removed outlier: 3.780A pdb=" N THR w 111 " --> pdb=" O LYS w 107 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL w 112 " --> pdb=" O LYS w 108 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU w 121 " --> pdb=" O ASP w 117 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN w 131 " --> pdb=" O LEU w 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 97 through 115 Processing helix chain 'y' and resid 158 through 184 Processing helix chain 'y' and resid 198 through 210 Processing sheet with id= A, first strand: chain 'A' and resid 557 through 562 Processing sheet with id= B, first strand: chain 'A' and resid 300 through 302 Processing sheet with id= C, first strand: chain 'A' and resid 591 through 593 removed outlier: 3.608A pdb=" N LYS A 600 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1247 through 1251 removed outlier: 6.773A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1089 through 1091 Processing sheet with id= F, first strand: chain 'A' and resid 1257 through 1262 removed outlier: 3.871A pdb=" N GLN A1295 " --> pdb=" O ASP A1290 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1406 through 1409 Processing sheet with id= H, first strand: chain 'A' and resid 1734 through 1739 removed outlier: 6.718A pdb=" N VAL A1773 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLN A1737 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A1775 " --> pdb=" O GLN A1737 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A1739 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A1777 " --> pdb=" O ARG A1739 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1849 through 1852 removed outlier: 6.838A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 1860 through 1864 Processing sheet with id= K, first strand: chain 'A' and resid 1877 through 1882 removed outlier: 3.778A pdb=" N THR A1881 " --> pdb=" O PHE A1890 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 6.938A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 134 through 138 Processing sheet with id= N, first strand: chain 'C' and resid 234 through 236 removed outlier: 6.541A pdb=" N ALA C 262 " --> pdb=" O VAL C 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 265 through 267 removed outlier: 3.632A pdb=" N SER C 315 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE C 320 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 575 through 577 removed outlier: 6.632A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 474 through 476 removed outlier: 3.812A pdb=" N LYS C 474 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 543 through 545 removed outlier: 3.927A pdb=" N TYR C 551 " --> pdb=" O LEU C 544 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= T, first strand: chain 'C' and resid 679 through 681 Processing sheet with id= U, first strand: chain 'C' and resid 710 through 714 removed outlier: 3.504A pdb=" N LYS C 819 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 773 " --> pdb=" O TYR C 818 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU C 820 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE C 775 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 858 through 860 Processing sheet with id= W, first strand: chain 'C' and resid 905 through 907 Processing sheet with id= X, first strand: chain 'C' and resid 866 through 869 Processing sheet with id= Y, first strand: chain 'J' and resid 142 through 147 removed outlier: 7.145A pdb=" N GLY J 158 " --> pdb=" O ARG J 143 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL J 145 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE J 156 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR J 176 " --> pdb=" O VAL J 166 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 185 through 190 removed outlier: 6.885A pdb=" N VAL J 200 " --> pdb=" O ARG J 186 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL J 188 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE J 198 " --> pdb=" O VAL J 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS J 207 " --> pdb=" O SER J 199 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL J 206 " --> pdb=" O TYR J 220 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG J 218 " --> pdb=" O CYS J 208 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP J 210 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE J 216 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= AB, first strand: chain 'J' and resid 269 through 273 removed outlier: 7.010A pdb=" N SER J 284 " --> pdb=" O ASN J 270 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL J 272 " --> pdb=" O VAL J 282 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL J 282 " --> pdb=" O VAL J 272 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL J 281 " --> pdb=" O TRP J 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 302 " --> pdb=" O LEU J 292 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 313 through 316 removed outlier: 3.999A pdb=" N ALA J 313 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP J 330 " --> pdb=" O CYS J 327 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR J 343 " --> pdb=" O SER J 333 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY J 335 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU J 341 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 356 through 358 removed outlier: 3.650A pdb=" N SER J 357 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 129 through 135 removed outlier: 6.604A pdb=" N ILE J 425 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL J 134 " --> pdb=" O ILE J 423 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE J 423 " --> pdb=" O VAL J 134 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 375 through 377 removed outlier: 3.682A pdb=" N GLN J 385 " --> pdb=" O PHE J 375 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP J 377 " --> pdb=" O LYS J 383 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS J 383 " --> pdb=" O ASP J 377 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 103 through 105 removed outlier: 3.522A pdb=" N ILE K 112 " --> pdb=" O LEU K 104 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 29 through 31 removed outlier: 4.241A pdb=" N THR M 29 " --> pdb=" O SER M 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER M 38 " --> pdb=" O THR M 29 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 222 through 225 removed outlier: 3.515A pdb=" N ARG M 174 " --> pdb=" O PHE M 183 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 26 through 28 Processing sheet with id= AK, first strand: chain 'N' and resid 290 through 292 Processing sheet with id= AL, first strand: chain 'N' and resid 280 through 282 Processing sheet with id= AM, first strand: chain 'V' and resid 652 through 654 removed outlier: 9.012A pdb=" N ILE V 653 " --> pdb=" O PHE V 501 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL V 503 " --> pdb=" O ILE V 653 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL V 631 " --> pdb=" O LEU V 502 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE V 504 " --> pdb=" O VAL V 631 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL V 633 " --> pdb=" O ILE V 504 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET V 530 " --> pdb=" O SER V 598 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE V 600 " --> pdb=" O MET V 530 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY V 532 " --> pdb=" O ILE V 600 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU V 602 " --> pdb=" O GLY V 532 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR V 534 " --> pdb=" O LEU V 602 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'V' and resid 663 through 666 Processing sheet with id= AO, first strand: chain 'V' and resid 724 through 730 removed outlier: 6.446A pdb=" N ILE V 694 " --> pdb=" O VAL V 754 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA V 756 " --> pdb=" O ILE V 694 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL V 696 " --> pdb=" O ALA V 756 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU V 695 " --> pdb=" O TYR V 770 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL V 772 " --> pdb=" O LEU V 695 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE V 697 " --> pdb=" O VAL V 772 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 777 through 784 Processing sheet with id= AQ, first strand: chain 'V' and resid 1042 through 1044 Processing sheet with id= AR, first strand: chain 'V' and resid 1071 through 1074 Processing sheet with id= AS, first strand: chain 'W' and resid 56 through 58 removed outlier: 6.676A pdb=" N THR W 78 " --> pdb=" O LEU W 57 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASN W 100 " --> pdb=" O LEU W 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'Y' and resid 100 through 103 Processing sheet with id= AU, first strand: chain 'b' and resid 77 through 83 removed outlier: 5.962A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG b 28 " --> pdb=" O THR b 24 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'd' and resid 56 through 59 removed outlier: 3.914A pdb=" N VAL d 47 " --> pdb=" O MET d 59 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'd' and resid 42 through 45 Processing sheet with id= AX, first strand: chain 'e' and resid 38 through 40 removed outlier: 3.746A pdb=" N VAL e 58 " --> pdb=" O LYS e 40 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'e' and resid 52 through 54 Processing sheet with id= AZ, first strand: chain 'f' and resid 80 through 82 removed outlier: 3.926A pdb=" N TYR f 80 " --> pdb=" O LYS f 30 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'f' and resid 41 through 45 removed outlier: 7.026A pdb=" N GLN f 52 " --> pdb=" O VAL f 43 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= BC, first strand: chain 'g' and resid 60 through 63 removed outlier: 3.641A pdb=" N GLY g 31 " --> pdb=" O VAL g 39 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP g 41 " --> pdb=" O LEU g 29 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU g 29 " --> pdb=" O ASP g 41 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'h' and resid 94 through 96 removed outlier: 3.789A pdb=" N GLN h 94 " --> pdb=" O GLU h 18 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR h 16 " --> pdb=" O ILE h 96 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS h 44 " --> pdb=" O TRP h 26 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'h' and resid 39 through 41 Processing sheet with id= BF, first strand: chain 'j' and resid 103 through 105 removed outlier: 3.659A pdb=" N VAL j 103 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU j 74 " --> pdb=" O ARG j 89 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'j' and resid 68 through 70 Processing sheet with id= BH, first strand: chain 'k' and resid 79 through 83 removed outlier: 5.995A pdb=" N CYS k 48 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS k 19 " --> pdb=" O ASP k 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP k 99 " --> pdb=" O LYS k 19 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG k 21 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL k 97 " --> pdb=" O ARG k 21 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU k 23 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR k 95 " --> pdb=" O LEU k 23 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'k' and resid 85 through 87 removed outlier: 3.948A pdb=" N ALA k 36 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN k 46 " --> pdb=" O LEU k 34 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU k 34 " --> pdb=" O ASN k 46 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'l' and resid 79 through 82 removed outlier: 3.691A pdb=" N VAL l 43 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP l 26 " --> pdb=" O LYS l 44 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'l' and resid 84 through 87 removed outlier: 3.860A pdb=" N SER l 31 " --> pdb=" O ILE l 39 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR l 41 " --> pdb=" O LEU l 29 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU l 29 " --> pdb=" O THR l 41 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'm' and resid 85 through 91 removed outlier: 3.629A pdb=" N ILE m 85 " --> pdb=" O GLU m 78 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU m 78 " --> pdb=" O ILE m 85 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE m 55 " --> pdb=" O LYS m 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL m 103 " --> pdb=" O SER m 47 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'm' and resid 93 through 96 removed outlier: 3.596A pdb=" N VAL m 68 " --> pdb=" O ALA m 60 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA m 60 " --> pdb=" O VAL m 68 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU m 70 " --> pdb=" O VAL m 58 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL m 58 " --> pdb=" O GLU m 70 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'n' and resid 56 through 59 Processing sheet with id= BO, first strand: chain 'n' and resid 61 through 64 removed outlier: 3.616A pdb=" N VAL n 64 " --> pdb=" O VAL n 42 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL n 42 " --> pdb=" O VAL n 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU n 35 " --> pdb=" O GLN n 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG n 45 " --> pdb=" O LEU n 33 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU n 33 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'o' and resid 243 through 245 removed outlier: 4.595A pdb=" N SER o 229 " --> pdb=" O SER o 225 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER o 225 " --> pdb=" O SER o 229 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS o 231 " --> pdb=" O SER o 223 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA o 211 " --> pdb=" O SER o 224 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'o' and resid 253 through 255 removed outlier: 3.589A pdb=" N GLN o 287 " --> pdb=" O HIS o 274 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'o' and resid 317 through 321 Processing sheet with id= BS, first strand: chain 'o' and resid 350 through 355 Processing sheet with id= BT, first strand: chain 'o' and resid 398 through 401 Processing sheet with id= BU, first strand: chain 'o' and resid 431 through 434 Processing sheet with id= BV, first strand: chain 'p' and resid 26 through 30 Processing sheet with id= BW, first strand: chain 'p' and resid 80 through 82 removed outlier: 5.786A pdb=" N ASP p 55 " --> pdb=" O ILE p 43 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE p 43 " --> pdb=" O ASP p 55 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'q' and resid 66 through 69 removed outlier: 3.623A pdb=" N GLY q 66 " --> pdb=" O GLU q 58 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA q 56 " --> pdb=" O LEU q 68 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR q 36 " --> pdb=" O LEU q 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR q 80 " --> pdb=" O LYS q 30 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'q' and resid 71 through 73 removed outlier: 3.591A pdb=" N SER q 44 " --> pdb=" O GLN q 52 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN q 54 " --> pdb=" O LEU q 42 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU q 42 " --> pdb=" O ASN q 54 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'r' and resid 53 through 56 removed outlier: 6.453A pdb=" N ALA r 43 " --> pdb=" O HIS r 55 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS r 24 " --> pdb=" O ILE r 46 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER r 70 " --> pdb=" O ASN r 18 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'r' and resid 61 through 63 removed outlier: 3.501A pdb=" N GLY r 31 " --> pdb=" O VAL r 39 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP r 41 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU r 29 " --> pdb=" O ASP r 41 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 't' and resid 13 through 15 Processing sheet with id= CC, first strand: chain 'u' and resid 13 through 16 removed outlier: 4.064A pdb=" N THR u 21 " --> pdb=" O SER u 16 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'v' and resid 13 through 15 Processing sheet with id= CE, first strand: chain 'w' and resid 13 through 15 Processing sheet with id= CF, first strand: chain 'y' and resid 143 through 145 3128 hydrogen bonds defined for protein. 8802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 336 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 49.06 Time building geometry restraints manager: 29.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12510 1.30 - 1.43: 23549 1.43 - 1.56: 45519 1.56 - 1.69: 972 1.69 - 1.83: 424 Bond restraints: 82974 Sorted by residual: bond pdb=" CA ILE V 493 " pdb=" CB ILE V 493 " ideal model delta sigma weight residual 1.539 1.631 -0.092 1.11e-02 8.12e+03 6.88e+01 bond pdb=" C LEU v 109 " pdb=" N SER v 110 " ideal model delta sigma weight residual 1.335 1.439 -0.105 1.31e-02 5.83e+03 6.37e+01 bond pdb=" C ILE T 612 " pdb=" N PRO T 613 " ideal model delta sigma weight residual 1.336 1.407 -0.071 1.23e-02 6.61e+03 3.33e+01 bond pdb=" C SER v 134 " pdb=" O SER v 134 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.19e-02 7.06e+03 3.20e+01 bond pdb=" CA PRO s 133 " pdb=" C PRO s 133 " ideal model delta sigma weight residual 1.520 1.600 -0.080 1.42e-02 4.96e+03 3.18e+01 ... (remaining 82969 not shown) Histogram of bond angle deviations from ideal: 92.65 - 101.27: 312 101.27 - 109.89: 18351 109.89 - 118.51: 49845 118.51 - 127.13: 44359 127.13 - 135.75: 1793 Bond angle restraints: 114660 Sorted by residual: angle pdb=" N ILE V 493 " pdb=" CA ILE V 493 " pdb=" CB ILE V 493 " ideal model delta sigma weight residual 110.62 131.72 -21.10 1.09e+00 8.42e-01 3.75e+02 angle pdb=" C ILE V 493 " pdb=" CA ILE V 493 " pdb=" CB ILE V 493 " ideal model delta sigma weight residual 111.81 92.65 19.16 1.25e+00 6.40e-01 2.35e+02 angle pdb=" C ILE H 87 " pdb=" N PRO H 88 " pdb=" CA PRO H 88 " ideal model delta sigma weight residual 118.85 134.48 -15.63 1.09e+00 8.42e-01 2.06e+02 angle pdb=" CA SER v 134 " pdb=" C SER v 134 " pdb=" O SER v 134 " ideal model delta sigma weight residual 120.42 108.17 12.25 1.06e+00 8.90e-01 1.34e+02 angle pdb=" O ASN V 833 " pdb=" C ASN V 833 " pdb=" N THR V 834 " ideal model delta sigma weight residual 123.27 135.75 -12.48 1.16e+00 7.43e-01 1.16e+02 ... (remaining 114655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 49239 35.94 - 71.87: 1453 71.87 - 107.81: 175 107.81 - 143.75: 11 143.75 - 179.68: 17 Dihedral angle restraints: 50895 sinusoidal: 23202 harmonic: 27693 Sorted by residual: dihedral pdb=" CA TYR V 562 " pdb=" C TYR V 562 " pdb=" N THR V 563 " pdb=" CA THR V 563 " ideal model delta harmonic sigma weight residual 180.00 99.70 80.30 0 5.00e+00 4.00e-02 2.58e+02 dihedral pdb=" CA PRO V 729 " pdb=" C PRO V 729 " pdb=" N VAL V 730 " pdb=" CA VAL V 730 " ideal model delta harmonic sigma weight residual 180.00 101.55 78.45 0 5.00e+00 4.00e-02 2.46e+02 dihedral pdb=" CA GLY V 749 " pdb=" C GLY V 749 " pdb=" N SER V 750 " pdb=" CA SER V 750 " ideal model delta harmonic sigma weight residual -180.00 -124.05 -55.95 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 50892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.998: 13671 0.998 - 1.995: 1 1.995 - 2.993: 0 2.993 - 3.991: 0 3.991 - 4.988: 2 Chirality restraints: 13674 Sorted by residual: chirality pdb=" C2 IHP A2500 " pdb=" C1 IHP A2500 " pdb=" C3 IHP A2500 " pdb=" O12 IHP A2500 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" C3 IHP A2500 " pdb=" C2 IHP A2500 " pdb=" C4 IHP A2500 " pdb=" O13 IHP A2500 " both_signs ideal model delta sigma weight residual False -2.34 2.47 -4.80 2.00e-01 2.50e+01 5.77e+02 chirality pdb=" CB ILE V 493 " pdb=" CA ILE V 493 " pdb=" CG1 ILE V 493 " pdb=" CG2 ILE V 493 " both_signs ideal model delta sigma weight residual False 2.64 1.05 1.59 2.00e-01 2.50e+01 6.33e+01 ... (remaining 13671 not shown) Planarity restraints: 12979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 818 " 0.191 2.00e-02 2.50e+03 1.02e-01 2.07e+02 pdb=" CG TYR V 818 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR V 818 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR V 818 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR V 818 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR V 818 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR V 818 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR V 818 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK X 27 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C UNK X 27 " 0.216 2.00e-02 2.50e+03 pdb=" O UNK X 27 " -0.080 2.00e-02 2.50e+03 pdb=" N UNK X 28 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK X 26 " 0.067 2.00e-02 2.50e+03 1.25e-01 1.55e+02 pdb=" C UNK X 26 " -0.216 2.00e-02 2.50e+03 pdb=" O UNK X 26 " 0.080 2.00e-02 2.50e+03 pdb=" N UNK X 27 " 0.069 2.00e-02 2.50e+03 ... (remaining 12976 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.59: 31 1.59 - 2.42: 443 2.42 - 3.25: 80767 3.25 - 4.07: 214669 4.07 - 4.90: 367683 Warning: very small nonbonded interaction distances. Nonbonded interactions: 663593 Sorted by model distance: nonbonded pdb=" CD1 LEU C 760 " pdb=" C GLU R 74 " model vdw 0.767 3.690 nonbonded pdb=" CD1 LEU C 760 " pdb=" N VAL R 75 " model vdw 0.784 3.540 nonbonded pdb=" CD2 LEU k 23 " pdb=" OG SER l 64 " model vdw 0.983 3.460 nonbonded pdb=" ND2 ASN W 61 " pdb=" NH2 ARG W 83 " model vdw 0.990 3.200 nonbonded pdb=" NZ LYS V 642 " pdb=" CG GLU V 832 " model vdw 1.040 3.520 ... (remaining 663588 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 'b' and (resid 12 through 55 or resid 77 through 102)) selection = (chain 'k' and (resid 12 through 54 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 97 or (resid 98 through 99 and (na \ me N or name CA or name C or name O or name CB )) or resid 100 through 102)) } ncs_group { reference = chain 'd' selection = (chain 'n' and (resid 4 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 45 or (resid 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 85)) } ncs_group { reference = (chain 'e' and (resid 10 through 63 or resid 73 through 92)) selection = (chain 'p' and (resid 10 through 55 or (resid 56 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 63 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )) or resid 74 through 92)) } ncs_group { reference = chain 'f' selection = (chain 'q' and (resid 12 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 83)) } ncs_group { reference = chain 'g' selection = (chain 'r' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 41 or (resid 42 through 43 and (name N \ or name CA or name C or name O or name CB )) or resid 44 through 47 or resid 54 \ through 76)) } ncs_group { reference = (chain 'h' and (resid 1 through 76 or resid 78 through 101)) selection = (chain 'l' and (resid 1 through 48 or resid 64 or resid 78 through 101)) } ncs_group { reference = (chain 'j' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 108)) selection = (chain 'm' and (resid 17 through 18 or (resid 19 through 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 or (resid 22 through 23 and (na \ me N or name CA or name C or name O or name CB )) or resid 24 or (resid 25 and ( \ name N or name CA or name C or name O or name CB )) or resid 26 through 35 or (r \ esid 36 through 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 through 73 or (resid 74 and (name N or name CA or name C or name O or na \ me CB )) or resid 75 through 87 or (resid 88 and (name N or name CA or name C or \ name O or name CB )) or resid 89 through 108)) } ncs_group { reference = (chain 't' and resid 1 through 139) selection = (chain 'u' and (resid 1 through 51 or resid 78 through 139)) selection = (chain 'v' and (resid 1 through 51 or resid 78 through 139)) selection = (chain 'w' and (resid 1 through 51 or resid 78 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 24.980 Check model and map are aligned: 0.870 Set scattering table: 0.560 Process input model: 210.940 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.480 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 248.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 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 : 0.008 0.105 82974 Z= 0.496 Angle : 1.235 21.099 114660 Z= 0.781 Chirality : 0.095 4.988 13674 Planarity : 0.010 0.305 12979 Dihedral : 16.227 179.683 32775 Min Nonbonded Distance : 0.767 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.31 % Favored : 93.22 % Rotamer: Outliers : 1.33 % Allowed : 4.47 % Favored : 94.20 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.23 % 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: -2.85 (0.08), residues: 9070 helix: -1.27 (0.07), residues: 4179 sheet: -2.07 (0.15), residues: 1064 loop : -2.46 (0.09), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP S 205 HIS 0.033 0.003 HIS V 558 PHE 0.119 0.004 PHE V1025 TYR 0.191 0.006 TYR V 818 ARG 0.028 0.001 ARG V 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2382 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 2292 time to evaluate : 6.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LEU cc_start: 0.9075 (mt) cc_final: 0.8874 (mt) REVERT: A 320 ASP cc_start: 0.7440 (m-30) cc_final: 0.7216 (m-30) REVERT: A 409 CYS cc_start: 0.8295 (m) cc_final: 0.8093 (p) REVERT: A 504 LYS cc_start: 0.8457 (mttt) cc_final: 0.8248 (mmtt) REVERT: A 514 TYR cc_start: 0.7875 (m-10) cc_final: 0.7633 (m-80) REVERT: A 651 ASP cc_start: 0.7877 (t0) cc_final: 0.7576 (t0) REVERT: A 676 GLN cc_start: 0.8041 (mp-120) cc_final: 0.7639 (mp10) REVERT: A 712 LEU cc_start: 0.9114 (mt) cc_final: 0.8903 (mm) REVERT: A 735 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 754 TYR cc_start: 0.8395 (t80) cc_final: 0.7716 (t80) REVERT: A 755 ASP cc_start: 0.6618 (t0) cc_final: 0.6388 (t0) REVERT: A 766 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9103 (mt) REVERT: A 791 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7697 (mtm110) REVERT: A 917 GLU cc_start: 0.5999 (mm-30) cc_final: 0.5208 (mm-30) REVERT: A 920 LYS cc_start: 0.5460 (mtpt) cc_final: 0.5211 (mtpt) REVERT: A 923 TYR cc_start: 0.7888 (m-80) cc_final: 0.7563 (m-80) REVERT: A 985 ASP cc_start: 0.7029 (t70) cc_final: 0.6657 (t0) REVERT: A 1122 ASP cc_start: 0.7815 (m-30) cc_final: 0.7485 (m-30) REVERT: A 1165 LEU cc_start: 0.9024 (mt) cc_final: 0.8388 (mt) REVERT: A 1210 ASP cc_start: 0.7500 (p0) cc_final: 0.7217 (p0) REVERT: A 1261 SER cc_start: 0.8854 (t) cc_final: 0.8373 (p) REVERT: A 1296 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7693 (mtt90) REVERT: A 1314 SER cc_start: 0.8832 (m) cc_final: 0.8264 (p) REVERT: A 1330 LYS cc_start: 0.8523 (tppp) cc_final: 0.8220 (mtmt) REVERT: A 1615 ASN cc_start: 0.8903 (t0) cc_final: 0.8574 (t0) REVERT: A 1616 ARG cc_start: 0.8717 (ptt90) cc_final: 0.8314 (ptt180) REVERT: A 1709 TRP cc_start: 0.7298 (m-10) cc_final: 0.6603 (m-10) REVERT: A 1802 MET cc_start: 0.7922 (mmm) cc_final: 0.7585 (mmm) REVERT: A 1804 THR cc_start: 0.8989 (m) cc_final: 0.8668 (p) REVERT: A 1806 MET cc_start: 0.8247 (mmm) cc_final: 0.7969 (mmm) REVERT: A 1908 LEU cc_start: 0.9148 (tp) cc_final: 0.8728 (mt) REVERT: A 1938 LYS cc_start: 0.8712 (tptt) cc_final: 0.8315 (pttm) REVERT: C 133 ILE cc_start: 0.8699 (mt) cc_final: 0.8465 (mt) REVERT: C 166 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7425 (tppt) REVERT: C 225 THR cc_start: 0.8549 (m) cc_final: 0.8162 (m) REVERT: C 260 ASN cc_start: 0.8100 (m-40) cc_final: 0.7887 (t0) REVERT: C 372 THR cc_start: 0.8963 (p) cc_final: 0.8741 (t) REVERT: C 423 HIS cc_start: 0.8321 (t-90) cc_final: 0.8076 (t-90) REVERT: C 427 LEU cc_start: 0.8943 (mt) cc_final: 0.8687 (mt) REVERT: C 477 ASP cc_start: 0.7636 (t0) cc_final: 0.6925 (t0) REVERT: C 679 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6662 (mt-10) REVERT: C 775 ILE cc_start: 0.7394 (mt) cc_final: 0.7115 (mm) REVERT: C 804 LYS cc_start: 0.8507 (tppt) cc_final: 0.8174 (ttpp) REVERT: C 837 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7722 (mm-40) REVERT: C 880 MET cc_start: 0.8850 (mmm) cc_final: 0.8366 (mmt) REVERT: C 960 ASN cc_start: 0.7926 (p0) cc_final: 0.7343 (t0) REVERT: C 961 SER cc_start: 0.8553 (p) cc_final: 0.8255 (p) REVERT: H 294 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7847 (tppt) REVERT: H 304 LEU cc_start: 0.9004 (tm) cc_final: 0.8664 (tp) REVERT: H 464 ASN cc_start: 0.7770 (m-40) cc_final: 0.7488 (t0) REVERT: J 161 ASP cc_start: 0.7306 (p0) cc_final: 0.6841 (p0) REVERT: J 163 THR cc_start: 0.8754 (p) cc_final: 0.8401 (p) REVERT: J 287 ASP cc_start: 0.7472 (p0) cc_final: 0.6918 (p0) REVERT: J 392 MET cc_start: 0.8195 (mmm) cc_final: 0.7986 (mmm) REVERT: J 402 VAL cc_start: 0.8774 (t) cc_final: 0.8533 (m) REVERT: J 420 ASP cc_start: 0.8410 (p0) cc_final: 0.7685 (p0) REVERT: K 197 ILE cc_start: 0.4210 (pt) cc_final: 0.4005 (pt) REVERT: L 25 ASP cc_start: 0.8350 (t0) cc_final: 0.7965 (t0) REVERT: L 28 ILE cc_start: 0.8898 (pt) cc_final: 0.8563 (mt) REVERT: L 100 TYR cc_start: 0.8736 (m-80) cc_final: 0.8425 (m-80) REVERT: M 76 PHE cc_start: 0.8610 (t80) cc_final: 0.8136 (t80) REVERT: M 235 GLN cc_start: 0.8541 (mt0) cc_final: 0.8195 (mt0) REVERT: N 34 CYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8342 (p) REVERT: N 140 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8390 (ttmt) REVERT: N 243 ASN cc_start: 0.7608 (t0) cc_final: 0.6797 (p0) REVERT: N 282 LEU cc_start: 0.7242 (mt) cc_final: 0.6787 (pt) REVERT: O 162 THR cc_start: 0.8027 (m) cc_final: 0.7682 (p) REVERT: P 9 LEU cc_start: 0.8159 (mt) cc_final: 0.7950 (mt) REVERT: S 57 TYR cc_start: 0.8123 (m-80) cc_final: 0.7871 (m-10) REVERT: S 67 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8128 (tp40) REVERT: S 105 TYR cc_start: 0.8852 (t80) cc_final: 0.8366 (t80) REVERT: S 121 LEU cc_start: 0.9058 (tt) cc_final: 0.8272 (tt) REVERT: S 212 HIS cc_start: 0.5450 (m-70) cc_final: 0.5173 (m90) REVERT: V 298 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6820 (tt0) REVERT: V 504 ILE cc_start: 0.5967 (tt) cc_final: 0.5644 (tt) REVERT: V 555 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6501 (tmtt) REVERT: V 580 THR cc_start: 0.3233 (OUTLIER) cc_final: 0.2915 (t) REVERT: V 583 MET cc_start: 0.2774 (mmm) cc_final: 0.2337 (mmt) REVERT: V 931 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.6769 (p) REVERT: V 937 TYR cc_start: 0.4001 (t80) cc_final: 0.3758 (t80) REVERT: V 970 TRP cc_start: 0.5430 (OUTLIER) cc_final: 0.4912 (t-100) REVERT: V 982 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7186 (t) REVERT: W 116 ARG cc_start: 0.3393 (mtm-85) cc_final: 0.2417 (mtt-85) REVERT: a 109 LEU cc_start: 0.8222 (tp) cc_final: 0.7824 (mt) REVERT: a 160 LEU cc_start: 0.8381 (tp) cc_final: 0.8140 (tp) REVERT: a 184 MET cc_start: 0.8277 (mmm) cc_final: 0.7917 (mmm) REVERT: a 195 ILE cc_start: 0.8764 (mp) cc_final: 0.8537 (mt) REVERT: a 237 ILE cc_start: 0.9158 (mt) cc_final: 0.8897 (mp) REVERT: b 33 GLN cc_start: 0.7512 (mt0) cc_final: 0.7006 (mm-40) REVERT: b 39 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7308 (tttp) REVERT: b 46 ASN cc_start: 0.8475 (t0) cc_final: 0.8064 (t0) REVERT: c 183 ASN cc_start: 0.8253 (m-40) cc_final: 0.8019 (m110) REVERT: c 219 MET cc_start: 0.0809 (ttm) cc_final: -0.0994 (ptt) REVERT: c 278 LEU cc_start: 0.8610 (mp) cc_final: 0.8186 (tt) REVERT: c 325 VAL cc_start: 0.8923 (t) cc_final: 0.8565 (t) REVERT: d 34 VAL cc_start: 0.8496 (t) cc_final: 0.8213 (t) REVERT: d 37 GLU cc_start: 0.6468 (mt-10) cc_final: 0.5536 (mt-10) REVERT: d 69 ILE cc_start: 0.8156 (mt) cc_final: 0.7911 (tt) REVERT: d 77 LEU cc_start: 0.8602 (mt) cc_final: 0.8341 (mm) REVERT: e 32 PHE cc_start: 0.7100 (t80) cc_final: 0.6655 (t80) REVERT: e 90 ILE cc_start: 0.4791 (mm) cc_final: 0.4357 (mm) REVERT: g 23 ARG cc_start: 0.4109 (mtm180) cc_final: 0.2932 (mmt180) REVERT: h 15 VAL cc_start: 0.6475 (m) cc_final: 0.5801 (m) REVERT: h 35 GLN cc_start: 0.6415 (mt0) cc_final: 0.6107 (mm-40) REVERT: h 77 ASP cc_start: 0.3310 (m-30) cc_final: 0.2561 (t0) REVERT: h 84 TYR cc_start: 0.6236 (t80) cc_final: 0.5869 (t80) REVERT: j 28 HIS cc_start: 0.5974 (m90) cc_final: 0.5678 (t-170) REVERT: j 41 ARG cc_start: 0.6839 (ptt180) cc_final: 0.5974 (mmm160) REVERT: j 58 VAL cc_start: 0.2280 (t) cc_final: 0.2014 (t) REVERT: j 59 LYS cc_start: 0.5206 (tppt) cc_final: 0.4766 (mmmt) REVERT: j 63 ARG cc_start: 0.4621 (mtp85) cc_final: 0.4352 (mtp180) REVERT: l 45 LEU cc_start: 0.1055 (OUTLIER) cc_final: 0.0764 (pt) REVERT: m 31 MET cc_start: 0.4096 (mmp) cc_final: 0.3624 (mmm) REVERT: o 275 TYR cc_start: 0.8786 (m-80) cc_final: 0.8445 (m-80) REVERT: o 356 MET cc_start: 0.7760 (mmp) cc_final: 0.7303 (mmm) REVERT: p 50 MET cc_start: 0.3743 (mtt) cc_final: 0.1352 (tpt) REVERT: y 200 ASN cc_start: 0.8846 (t0) cc_final: 0.8421 (t0) outliers start: 90 outliers final: 16 residues processed: 2354 average time/residue: 0.7942 time to fit residues: 3114.3638 Evaluate side-chains 1204 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1180 time to evaluate : 6.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain V residue 486 TYR Chi-restraints excluded: chain V residue 516 ILE Chi-restraints excluded: chain V residue 544 VAL Chi-restraints excluded: chain V residue 555 LYS Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 847 ILE Chi-restraints excluded: chain V residue 871 LEU Chi-restraints excluded: chain V residue 931 SER Chi-restraints excluded: chain V residue 970 TRP Chi-restraints excluded: chain V residue 979 TYR Chi-restraints excluded: chain V residue 982 THR Chi-restraints excluded: chain V residue 1059 LEU Chi-restraints excluded: chain V residue 1081 SER Chi-restraints excluded: chain V residue 1094 VAL Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain o residue 315 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 825 optimal weight: 10.0000 chunk 740 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 499 optimal weight: 7.9990 chunk 395 optimal weight: 0.9990 chunk 765 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 465 optimal weight: 6.9990 chunk 569 optimal weight: 7.9990 chunk 887 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 181 HIS A 233 HIS A 254 HIS A 326 ASN A 368 ASN A 392 ASN A 429 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN A 617 ASN A 685 HIS ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN A1140 ASN A1281 ASN A1424 HIS A1431 HIS ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 ASN ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1763 ASN A1863 HIS A1895 HIS A1902 GLN A1990 ASN C 84 GLN C 119 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS C 721 GLN C 776 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 ASN H 355 HIS H 369 ASN H 458 HIS ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 ASN J 270 ASN J 306 HIS J 382 HIS K 37 ASN K 75 GLN K 103 ASN K 108 ASN K 110 HIS L 29 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 HIS L 112 ASN L 147 HIS M 35 ASN M 44 ASN ** M 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN N 45 HIS N 69 ASN N 81 HIS N 134 ASN O 72 GLN O 96 GLN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN P 34 HIS ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN S 210 ASN S 212 HIS V 639 ASN V 781 ASN V 845 HIS V 874 ASN ** V 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 955 HIS ** V 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 989 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN W 157 GLN a 153 ASN a 181 GLN ** a 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 30 ASN ** c 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 ASN d 17 HIS d 41 ASN ** d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 ASN ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 54 ASN f 77 ASN g 18 ASN g 55 HIS g 66 ASN ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 71 ASN l 30 GLN l 78 ASN ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 ASN n 68 GLN o 176 HIS o 325 ASN o 337 HIS ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 358 ASN p 86 ASN q 25 HIS ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 GLN r 66 ASN y 200 ASN ** y 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 82974 Z= 0.311 Angle : 0.727 13.531 114660 Z= 0.375 Chirality : 0.045 0.439 13674 Planarity : 0.005 0.111 12979 Dihedral : 18.058 177.685 17410 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 3.82 % Allowed : 12.97 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % 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: -1.12 (0.09), residues: 9070 helix: 0.61 (0.08), residues: 4192 sheet: -1.78 (0.15), residues: 1063 loop : -1.98 (0.09), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 163 HIS 0.011 0.001 HIS V 989 PHE 0.033 0.002 PHE V 525 TYR 0.028 0.002 TYR S 192 ARG 0.012 0.001 ARG M 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1284 time to evaluate : 6.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASP cc_start: 0.7456 (m-30) cc_final: 0.7247 (m-30) REVERT: A 331 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: A 371 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: A 504 LYS cc_start: 0.8467 (mttt) cc_final: 0.8262 (mmtt) REVERT: A 651 ASP cc_start: 0.8069 (t0) cc_final: 0.7702 (t70) REVERT: A 712 LEU cc_start: 0.9238 (mt) cc_final: 0.8988 (mm) REVERT: A 754 TYR cc_start: 0.8352 (t80) cc_final: 0.7969 (t80) REVERT: A 766 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9055 (mt) REVERT: A 783 LEU cc_start: 0.8902 (mt) cc_final: 0.8401 (mt) REVERT: A 917 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5314 (mm-30) REVERT: A 941 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7216 (mt-10) REVERT: A 1085 LYS cc_start: 0.8932 (tptp) cc_final: 0.8584 (ttmm) REVERT: A 1122 ASP cc_start: 0.7648 (m-30) cc_final: 0.7371 (m-30) REVERT: A 1145 MET cc_start: 0.8349 (mtm) cc_final: 0.8039 (mtm) REVERT: A 1164 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 1261 SER cc_start: 0.8871 (t) cc_final: 0.8283 (p) REVERT: A 1330 LYS cc_start: 0.8750 (tppp) cc_final: 0.8095 (mtmt) REVERT: A 1445 THR cc_start: 0.9062 (m) cc_final: 0.8827 (p) REVERT: A 1616 ARG cc_start: 0.8909 (ptt90) cc_final: 0.8618 (ptt180) REVERT: A 1620 TYR cc_start: 0.7899 (t80) cc_final: 0.7664 (t80) REVERT: A 1806 MET cc_start: 0.8396 (mmm) cc_final: 0.8193 (mmm) REVERT: A 1908 LEU cc_start: 0.9255 (tp) cc_final: 0.8795 (mt) REVERT: A 1933 ILE cc_start: 0.9333 (mt) cc_final: 0.9065 (tt) REVERT: A 1937 ARG cc_start: 0.6991 (mmt180) cc_final: 0.6715 (mmt180) REVERT: A 1938 LYS cc_start: 0.8645 (tptt) cc_final: 0.8349 (pttm) REVERT: C 78 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6379 (mmm) REVERT: C 111 LYS cc_start: 0.8394 (pttt) cc_final: 0.8090 (mmtt) REVERT: C 166 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7683 (tppt) REVERT: C 432 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7934 (mm-40) REVERT: C 477 ASP cc_start: 0.7694 (t0) cc_final: 0.7264 (t70) REVERT: C 679 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6456 (mt-10) REVERT: C 773 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7898 (m) REVERT: C 775 ILE cc_start: 0.7439 (mt) cc_final: 0.7161 (mm) REVERT: C 837 GLN cc_start: 0.7969 (mm-40) cc_final: 0.5097 (pp30) REVERT: H 294 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7921 (tppt) REVERT: H 345 SER cc_start: 0.8825 (m) cc_final: 0.8031 (p) REVERT: H 430 ASN cc_start: 0.7396 (m-40) cc_final: 0.7057 (t0) REVERT: H 452 LEU cc_start: 0.7020 (tp) cc_final: 0.6745 (tp) REVERT: H 464 ASN cc_start: 0.7725 (m-40) cc_final: 0.7502 (t0) REVERT: H 477 MET cc_start: 0.6528 (mmp) cc_final: 0.6013 (mmt) REVERT: J 161 ASP cc_start: 0.7579 (p0) cc_final: 0.7221 (p0) REVERT: J 163 THR cc_start: 0.8601 (p) cc_final: 0.8067 (p) REVERT: J 329 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6101 (t0) REVERT: J 377 ASP cc_start: 0.8177 (t0) cc_final: 0.7532 (t0) REVERT: J 426 TRP cc_start: 0.9202 (m100) cc_final: 0.8272 (m100) REVERT: L 25 ASP cc_start: 0.8370 (t0) cc_final: 0.8121 (t0) REVERT: L 28 ILE cc_start: 0.8951 (pt) cc_final: 0.8727 (mt) REVERT: L 48 GLN cc_start: 0.8221 (mp10) cc_final: 0.8012 (mp10) REVERT: L 58 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: L 115 ASN cc_start: 0.7794 (p0) cc_final: 0.7545 (p0) REVERT: N 85 GLN cc_start: 0.7212 (pp30) cc_final: 0.6726 (pp30) REVERT: N 86 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8634 (tp) REVERT: N 140 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8438 (ttmt) REVERT: N 243 ASN cc_start: 0.7637 (t0) cc_final: 0.7411 (t0) REVERT: N 282 LEU cc_start: 0.7338 (mt) cc_final: 0.6824 (pt) REVERT: O 162 THR cc_start: 0.8178 (m) cc_final: 0.7860 (p) REVERT: P 9 LEU cc_start: 0.8215 (mt) cc_final: 0.7939 (mt) REVERT: S 41 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6706 (tm-30) REVERT: S 67 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8290 (tp-100) REVERT: S 126 ILE cc_start: 0.9054 (mm) cc_final: 0.8605 (mt) REVERT: V 512 LYS cc_start: 0.4000 (OUTLIER) cc_final: 0.2994 (ttmt) REVERT: V 613 ASP cc_start: 0.3560 (OUTLIER) cc_final: 0.3082 (t0) REVERT: V 702 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.5267 (tt0) REVERT: V 847 ILE cc_start: 0.5888 (OUTLIER) cc_final: 0.5354 (pt) REVERT: V 864 MET cc_start: 0.4053 (ptp) cc_final: 0.3814 (ptp) REVERT: V 970 TRP cc_start: 0.5817 (OUTLIER) cc_final: 0.4891 (t-100) REVERT: V 1015 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.4167 (t70) REVERT: V 1086 ILE cc_start: 0.8165 (tp) cc_final: 0.7895 (pt) REVERT: W 116 ARG cc_start: 0.3326 (mtm-85) cc_final: 0.2413 (mtp180) REVERT: a 109 LEU cc_start: 0.8436 (tp) cc_final: 0.8064 (mt) REVERT: b 33 GLN cc_start: 0.7361 (mt0) cc_final: 0.7065 (mm-40) REVERT: b 35 MET cc_start: 0.5124 (mmm) cc_final: 0.4409 (mmm) REVERT: b 46 ASN cc_start: 0.8303 (t0) cc_final: 0.8014 (t0) REVERT: c 33 ILE cc_start: 0.8111 (mm) cc_final: 0.7824 (mm) REVERT: c 219 MET cc_start: 0.0791 (ttm) cc_final: -0.0896 (ptt) REVERT: c 278 LEU cc_start: 0.8715 (mp) cc_final: 0.8260 (tt) REVERT: c 313 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5943 (tmm) REVERT: d 30 ARG cc_start: 0.7589 (ttp80) cc_final: 0.6818 (ttp80) REVERT: d 48 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6790 (pt) REVERT: d 69 ILE cc_start: 0.8108 (mt) cc_final: 0.7867 (tt) REVERT: e 50 MET cc_start: 0.5955 (mmm) cc_final: 0.5658 (mtt) REVERT: e 90 ILE cc_start: 0.4891 (mm) cc_final: 0.4558 (mm) REVERT: g 23 ARG cc_start: 0.3940 (mtm180) cc_final: 0.2438 (mmt180) REVERT: h 36 MET cc_start: 0.6822 (ttp) cc_final: 0.6498 (ttt) REVERT: h 46 THR cc_start: 0.7073 (m) cc_final: 0.6433 (p) REVERT: h 77 ASP cc_start: 0.3275 (m-30) cc_final: 0.2534 (t0) REVERT: j 41 ARG cc_start: 0.6834 (ptt180) cc_final: 0.5914 (mmt180) REVERT: j 48 LEU cc_start: 0.6640 (tp) cc_final: 0.6325 (tp) REVERT: k 35 MET cc_start: 0.2890 (mmm) cc_final: 0.2674 (mmm) REVERT: m 31 MET cc_start: 0.4359 (mmp) cc_final: 0.4031 (mmm) REVERT: o 275 TYR cc_start: 0.8939 (m-80) cc_final: 0.8398 (m-80) REVERT: o 323 GLN cc_start: 0.8092 (mm110) cc_final: 0.7870 (mm-40) REVERT: o 356 MET cc_start: 0.7913 (mmp) cc_final: 0.7453 (mmm) REVERT: o 438 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6596 (tm-30) REVERT: p 50 MET cc_start: 0.3662 (mtt) cc_final: 0.3389 (mtm) REVERT: y 195 PHE cc_start: 0.8550 (p90) cc_final: 0.8335 (p90) REVERT: y 200 ASN cc_start: 0.8723 (t0) cc_final: 0.8427 (t0) REVERT: y 205 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7518 (tm-30) outliers start: 258 outliers final: 136 residues processed: 1465 average time/residue: 0.7668 time to fit residues: 1962.1631 Evaluate side-chains 1165 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1012 time to evaluate : 6.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1164 TYR Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1401 SER Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1745 SER Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 842 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain H residue 302 SER Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 415 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 260 GLU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 239 SER Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 302 LEU Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 494 GLN Chi-restraints excluded: chain V residue 512 LYS Chi-restraints excluded: chain V residue 544 VAL Chi-restraints excluded: chain V residue 556 VAL Chi-restraints excluded: chain V residue 559 ASP Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 613 ASP Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 675 ILE Chi-restraints excluded: chain V residue 681 CYS Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 702 GLU Chi-restraints excluded: chain V residue 773 VAL Chi-restraints excluded: chain V residue 847 ILE Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 970 TRP Chi-restraints excluded: chain V residue 1015 HIS Chi-restraints excluded: chain V residue 1059 LEU Chi-restraints excluded: chain V residue 1073 VAL Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain V residue 1087 GLU Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 111 PHE Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 158 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain c residue 97 MET Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain c residue 302 LEU Chi-restraints excluded: chain c residue 309 HIS Chi-restraints excluded: chain c residue 313 MET Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 31 MET Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 235 THR Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain o residue 444 CYS Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 166 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 493 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 738 optimal weight: 3.9990 chunk 604 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 888 optimal weight: 0.9980 chunk 960 optimal weight: 50.0000 chunk 791 optimal weight: 4.9990 chunk 881 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 713 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 368 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 ASN ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 290 HIS C 403 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 369 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN M 235 GLN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 GLN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 HIS ** P 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN S 73 GLN ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 558 HIS V 983 ASN ** V1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 153 ASN ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 ASN c 309 HIS c 327 HIS ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 34 GLN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 82974 Z= 0.352 Angle : 0.724 12.895 114660 Z= 0.369 Chirality : 0.045 0.367 13674 Planarity : 0.005 0.109 12979 Dihedral : 17.865 179.235 17391 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.84 % Rotamer: Outliers : 4.94 % Allowed : 15.06 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.06 % 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: -0.64 (0.09), residues: 9070 helix: 1.08 (0.08), residues: 4167 sheet: -1.62 (0.16), residues: 1033 loop : -1.78 (0.10), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP o 410 HIS 0.011 0.002 HIS W 150 PHE 0.030 0.002 PHE o 308 TYR 0.031 0.002 TYR S 105 ARG 0.010 0.001 ARG M 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1145 time to evaluate : 6.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7270 (pp20) cc_final: 0.6586 (pp20) REVERT: A 331 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: A 409 CYS cc_start: 0.8003 (m) cc_final: 0.7673 (p) REVERT: A 651 ASP cc_start: 0.8051 (t0) cc_final: 0.7831 (t70) REVERT: A 743 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8285 (mtpp) REVERT: A 754 TYR cc_start: 0.8433 (t80) cc_final: 0.8040 (t80) REVERT: A 763 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7952 (tpt) REVERT: A 912 LEU cc_start: 0.9178 (tp) cc_final: 0.8935 (tp) REVERT: A 917 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5384 (mm-30) REVERT: A 941 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 1067 ASN cc_start: 0.8847 (t0) cc_final: 0.8397 (t0) REVERT: A 1095 MET cc_start: 0.8665 (ptp) cc_final: 0.8417 (ptp) REVERT: A 1122 ASP cc_start: 0.7573 (m-30) cc_final: 0.7144 (m-30) REVERT: A 1145 MET cc_start: 0.8462 (mtm) cc_final: 0.8262 (mtm) REVERT: A 1261 SER cc_start: 0.9078 (t) cc_final: 0.8598 (p) REVERT: A 1330 LYS cc_start: 0.8815 (tppp) cc_final: 0.8247 (mtmt) REVERT: A 1429 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6793 (mtm) REVERT: A 1550 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 1616 ARG cc_start: 0.8994 (ptt90) cc_final: 0.8794 (ptt180) REVERT: A 1703 MET cc_start: 0.8280 (mtp) cc_final: 0.8005 (mtp) REVERT: A 1732 MET cc_start: 0.8279 (mtp) cc_final: 0.7778 (ttm) REVERT: A 1933 ILE cc_start: 0.9381 (mt) cc_final: 0.9075 (tt) REVERT: A 1938 LYS cc_start: 0.8748 (tptt) cc_final: 0.8370 (pttm) REVERT: A 2024 MET cc_start: 0.7472 (mmt) cc_final: 0.7076 (mmp) REVERT: C 111 LYS cc_start: 0.8460 (pttt) cc_final: 0.8053 (tptp) REVERT: C 166 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7739 (tppt) REVERT: C 264 CYS cc_start: 0.7129 (m) cc_final: 0.6797 (m) REVERT: C 477 ASP cc_start: 0.7640 (t0) cc_final: 0.7250 (t70) REVERT: C 679 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6782 (mt-10) REVERT: C 775 ILE cc_start: 0.7489 (mt) cc_final: 0.7247 (mm) REVERT: C 804 LYS cc_start: 0.8942 (tppt) cc_final: 0.8491 (ttpp) REVERT: C 817 GLN cc_start: 0.5976 (pm20) cc_final: 0.5690 (pm20) REVERT: H 294 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7897 (tppt) REVERT: H 351 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: H 452 LEU cc_start: 0.7116 (tp) cc_final: 0.6852 (tp) REVERT: H 464 ASN cc_start: 0.7678 (m-40) cc_final: 0.7448 (t0) REVERT: H 477 MET cc_start: 0.6825 (mmp) cc_final: 0.6133 (mmt) REVERT: J 161 ASP cc_start: 0.7659 (p0) cc_final: 0.7353 (p0) REVERT: J 163 THR cc_start: 0.8596 (p) cc_final: 0.8288 (p) REVERT: J 329 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6650 (t70) REVERT: J 377 ASP cc_start: 0.8182 (t0) cc_final: 0.7663 (t0) REVERT: J 426 TRP cc_start: 0.9253 (m100) cc_final: 0.8417 (m100) REVERT: L 25 ASP cc_start: 0.8505 (t0) cc_final: 0.8199 (t0) REVERT: L 28 ILE cc_start: 0.8989 (pt) cc_final: 0.8786 (mt) REVERT: L 58 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: L 88 ASP cc_start: 0.5626 (m-30) cc_final: 0.5138 (m-30) REVERT: M 41 PHE cc_start: 0.6527 (t80) cc_final: 0.6303 (t80) REVERT: M 48 VAL cc_start: 0.9064 (t) cc_final: 0.8834 (m) REVERT: M 109 LEU cc_start: 0.8372 (mt) cc_final: 0.8163 (mt) REVERT: M 241 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7100 (mt-10) REVERT: N 56 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8437 (mt) REVERT: N 72 GLN cc_start: 0.8605 (mt0) cc_final: 0.8200 (mt0) REVERT: N 85 GLN cc_start: 0.7504 (pp30) cc_final: 0.7281 (pp30) REVERT: N 108 MET cc_start: 0.8115 (mmm) cc_final: 0.7893 (mmt) REVERT: N 140 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8443 (ttmt) REVERT: N 243 ASN cc_start: 0.7744 (t0) cc_final: 0.7534 (t0) REVERT: N 282 LEU cc_start: 0.7365 (mt) cc_final: 0.6890 (pt) REVERT: S 38 LEU cc_start: 0.8792 (pt) cc_final: 0.8333 (mm) REVERT: S 41 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6623 (tm-30) REVERT: S 64 ASP cc_start: 0.7262 (p0) cc_final: 0.7060 (p0) REVERT: S 120 ASN cc_start: 0.7996 (m-40) cc_final: 0.7635 (m110) REVERT: S 163 GLU cc_start: 0.8016 (pp20) cc_final: 0.7704 (pp20) REVERT: V 512 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.3738 (ttmt) REVERT: V 530 MET cc_start: 0.3932 (mpp) cc_final: 0.3056 (mpp) REVERT: V 613 ASP cc_start: 0.3648 (OUTLIER) cc_final: 0.3155 (t0) REVERT: V 672 MET cc_start: 0.0875 (mmp) cc_final: 0.0481 (mmp) REVERT: V 872 MET cc_start: 0.4884 (tpt) cc_final: 0.4251 (mtm) REVERT: V 960 HIS cc_start: 0.5815 (m170) cc_final: 0.5593 (m170) REVERT: V 1029 PHE cc_start: 0.5107 (OUTLIER) cc_final: 0.3210 (m-80) REVERT: V 1064 TYR cc_start: 0.1842 (OUTLIER) cc_final: 0.1032 (t80) REVERT: V 1068 MET cc_start: 0.7272 (ppp) cc_final: 0.7046 (ppp) REVERT: V 1086 ILE cc_start: 0.8273 (tp) cc_final: 0.8018 (pt) REVERT: a 109 LEU cc_start: 0.8490 (tp) cc_final: 0.7963 (mt) REVERT: a 119 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6881 (tp30) REVERT: a 237 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8911 (mp) REVERT: b 17 ASP cc_start: 0.7464 (t0) cc_final: 0.7200 (t0) REVERT: b 46 ASN cc_start: 0.8270 (t0) cc_final: 0.7963 (t0) REVERT: c 219 MET cc_start: 0.1363 (ttm) cc_final: -0.0515 (ptm) REVERT: d 30 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7443 (ttp80) REVERT: d 35 GLU cc_start: 0.7692 (tp30) cc_final: 0.7363 (tp30) REVERT: d 48 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6837 (pt) REVERT: e 30 TRP cc_start: 0.2603 (OUTLIER) cc_final: 0.1999 (t-100) REVERT: e 90 ILE cc_start: 0.4952 (mm) cc_final: 0.4589 (mm) REVERT: g 23 ARG cc_start: 0.3825 (mtm180) cc_final: 0.2420 (mmt180) REVERT: g 35 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5943 (t80) REVERT: h 77 ASP cc_start: 0.3538 (m-30) cc_final: 0.2733 (t0) REVERT: j 50 ASN cc_start: 0.5217 (OUTLIER) cc_final: 0.4451 (m-40) REVERT: o 275 TYR cc_start: 0.9138 (m-80) cc_final: 0.8583 (m-80) REVERT: o 438 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6887 (tm-30) REVERT: p 50 MET cc_start: 0.3856 (mtt) cc_final: 0.3084 (ttm) REVERT: q 49 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.3565 (t80) REVERT: y 205 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7716 (tm-30) outliers start: 334 outliers final: 186 residues processed: 1371 average time/residue: 0.7103 time to fit residues: 1708.9926 Evaluate side-chains 1177 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 972 time to evaluate : 6.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1164 TYR Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1401 SER Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1429 MET Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1745 SER Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1906 SER Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain H residue 351 MET Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 405 SER Chi-restraints excluded: chain J residue 415 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 239 SER Chi-restraints excluded: chain S residue 240 ASP Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain S residue 248 ASN Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 512 LYS Chi-restraints excluded: chain V residue 517 THR Chi-restraints excluded: chain V residue 525 PHE Chi-restraints excluded: chain V residue 559 ASP Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 613 ASP Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 767 ASP Chi-restraints excluded: chain V residue 789 ILE Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 911 LEU Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 1029 PHE Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain V residue 1087 GLU Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 103 THR Chi-restraints excluded: chain a residue 158 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 97 MET Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 30 TRP Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 94 SER Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 235 THR Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain o residue 407 LEU Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain o residue 444 CYS Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 156 ASP Chi-restraints excluded: chain y residue 166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 878 optimal weight: 0.9980 chunk 668 optimal weight: 9.9990 chunk 461 optimal weight: 9.9990 chunk 98 optimal weight: 0.0030 chunk 424 optimal weight: 0.4980 chunk 596 optimal weight: 50.0000 chunk 892 optimal weight: 5.9990 chunk 944 optimal weight: 40.0000 chunk 466 optimal weight: 8.9990 chunk 845 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 713 ASN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1449 ASN A1603 ASN ** A1635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1763 ASN C 101 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 869 HIS ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 ASN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS S 78 GLN ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 933 GLN V 999 GLN ** V1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 HIS ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 327 HIS ** c 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 43 GLN o 176 HIS ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 82974 Z= 0.201 Angle : 0.618 14.140 114660 Z= 0.313 Chirality : 0.042 0.297 13674 Planarity : 0.004 0.108 12979 Dihedral : 17.664 176.949 17382 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 4.26 % Allowed : 16.80 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.09), residues: 9070 helix: 1.45 (0.08), residues: 4184 sheet: -1.50 (0.16), residues: 1059 loop : -1.54 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP o 410 HIS 0.011 0.001 HIS S 117 PHE 0.036 0.002 PHE V1025 TYR 0.029 0.002 TYR S 105 ARG 0.008 0.001 ARG P 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1149 time to evaluate : 6.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7067 (pp20) cc_final: 0.6846 (pp20) REVERT: A 409 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 497 GLN cc_start: 0.8301 (pt0) cc_final: 0.8048 (pt0) REVERT: A 593 LEU cc_start: 0.9590 (tm) cc_final: 0.9196 (tt) REVERT: A 754 TYR cc_start: 0.8134 (t80) cc_final: 0.7855 (t80) REVERT: A 763 MET cc_start: 0.8337 (tpp) cc_final: 0.7969 (tpt) REVERT: A 848 ASN cc_start: 0.8968 (t0) cc_final: 0.8658 (t0) REVERT: A 912 LEU cc_start: 0.9110 (tp) cc_final: 0.8897 (tp) REVERT: A 941 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 1122 ASP cc_start: 0.7543 (m-30) cc_final: 0.7288 (m-30) REVERT: A 1145 MET cc_start: 0.8444 (mtm) cc_final: 0.8243 (mtm) REVERT: A 1261 SER cc_start: 0.9045 (t) cc_final: 0.8494 (p) REVERT: A 1262 MET cc_start: 0.7913 (ttm) cc_final: 0.7695 (ttm) REVERT: A 1330 LYS cc_start: 0.8816 (tppp) cc_final: 0.8184 (mtpt) REVERT: A 1616 ARG cc_start: 0.8920 (ptt90) cc_final: 0.8700 (ptt180) REVERT: A 1703 MET cc_start: 0.8242 (mtp) cc_final: 0.7938 (mtp) REVERT: A 1732 MET cc_start: 0.8123 (mtp) cc_final: 0.7825 (ttt) REVERT: A 1802 MET cc_start: 0.7809 (mmm) cc_final: 0.7336 (mmm) REVERT: A 1806 MET cc_start: 0.8287 (mtp) cc_final: 0.7960 (mtp) REVERT: A 1844 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6921 (p90) REVERT: A 1908 LEU cc_start: 0.9284 (tp) cc_final: 0.8844 (mt) REVERT: A 1933 ILE cc_start: 0.9385 (mt) cc_final: 0.9089 (tt) REVERT: A 1938 LYS cc_start: 0.8699 (tptt) cc_final: 0.8328 (pttm) REVERT: A 2024 MET cc_start: 0.7589 (mmt) cc_final: 0.7268 (mmp) REVERT: C 111 LYS cc_start: 0.8433 (pttt) cc_final: 0.8015 (tptp) REVERT: C 166 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7651 (tppt) REVERT: C 679 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6918 (mt-10) REVERT: C 775 ILE cc_start: 0.7466 (mt) cc_final: 0.7195 (mm) REVERT: C 804 LYS cc_start: 0.8833 (tppt) cc_final: 0.8321 (mtmm) REVERT: C 817 GLN cc_start: 0.6098 (pm20) cc_final: 0.5845 (pm20) REVERT: H 294 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7729 (tppt) REVERT: H 351 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7844 (mtp) REVERT: H 452 LEU cc_start: 0.7068 (tp) cc_final: 0.6864 (tp) REVERT: H 477 MET cc_start: 0.6695 (mmp) cc_final: 0.5996 (mmt) REVERT: J 163 THR cc_start: 0.8554 (p) cc_final: 0.8221 (p) REVERT: J 329 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6435 (t70) REVERT: J 362 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7083 (t70) REVERT: J 377 ASP cc_start: 0.8276 (t0) cc_final: 0.7740 (t0) REVERT: K 73 TYR cc_start: 0.8416 (t80) cc_final: 0.8131 (t80) REVERT: L 18 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7793 (mmtm) REVERT: L 25 ASP cc_start: 0.8458 (t0) cc_final: 0.8139 (t0) REVERT: L 53 MET cc_start: 0.8239 (mmm) cc_final: 0.7995 (tpp) REVERT: L 58 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: M 33 TRP cc_start: 0.9004 (t-100) cc_final: 0.8737 (t-100) REVERT: M 240 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: N 26 THR cc_start: 0.9315 (m) cc_final: 0.9099 (m) REVERT: N 72 GLN cc_start: 0.8564 (mt0) cc_final: 0.8232 (mt0) REVERT: N 108 MET cc_start: 0.7902 (mmm) cc_final: 0.7671 (mmt) REVERT: N 140 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8434 (ttmt) REVERT: N 282 LEU cc_start: 0.7419 (mt) cc_final: 0.6866 (pt) REVERT: O 18 ASP cc_start: 0.8253 (m-30) cc_final: 0.8037 (m-30) REVERT: O 136 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5631 (mtp) REVERT: P 9 LEU cc_start: 0.8202 (mt) cc_final: 0.7898 (mt) REVERT: P 12 ARG cc_start: 0.8428 (tpt-90) cc_final: 0.7911 (tpp80) REVERT: S 38 LEU cc_start: 0.8738 (pt) cc_final: 0.8326 (mm) REVERT: S 41 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6663 (tm-30) REVERT: S 49 ARG cc_start: 0.6968 (tmm-80) cc_final: 0.6623 (ttt90) REVERT: S 156 TYR cc_start: 0.8335 (m-80) cc_final: 0.8061 (m-80) REVERT: S 163 GLU cc_start: 0.8067 (pp20) cc_final: 0.7768 (pp20) REVERT: S 246 LEU cc_start: 0.8889 (tp) cc_final: 0.8593 (tp) REVERT: V 502 LEU cc_start: 0.5456 (tp) cc_final: 0.4988 (mm) REVERT: V 527 ASN cc_start: 0.0548 (OUTLIER) cc_final: 0.0261 (p0) REVERT: V 530 MET cc_start: 0.3760 (mpp) cc_final: 0.2758 (mpp) REVERT: V 613 ASP cc_start: 0.3646 (OUTLIER) cc_final: 0.3296 (t0) REVERT: V 665 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4704 (mt) REVERT: V 672 MET cc_start: 0.0693 (mmp) cc_final: 0.0089 (mmp) REVERT: V 849 MET cc_start: 0.6471 (mmp) cc_final: 0.6163 (mmp) REVERT: V 864 MET cc_start: 0.4140 (ptp) cc_final: 0.3823 (ptp) REVERT: V 872 MET cc_start: 0.4648 (tpt) cc_final: 0.4387 (mtm) REVERT: V 903 MET cc_start: 0.4786 (pmm) cc_final: 0.4522 (pmm) REVERT: V 1029 PHE cc_start: 0.4699 (OUTLIER) cc_final: 0.3648 (m-80) REVERT: V 1064 TYR cc_start: 0.1477 (OUTLIER) cc_final: 0.0510 (t80) REVERT: V 1068 MET cc_start: 0.7252 (ppp) cc_final: 0.6109 (ttm) REVERT: V 1074 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7718 (tt) REVERT: V 1081 SER cc_start: 0.6396 (m) cc_final: 0.5744 (p) REVERT: a 109 LEU cc_start: 0.8347 (tp) cc_final: 0.7776 (mt) REVERT: a 184 MET cc_start: 0.8507 (mmm) cc_final: 0.8098 (mmm) REVERT: b 17 ASP cc_start: 0.7596 (t0) cc_final: 0.7282 (t0) REVERT: c 219 MET cc_start: 0.1112 (ttm) cc_final: -0.0355 (ptm) REVERT: c 304 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8372 (mm-40) REVERT: d 30 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7442 (ttp80) REVERT: d 35 GLU cc_start: 0.7161 (tp30) cc_final: 0.6794 (tp30) REVERT: d 48 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7084 (tp) REVERT: e 30 TRP cc_start: 0.2876 (OUTLIER) cc_final: 0.2504 (t-100) REVERT: e 90 ILE cc_start: 0.4362 (mm) cc_final: 0.4094 (mm) REVERT: g 23 ARG cc_start: 0.3809 (mtm180) cc_final: 0.2581 (mmt180) REVERT: g 35 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5539 (t80) REVERT: j 31 MET cc_start: 0.5536 (mpp) cc_final: 0.4442 (mtt) REVERT: j 50 ASN cc_start: 0.5268 (OUTLIER) cc_final: 0.4625 (m-40) REVERT: l 40 LEU cc_start: 0.1182 (tp) cc_final: 0.0566 (tp) REVERT: o 273 LEU cc_start: 0.8017 (mt) cc_final: 0.7759 (mt) REVERT: o 275 TYR cc_start: 0.9079 (m-80) cc_final: 0.8532 (m-80) REVERT: o 300 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6913 (tptt) REVERT: o 339 MET cc_start: 0.7520 (mmt) cc_final: 0.6971 (mmp) REVERT: o 351 PHE cc_start: 0.8137 (t80) cc_final: 0.7908 (t80) REVERT: o 438 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6950 (tm-30) REVERT: p 50 MET cc_start: 0.3802 (mtt) cc_final: 0.3017 (ttm) REVERT: y 159 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7582 (mmmm) REVERT: y 205 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7541 (tm-30) outliers start: 288 outliers final: 156 residues processed: 1350 average time/residue: 0.7019 time to fit residues: 1668.2115 Evaluate side-chains 1163 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 987 time to evaluate : 7.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1657 ILE Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain H residue 302 SER Chi-restraints excluded: chain H residue 351 MET Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 474 THR Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 182 ILE Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 493 ILE Chi-restraints excluded: chain V residue 525 PHE Chi-restraints excluded: chain V residue 527 ASN Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 609 THR Chi-restraints excluded: chain V residue 613 ASP Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 665 LEU Chi-restraints excluded: chain V residue 681 CYS Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 737 GLU Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 767 ASP Chi-restraints excluded: chain V residue 773 VAL Chi-restraints excluded: chain V residue 789 ILE Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 911 LEU Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 933 GLN Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 1029 PHE Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1074 LEU Chi-restraints excluded: chain V residue 1084 THR Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain V residue 1087 GLU Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 158 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain c residue 97 MET Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 158 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 248 LEU Chi-restraints excluded: chain c residue 325 VAL Chi-restraints excluded: chain c residue 332 ASN Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 30 TRP Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 398 ILE Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain o residue 407 LEU Chi-restraints excluded: chain o residue 410 TRP Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain p residue 35 ILE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain y residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 786 optimal weight: 6.9990 chunk 536 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 703 optimal weight: 0.9980 chunk 389 optimal weight: 0.9990 chunk 805 optimal weight: 9.9990 chunk 652 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 482 optimal weight: 0.6980 chunk 847 optimal weight: 0.8980 chunk 238 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1883 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN C 514 GLN C 647 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 671 GLN ** V 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 208 HIS c 124 ASN ** c 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 ASN n 4 ASN n 12 ASN n 17 HIS n 43 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 82974 Z= 0.173 Angle : 0.597 11.154 114660 Z= 0.301 Chirality : 0.041 0.279 13674 Planarity : 0.004 0.192 12979 Dihedral : 17.527 179.723 17380 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 3.85 % Allowed : 17.99 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.09), residues: 9070 helix: 1.68 (0.08), residues: 4188 sheet: -1.42 (0.15), residues: 1086 loop : -1.44 (0.10), residues: 3796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP o 434 HIS 0.011 0.001 HIS j 28 PHE 0.031 0.001 PHE A1114 TYR 0.036 0.002 TYR S 105 ARG 0.011 0.000 ARG V 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1095 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7150 (pp20) cc_final: 0.6823 (pp20) REVERT: A 497 GLN cc_start: 0.8359 (pt0) cc_final: 0.8144 (pt0) REVERT: A 593 LEU cc_start: 0.9609 (tm) cc_final: 0.9190 (tt) REVERT: A 629 MET cc_start: 0.8472 (tmm) cc_final: 0.8216 (tmm) REVERT: A 651 ASP cc_start: 0.7957 (t0) cc_final: 0.7749 (t0) REVERT: A 754 TYR cc_start: 0.8172 (t80) cc_final: 0.7870 (t80) REVERT: A 912 LEU cc_start: 0.9072 (tp) cc_final: 0.8870 (tp) REVERT: A 917 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5145 (mm-30) REVERT: A 941 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7078 (mt-10) REVERT: A 1085 LYS cc_start: 0.8949 (tptp) cc_final: 0.8687 (tptp) REVERT: A 1122 ASP cc_start: 0.7659 (m-30) cc_final: 0.7359 (m-30) REVERT: A 1261 SER cc_start: 0.8983 (t) cc_final: 0.8426 (p) REVERT: A 1288 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 1330 LYS cc_start: 0.8810 (tppp) cc_final: 0.8197 (mtpt) REVERT: A 1517 TYR cc_start: 0.8947 (m-80) cc_final: 0.7990 (m-80) REVERT: A 1616 ARG cc_start: 0.8971 (ptt90) cc_final: 0.8747 (ptm160) REVERT: A 1659 GLU cc_start: 0.8435 (pt0) cc_final: 0.8233 (pt0) REVERT: A 1732 MET cc_start: 0.7970 (mtp) cc_final: 0.7658 (ttm) REVERT: A 1844 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6690 (p90) REVERT: A 1908 LEU cc_start: 0.9195 (tp) cc_final: 0.8910 (mt) REVERT: A 1933 ILE cc_start: 0.9336 (mt) cc_final: 0.9056 (tt) REVERT: A 1938 LYS cc_start: 0.8667 (tptt) cc_final: 0.8289 (pttm) REVERT: A 2024 MET cc_start: 0.7685 (mmt) cc_final: 0.7353 (mmp) REVERT: C 111 LYS cc_start: 0.8455 (pttt) cc_final: 0.8011 (tptp) REVERT: C 166 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7502 (tppt) REVERT: C 379 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8989 (mp) REVERT: C 477 ASP cc_start: 0.7932 (t0) cc_final: 0.7479 (t70) REVERT: C 773 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7751 (m) REVERT: C 775 ILE cc_start: 0.7477 (mt) cc_final: 0.7206 (mm) REVERT: C 804 LYS cc_start: 0.8848 (tppt) cc_final: 0.8333 (mtmm) REVERT: C 910 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7222 (mm-30) REVERT: H 294 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7744 (tppt) REVERT: H 351 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7830 (mtp) REVERT: H 452 LEU cc_start: 0.7007 (tp) cc_final: 0.6795 (tp) REVERT: H 477 MET cc_start: 0.6615 (mmp) cc_final: 0.5941 (mmt) REVERT: J 329 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6426 (t70) REVERT: J 362 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7068 (t70) REVERT: J 377 ASP cc_start: 0.8270 (t0) cc_final: 0.7751 (t0) REVERT: K 73 TYR cc_start: 0.8463 (t80) cc_final: 0.8186 (t80) REVERT: L 25 ASP cc_start: 0.8453 (t0) cc_final: 0.8116 (t0) REVERT: L 58 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: L 128 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7401 (tp-100) REVERT: L 131 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8091 (tm-30) REVERT: N 72 GLN cc_start: 0.8566 (mt0) cc_final: 0.8266 (mt0) REVERT: N 74 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7293 (p) REVERT: N 108 MET cc_start: 0.7850 (mmm) cc_final: 0.7450 (mmm) REVERT: N 140 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8465 (ttmt) REVERT: N 243 ASN cc_start: 0.7744 (t0) cc_final: 0.7508 (t0) REVERT: O 18 ASP cc_start: 0.8215 (m-30) cc_final: 0.7993 (m-30) REVERT: O 136 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.5576 (mtp) REVERT: P 9 LEU cc_start: 0.8232 (mt) cc_final: 0.7946 (mt) REVERT: S 38 LEU cc_start: 0.8702 (pt) cc_final: 0.8277 (mm) REVERT: S 41 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6616 (tm-30) REVERT: S 156 TYR cc_start: 0.8353 (m-80) cc_final: 0.8039 (m-80) REVERT: S 163 GLU cc_start: 0.8069 (pp20) cc_final: 0.7779 (pp20) REVERT: V 522 GLU cc_start: 0.3727 (OUTLIER) cc_final: 0.3349 (tp30) REVERT: V 530 MET cc_start: 0.3545 (mpp) cc_final: 0.2744 (mpp) REVERT: V 613 ASP cc_start: 0.3740 (OUTLIER) cc_final: 0.3314 (t0) REVERT: V 672 MET cc_start: 0.0667 (mmp) cc_final: 0.0065 (mmp) REVERT: V 872 MET cc_start: 0.4813 (tpt) cc_final: 0.4416 (mtm) REVERT: V 1064 TYR cc_start: 0.1417 (OUTLIER) cc_final: 0.0564 (t80) REVERT: V 1074 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7725 (tt) REVERT: a 109 LEU cc_start: 0.8368 (tp) cc_final: 0.7832 (mt) REVERT: a 119 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6852 (tp30) REVERT: a 141 LYS cc_start: 0.8318 (mttt) cc_final: 0.7755 (tptt) REVERT: a 208 HIS cc_start: 0.7744 (t-90) cc_final: 0.7226 (t-170) REVERT: b 17 ASP cc_start: 0.7660 (t0) cc_final: 0.7340 (t0) REVERT: b 35 MET cc_start: 0.5343 (mmm) cc_final: 0.5087 (mmt) REVERT: c 219 MET cc_start: 0.1124 (ttm) cc_final: -0.0368 (ptm) REVERT: c 304 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8374 (mm-40) REVERT: c 337 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: d 30 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7394 (ttp80) REVERT: d 48 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6984 (tp) REVERT: d 69 ILE cc_start: 0.7804 (mt) cc_final: 0.7401 (tp) REVERT: e 30 TRP cc_start: 0.2786 (OUTLIER) cc_final: 0.2216 (t-100) REVERT: e 90 ILE cc_start: 0.4970 (mm) cc_final: 0.4713 (mm) REVERT: g 23 ARG cc_start: 0.3659 (mtm180) cc_final: 0.2407 (mmt180) REVERT: g 35 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.5505 (t80) REVERT: h 21 ASN cc_start: 0.2947 (OUTLIER) cc_final: 0.1514 (t0) REVERT: j 99 ASP cc_start: 0.4813 (p0) cc_final: 0.4531 (t0) REVERT: m 31 MET cc_start: 0.3590 (mmm) cc_final: 0.3208 (mmm) REVERT: o 273 LEU cc_start: 0.8007 (mt) cc_final: 0.7790 (mt) REVERT: o 275 TYR cc_start: 0.9013 (m-80) cc_final: 0.8554 (m-80) REVERT: o 300 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6889 (tptt) REVERT: o 321 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8338 (mm-30) REVERT: o 333 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6520 (p0) REVERT: o 339 MET cc_start: 0.7445 (mmt) cc_final: 0.7023 (mmp) REVERT: o 351 PHE cc_start: 0.8081 (t80) cc_final: 0.7846 (t80) REVERT: o 356 MET cc_start: 0.8455 (mmm) cc_final: 0.7806 (mmm) REVERT: o 366 LYS cc_start: 0.7687 (mptt) cc_final: 0.7303 (tppt) REVERT: p 50 MET cc_start: 0.3674 (mtt) cc_final: 0.2908 (ttm) REVERT: q 49 PHE cc_start: 0.5402 (OUTLIER) cc_final: 0.3593 (t80) REVERT: y 106 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7271 (pp20) REVERT: y 177 GLU cc_start: 0.7255 (tp30) cc_final: 0.6521 (tm-30) REVERT: y 205 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7499 (tm-30) outliers start: 260 outliers final: 160 residues processed: 1272 average time/residue: 0.7078 time to fit residues: 1583.8889 Evaluate side-chains 1144 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 962 time to evaluate : 6.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 351 MET Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 260 GLU Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 497 ARG Chi-restraints excluded: chain V residue 522 GLU Chi-restraints excluded: chain V residue 525 PHE Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 613 ASP Chi-restraints excluded: chain V residue 681 CYS Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 737 GLU Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 767 ASP Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1074 LEU Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 174 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 248 LEU Chi-restraints excluded: chain c residue 325 VAL Chi-restraints excluded: chain c residue 337 GLU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 30 TRP Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 308 PHE Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 333 ASP Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain p residue 35 ILE Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 317 optimal weight: 0.9980 chunk 850 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 554 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 945 optimal weight: 8.9990 chunk 784 optimal weight: 2.9990 chunk 437 optimal weight: 7.9990 chunk 78 optimal weight: 0.0050 chunk 312 optimal weight: 4.9990 chunk 496 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 429 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 ASN ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN C 929 GLN H 363 ASN J 113 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 671 GLN ** V 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 43 GLN o 291 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 82974 Z= 0.171 Angle : 0.589 15.772 114660 Z= 0.296 Chirality : 0.041 0.301 13674 Planarity : 0.004 0.152 12979 Dihedral : 17.433 177.177 17378 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 4.02 % Allowed : 18.46 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 9070 helix: 1.85 (0.08), residues: 4187 sheet: -1.34 (0.15), residues: 1099 loop : -1.33 (0.10), residues: 3784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP o 434 HIS 0.008 0.001 HIS j 28 PHE 0.037 0.001 PHE V 953 TYR 0.033 0.001 TYR M 34 ARG 0.010 0.000 ARG j 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1060 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7060 (pp20) cc_final: 0.6823 (pp20) REVERT: A 497 GLN cc_start: 0.8419 (pt0) cc_final: 0.8145 (pt0) REVERT: A 629 MET cc_start: 0.8403 (tmm) cc_final: 0.8195 (tmm) REVERT: A 651 ASP cc_start: 0.7942 (t0) cc_final: 0.7696 (t0) REVERT: A 754 TYR cc_start: 0.8141 (t80) cc_final: 0.7780 (t80) REVERT: A 917 GLU cc_start: 0.5898 (mm-30) cc_final: 0.5202 (mm-30) REVERT: A 941 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7067 (mt-10) REVERT: A 1085 LYS cc_start: 0.8988 (tptp) cc_final: 0.8733 (tptp) REVERT: A 1122 ASP cc_start: 0.7661 (m-30) cc_final: 0.7374 (m-30) REVERT: A 1261 SER cc_start: 0.9031 (t) cc_final: 0.8477 (p) REVERT: A 1266 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7549 (mt-10) REVERT: A 1288 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 1291 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7563 (tp30) REVERT: A 1330 LYS cc_start: 0.8821 (tppp) cc_final: 0.8212 (mtpt) REVERT: A 1517 TYR cc_start: 0.8950 (m-80) cc_final: 0.8061 (m-80) REVERT: A 1521 ARG cc_start: 0.7290 (mtp180) cc_final: 0.6878 (mtp85) REVERT: A 1732 MET cc_start: 0.7988 (mtp) cc_final: 0.7691 (ttm) REVERT: A 1844 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.6894 (p90) REVERT: A 1908 LEU cc_start: 0.9155 (tp) cc_final: 0.8835 (mt) REVERT: A 1933 ILE cc_start: 0.9349 (mt) cc_final: 0.9064 (tt) REVERT: A 1938 LYS cc_start: 0.8516 (tptt) cc_final: 0.8195 (pttm) REVERT: A 2024 MET cc_start: 0.7660 (mmt) cc_final: 0.7347 (mmp) REVERT: C 111 LYS cc_start: 0.8464 (pttt) cc_final: 0.7996 (tptp) REVERT: C 166 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7484 (tppt) REVERT: C 773 VAL cc_start: 0.7967 (m) cc_final: 0.7669 (m) REVERT: C 775 ILE cc_start: 0.7586 (mt) cc_final: 0.7357 (mm) REVERT: C 804 LYS cc_start: 0.8828 (tppt) cc_final: 0.8377 (mtmm) REVERT: C 910 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7242 (mm-30) REVERT: C 911 SER cc_start: 0.8869 (p) cc_final: 0.8660 (p) REVERT: H 294 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7750 (tppt) REVERT: H 351 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7820 (mtp) REVERT: H 477 MET cc_start: 0.6586 (mmp) cc_final: 0.5943 (mmt) REVERT: J 220 TYR cc_start: 0.9046 (m-80) cc_final: 0.8809 (m-80) REVERT: J 329 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6438 (t70) REVERT: J 362 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.6745 (t0) REVERT: J 377 ASP cc_start: 0.8312 (t0) cc_final: 0.7763 (t0) REVERT: K 73 TYR cc_start: 0.8465 (t80) cc_final: 0.8211 (t80) REVERT: K 202 MET cc_start: 0.8015 (tpp) cc_final: 0.7455 (mmm) REVERT: L 18 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7725 (mmtm) REVERT: L 25 ASP cc_start: 0.8331 (t0) cc_final: 0.8058 (t0) REVERT: L 53 MET cc_start: 0.8195 (mmm) cc_final: 0.7890 (tpp) REVERT: L 58 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: L 128 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7286 (tp-100) REVERT: L 131 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8075 (tm-30) REVERT: M 240 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: N 74 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7290 (p) REVERT: N 108 MET cc_start: 0.7831 (mmm) cc_final: 0.7477 (mmm) REVERT: N 243 ASN cc_start: 0.7739 (t0) cc_final: 0.7498 (t0) REVERT: O 79 GLU cc_start: 0.7615 (tt0) cc_final: 0.7325 (tt0) REVERT: P 9 LEU cc_start: 0.8236 (mt) cc_final: 0.7959 (mt) REVERT: S 38 LEU cc_start: 0.8649 (pt) cc_final: 0.8207 (mm) REVERT: S 41 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6566 (tm-30) REVERT: S 156 TYR cc_start: 0.8243 (m-80) cc_final: 0.8030 (m-80) REVERT: S 163 GLU cc_start: 0.8060 (pp20) cc_final: 0.7779 (pp20) REVERT: V 497 ARG cc_start: 0.2241 (OUTLIER) cc_final: 0.0663 (mmt90) REVERT: V 522 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.3157 (tp30) REVERT: V 601 MET cc_start: 0.0914 (tpp) cc_final: 0.0425 (tpp) REVERT: V 613 ASP cc_start: 0.4007 (OUTLIER) cc_final: 0.3573 (t0) REVERT: V 672 MET cc_start: 0.0704 (mmp) cc_final: 0.0130 (mmp) REVERT: V 872 MET cc_start: 0.4806 (tpt) cc_final: 0.4299 (mtm) REVERT: V 898 MET cc_start: 0.4635 (ptm) cc_final: 0.4405 (tmm) REVERT: V 903 MET cc_start: 0.3965 (pmm) cc_final: 0.3632 (pmm) REVERT: V 1064 TYR cc_start: 0.1564 (OUTLIER) cc_final: 0.0676 (t80) REVERT: V 1074 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7731 (tt) REVERT: a 109 LEU cc_start: 0.8335 (tp) cc_final: 0.7840 (mt) REVERT: a 119 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6836 (tp30) REVERT: a 141 LYS cc_start: 0.8303 (mttt) cc_final: 0.7726 (tptt) REVERT: a 208 HIS cc_start: 0.7585 (t-90) cc_final: 0.7030 (t-170) REVERT: b 17 ASP cc_start: 0.7591 (t0) cc_final: 0.7290 (t0) REVERT: c 219 MET cc_start: 0.1084 (ttm) cc_final: -0.0351 (ptm) REVERT: c 304 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8418 (mm-40) REVERT: c 337 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: d 30 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7426 (ttp80) REVERT: d 35 GLU cc_start: 0.7086 (tp30) cc_final: 0.6840 (tp30) REVERT: d 40 MET cc_start: 0.8229 (mpp) cc_final: 0.7778 (mpp) REVERT: d 48 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6974 (tp) REVERT: d 69 ILE cc_start: 0.7753 (mt) cc_final: 0.7369 (tp) REVERT: e 30 TRP cc_start: 0.2967 (OUTLIER) cc_final: 0.2481 (t-100) REVERT: e 90 ILE cc_start: 0.4719 (mm) cc_final: 0.4417 (mm) REVERT: g 23 ARG cc_start: 0.3687 (mtm180) cc_final: 0.2295 (mmt180) REVERT: g 35 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5427 (t80) REVERT: h 21 ASN cc_start: 0.2706 (OUTLIER) cc_final: 0.1328 (t0) REVERT: j 99 ASP cc_start: 0.4699 (p0) cc_final: 0.4480 (t0) REVERT: o 236 GLU cc_start: 0.6749 (mp0) cc_final: 0.6339 (mp0) REVERT: o 247 ASN cc_start: 0.7786 (p0) cc_final: 0.6680 (m-40) REVERT: o 273 LEU cc_start: 0.7833 (mt) cc_final: 0.7585 (mt) REVERT: o 275 TYR cc_start: 0.8964 (m-80) cc_final: 0.8492 (m-80) REVERT: o 300 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6940 (tptt) REVERT: o 321 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8308 (mm-30) REVERT: o 351 PHE cc_start: 0.8114 (t80) cc_final: 0.7898 (t80) REVERT: o 356 MET cc_start: 0.8485 (mmm) cc_final: 0.7896 (mmm) REVERT: o 366 LYS cc_start: 0.7960 (mptt) cc_final: 0.7340 (tppt) REVERT: o 367 PRO cc_start: 0.7382 (Cg_exo) cc_final: 0.6913 (Cg_endo) REVERT: p 50 MET cc_start: 0.3629 (mtt) cc_final: 0.2873 (ttm) REVERT: p 91 THR cc_start: 0.2899 (OUTLIER) cc_final: 0.2466 (t) REVERT: q 49 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.3392 (t80) REVERT: y 177 GLU cc_start: 0.7220 (tp30) cc_final: 0.6869 (tm-30) REVERT: y 205 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7534 (tm-30) outliers start: 272 outliers final: 175 residues processed: 1259 average time/residue: 0.7020 time to fit residues: 1558.4878 Evaluate side-chains 1165 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 967 time to evaluate : 6.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1600 GLN Chi-restraints excluded: chain A residue 1603 ASN Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1875 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain H residue 351 MET Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 474 THR Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 497 ARG Chi-restraints excluded: chain V residue 505 VAL Chi-restraints excluded: chain V residue 522 GLU Chi-restraints excluded: chain V residue 525 PHE Chi-restraints excluded: chain V residue 564 ILE Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 613 ASP Chi-restraints excluded: chain V residue 652 ILE Chi-restraints excluded: chain V residue 681 CYS Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 911 LEU Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 953 PHE Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 989 HIS Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1074 LEU Chi-restraints excluded: chain V residue 1081 SER Chi-restraints excluded: chain V residue 1084 THR Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 99 ILE Chi-restraints excluded: chain c residue 158 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 248 LEU Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain c residue 325 VAL Chi-restraints excluded: chain c residue 332 ASN Chi-restraints excluded: chain c residue 337 GLU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 30 TRP Chi-restraints excluded: chain e residue 35 ILE Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 191 ASP Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 308 PHE Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 398 ILE Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain r residue 47 ASN Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 205 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 911 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 538 optimal weight: 7.9990 chunk 690 optimal weight: 6.9990 chunk 534 optimal weight: 9.9990 chunk 795 optimal weight: 6.9990 chunk 527 optimal weight: 9.9990 chunk 941 optimal weight: 0.7980 chunk 589 optimal weight: 7.9990 chunk 574 optimal weight: 30.0000 chunk 434 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 643 ASN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1763 ASN A1883 ASN C 112 ASN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 HIS ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN N 72 GLN ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 606 HIS V 671 GLN ** V 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 35 GLN ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 309 HIS ** c 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 54 ASN ** m 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 12 ASN o 336 GLN ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 82974 Z= 0.408 Angle : 0.737 15.501 114660 Z= 0.374 Chirality : 0.046 0.325 13674 Planarity : 0.005 0.141 12979 Dihedral : 17.603 179.965 17378 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.48 % Favored : 93.44 % Rotamer: Outliers : 4.66 % Allowed : 18.42 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 9070 helix: 1.51 (0.08), residues: 4170 sheet: -1.40 (0.16), residues: 1054 loop : -1.48 (0.10), residues: 3846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP o 434 HIS 0.011 0.002 HIS S 117 PHE 0.054 0.003 PHE A 557 TYR 0.040 0.003 TYR S 105 ARG 0.010 0.001 ARG P 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 960 time to evaluate : 6.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8241 (tpp) cc_final: 0.7888 (ttt) REVERT: A 372 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: A 651 ASP cc_start: 0.8187 (t0) cc_final: 0.7983 (t0) REVERT: A 754 TYR cc_start: 0.8466 (t80) cc_final: 0.8041 (t80) REVERT: A 912 LEU cc_start: 0.9157 (tp) cc_final: 0.8918 (tp) REVERT: A 917 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5437 (mm-30) REVERT: A 941 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7125 (mt-10) REVERT: A 988 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 1122 ASP cc_start: 0.7778 (m-30) cc_final: 0.7462 (m-30) REVERT: A 1261 SER cc_start: 0.9212 (t) cc_final: 0.8577 (p) REVERT: A 1291 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7537 (tp30) REVERT: A 1330 LYS cc_start: 0.8890 (tppp) cc_final: 0.8225 (mtpt) REVERT: A 1520 GLU cc_start: 0.6753 (pm20) cc_final: 0.6484 (pm20) REVERT: A 1521 ARG cc_start: 0.7380 (mtp180) cc_final: 0.6839 (mtp85) REVERT: A 1603 ASN cc_start: 0.8734 (m-40) cc_final: 0.8534 (m-40) REVERT: A 1659 GLU cc_start: 0.8459 (pt0) cc_final: 0.8195 (pt0) REVERT: A 1732 MET cc_start: 0.8186 (mtp) cc_final: 0.7949 (ttm) REVERT: A 1740 TYR cc_start: 0.8192 (t80) cc_final: 0.7563 (t80) REVERT: A 1844 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7756 (p90) REVERT: A 1916 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7585 (tp30) REVERT: A 1933 ILE cc_start: 0.9392 (mt) cc_final: 0.9122 (tt) REVERT: A 1938 LYS cc_start: 0.8667 (tptt) cc_final: 0.8211 (pptt) REVERT: A 1979 MET cc_start: 0.8591 (mmm) cc_final: 0.8016 (mmp) REVERT: A 2010 LEU cc_start: 0.8782 (tp) cc_final: 0.8282 (mt) REVERT: C 111 LYS cc_start: 0.8567 (pttt) cc_final: 0.8087 (tptp) REVERT: C 166 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7628 (tppt) REVERT: C 276 ASP cc_start: 0.7662 (m-30) cc_final: 0.7199 (m-30) REVERT: C 804 LYS cc_start: 0.8848 (tppt) cc_final: 0.8199 (mtmm) REVERT: C 880 MET cc_start: 0.8872 (mmm) cc_final: 0.8486 (mmt) REVERT: H 294 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8205 (tttt) REVERT: H 477 MET cc_start: 0.6698 (mmp) cc_final: 0.5993 (mmt) REVERT: H 478 ARG cc_start: 0.8054 (mmt90) cc_final: 0.7568 (tpp80) REVERT: J 329 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6501 (t0) REVERT: J 377 ASP cc_start: 0.8178 (t0) cc_final: 0.7748 (t0) REVERT: L 25 ASP cc_start: 0.8567 (t0) cc_final: 0.8237 (t0) REVERT: L 58 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: L 128 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7419 (tp-100) REVERT: M 240 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: M 241 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6760 (tt0) REVERT: M 242 LEU cc_start: 0.9264 (tp) cc_final: 0.9033 (tt) REVERT: N 56 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8510 (mp) REVERT: N 72 GLN cc_start: 0.8432 (mt0) cc_final: 0.8066 (mt0) REVERT: N 108 MET cc_start: 0.7996 (mmm) cc_final: 0.7551 (mmm) REVERT: N 243 ASN cc_start: 0.7904 (t0) cc_final: 0.7693 (t0) REVERT: S 38 LEU cc_start: 0.8735 (pt) cc_final: 0.8219 (mt) REVERT: S 41 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6843 (tm-30) REVERT: S 53 GLU cc_start: 0.8448 (tt0) cc_final: 0.8185 (tm-30) REVERT: S 120 ASN cc_start: 0.7722 (m-40) cc_final: 0.7514 (m110) REVERT: S 163 GLU cc_start: 0.8254 (pp20) cc_final: 0.7837 (pp20) REVERT: V 525 PHE cc_start: 0.3001 (OUTLIER) cc_final: 0.2784 (t80) REVERT: V 613 ASP cc_start: 0.4217 (OUTLIER) cc_final: 0.3840 (t0) REVERT: V 672 MET cc_start: 0.0645 (mmp) cc_final: 0.0161 (mmp) REVERT: V 711 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.3969 (tp) REVERT: V 898 MET cc_start: 0.4958 (ptm) cc_final: 0.4681 (tmm) REVERT: V 1064 TYR cc_start: 0.2193 (OUTLIER) cc_final: 0.0718 (t80) REVERT: V 1068 MET cc_start: 0.7167 (ppp) cc_final: 0.6812 (ttm) REVERT: a 119 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6948 (tp30) REVERT: a 141 LYS cc_start: 0.8379 (mttt) cc_final: 0.7848 (tptt) REVERT: a 190 ASN cc_start: 0.6254 (OUTLIER) cc_final: 0.5829 (t0) REVERT: b 17 ASP cc_start: 0.7315 (t0) cc_final: 0.7065 (t0) REVERT: c 43 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.5849 (p90) REVERT: c 219 MET cc_start: 0.1106 (ttm) cc_final: -0.0412 (ptm) REVERT: c 304 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8445 (mm-40) REVERT: d 30 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7690 (ttp80) REVERT: d 40 MET cc_start: 0.8271 (mpp) cc_final: 0.7455 (mpp) REVERT: d 48 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.6994 (tp) REVERT: d 84 PHE cc_start: 0.7691 (m-80) cc_final: 0.7383 (m-80) REVERT: e 90 ILE cc_start: 0.5083 (mm) cc_final: 0.4768 (mm) REVERT: g 35 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5578 (t80) REVERT: j 50 ASN cc_start: 0.5570 (OUTLIER) cc_final: 0.4435 (m-40) REVERT: o 275 TYR cc_start: 0.9234 (m-80) cc_final: 0.8627 (m-80) REVERT: o 300 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7535 (tptt) REVERT: o 321 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8381 (mm-30) REVERT: o 356 MET cc_start: 0.8393 (mmm) cc_final: 0.8031 (mmp) REVERT: o 410 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.7042 (m-10) REVERT: p 50 MET cc_start: 0.3714 (mtt) cc_final: 0.2928 (ttm) REVERT: q 49 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.3499 (t80) REVERT: y 205 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7728 (tm-30) outliers start: 315 outliers final: 221 residues processed: 1188 average time/residue: 0.7181 time to fit residues: 1514.6665 Evaluate side-chains 1129 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 890 time to evaluate : 6.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 GLN Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1695 ASN Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1745 SER Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1875 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain A residue 2078 GLU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 474 THR Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 405 SER Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 238 TRP Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 505 VAL Chi-restraints excluded: chain V residue 517 THR Chi-restraints excluded: chain V residue 525 PHE Chi-restraints excluded: chain V residue 564 ILE Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 613 ASP Chi-restraints excluded: chain V residue 652 ILE Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 711 LEU Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 767 ASP Chi-restraints excluded: chain V residue 773 VAL Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 906 THR Chi-restraints excluded: chain V residue 915 VAL Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 953 PHE Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1081 SER Chi-restraints excluded: chain V residue 1084 THR Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 103 THR Chi-restraints excluded: chain a residue 190 ASN Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 197 VAL Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 43 TYR Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 97 MET Chi-restraints excluded: chain c residue 158 VAL Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain c residue 309 HIS Chi-restraints excluded: chain c residue 337 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 191 ASP Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 235 THR Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 253 VAL Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 308 PHE Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 398 ILE Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain o residue 410 TRP Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain r residue 47 ASN Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 156 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 582 optimal weight: 40.0000 chunk 376 optimal weight: 10.0000 chunk 562 optimal weight: 0.8980 chunk 283 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 598 optimal weight: 8.9990 chunk 641 optimal weight: 40.0000 chunk 465 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 740 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN A 643 ASN A 739 ASN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1763 ASN A1883 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 ASN N 69 ASN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 833 ASN V 999 GLN ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 12 ASN ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 82974 Z= 0.213 Angle : 0.624 17.240 114660 Z= 0.313 Chirality : 0.042 0.291 13674 Planarity : 0.004 0.104 12979 Dihedral : 17.506 178.941 17378 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 3.73 % Allowed : 20.13 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.09), residues: 9070 helix: 1.78 (0.08), residues: 4169 sheet: -1.34 (0.16), residues: 1067 loop : -1.34 (0.10), residues: 3834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP o 434 HIS 0.021 0.001 HIS c 309 PHE 0.049 0.002 PHE A 557 TYR 0.028 0.002 TYR S 105 ARG 0.021 0.001 ARG V 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1012 time to evaluate : 6.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7130 (pp20) cc_final: 0.6369 (pp20) REVERT: A 179 MET cc_start: 0.8197 (tpp) cc_final: 0.7793 (ttt) REVERT: A 372 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7513 (mtp85) REVERT: A 593 LEU cc_start: 0.9554 (tm) cc_final: 0.9193 (tt) REVERT: A 651 ASP cc_start: 0.8034 (t0) cc_final: 0.7801 (t0) REVERT: A 754 TYR cc_start: 0.8170 (t80) cc_final: 0.7853 (t80) REVERT: A 912 LEU cc_start: 0.9082 (tp) cc_final: 0.8848 (tp) REVERT: A 917 GLU cc_start: 0.6101 (mm-30) cc_final: 0.5297 (mm-30) REVERT: A 941 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 988 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 1067 ASN cc_start: 0.8761 (t0) cc_final: 0.8390 (t0) REVERT: A 1261 SER cc_start: 0.9071 (t) cc_final: 0.8482 (p) REVERT: A 1291 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7395 (tp30) REVERT: A 1330 LYS cc_start: 0.8848 (tppp) cc_final: 0.8207 (mtpt) REVERT: A 1520 GLU cc_start: 0.6803 (pm20) cc_final: 0.6534 (pm20) REVERT: A 1521 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6932 (mtp85) REVERT: A 1732 MET cc_start: 0.8090 (mtp) cc_final: 0.7765 (ttm) REVERT: A 1740 TYR cc_start: 0.8109 (t80) cc_final: 0.7456 (t80) REVERT: A 1806 MET cc_start: 0.8251 (mtp) cc_final: 0.7971 (mtp) REVERT: A 1844 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7590 (p90) REVERT: A 1908 LEU cc_start: 0.9193 (tp) cc_final: 0.8881 (mt) REVERT: A 1933 ILE cc_start: 0.9368 (mt) cc_final: 0.9109 (tt) REVERT: A 1938 LYS cc_start: 0.8519 (tptt) cc_final: 0.8164 (pttm) REVERT: A 2063 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6980 (t80) REVERT: C 111 LYS cc_start: 0.8505 (pttt) cc_final: 0.8010 (mmtt) REVERT: C 166 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7452 (tppt) REVERT: C 276 ASP cc_start: 0.7551 (m-30) cc_final: 0.7061 (m-30) REVERT: C 797 GLN cc_start: 0.8240 (mt0) cc_final: 0.7596 (tm-30) REVERT: C 804 LYS cc_start: 0.8854 (tppt) cc_final: 0.8242 (mtmm) REVERT: C 880 MET cc_start: 0.8895 (mmm) cc_final: 0.8540 (mmt) REVERT: C 910 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7148 (mm-30) REVERT: H 294 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8099 (tttt) REVERT: H 477 MET cc_start: 0.6593 (mmp) cc_final: 0.5995 (mmt) REVERT: J 329 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6578 (t70) REVERT: J 362 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7047 (t70) REVERT: J 377 ASP cc_start: 0.8204 (t0) cc_final: 0.7788 (t0) REVERT: J 420 ASP cc_start: 0.8623 (p0) cc_final: 0.8255 (p0) REVERT: K 73 TYR cc_start: 0.8459 (t80) cc_final: 0.8221 (t80) REVERT: K 202 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8071 (mmm) REVERT: L 25 ASP cc_start: 0.8568 (t0) cc_final: 0.8275 (t0) REVERT: L 58 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: L 128 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7368 (tp-100) REVERT: M 33 TRP cc_start: 0.9127 (t-100) cc_final: 0.8793 (t60) REVERT: M 241 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6591 (tt0) REVERT: N 243 ASN cc_start: 0.7867 (t0) cc_final: 0.7652 (t0) REVERT: P 9 LEU cc_start: 0.8275 (mt) cc_final: 0.7925 (mt) REVERT: S 38 LEU cc_start: 0.8650 (pt) cc_final: 0.8231 (mm) REVERT: S 41 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6581 (tm-30) REVERT: S 53 GLU cc_start: 0.8398 (tt0) cc_final: 0.8120 (tm-30) REVERT: S 163 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7869 (pp20) REVERT: V 489 ARG cc_start: 0.4594 (ttt-90) cc_final: 0.4378 (mtp180) REVERT: V 583 MET cc_start: 0.4334 (mmm) cc_final: 0.3569 (mmt) REVERT: V 672 MET cc_start: 0.1021 (mmp) cc_final: 0.0563 (mmp) REVERT: V 711 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.3956 (tp) REVERT: V 849 MET cc_start: 0.5923 (mmp) cc_final: 0.5606 (mmm) REVERT: V 872 MET cc_start: 0.4401 (mmm) cc_final: 0.3768 (mtt) REVERT: V 1064 TYR cc_start: 0.1970 (OUTLIER) cc_final: 0.0653 (t80) REVERT: a 109 LEU cc_start: 0.8250 (tp) cc_final: 0.7822 (mt) REVERT: a 119 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6899 (tp30) REVERT: a 141 LYS cc_start: 0.8314 (mttt) cc_final: 0.7799 (tptt) REVERT: a 190 ASN cc_start: 0.6131 (p0) cc_final: 0.5744 (t0) REVERT: b 46 ASN cc_start: 0.8157 (m-40) cc_final: 0.7596 (m-40) REVERT: c 219 MET cc_start: 0.1127 (ttm) cc_final: -0.0342 (ptm) REVERT: c 300 ASN cc_start: 0.8538 (m-40) cc_final: 0.7897 (m110) REVERT: c 304 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8416 (mm-40) REVERT: d 30 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7763 (ttp80) REVERT: d 35 GLU cc_start: 0.7074 (tp30) cc_final: 0.6749 (tp30) REVERT: d 40 MET cc_start: 0.8244 (mpp) cc_final: 0.7539 (mpp) REVERT: d 48 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7026 (tp) REVERT: e 90 ILE cc_start: 0.4479 (mm) cc_final: 0.4160 (mm) REVERT: g 35 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5399 (t80) REVERT: h 21 ASN cc_start: 0.3292 (OUTLIER) cc_final: 0.1760 (t0) REVERT: j 31 MET cc_start: 0.5541 (mpp) cc_final: 0.3848 (mtt) REVERT: j 50 ASN cc_start: 0.5570 (OUTLIER) cc_final: 0.4410 (m-40) REVERT: j 99 ASP cc_start: 0.4704 (p0) cc_final: 0.4425 (t0) REVERT: l 40 LEU cc_start: 0.1128 (tp) cc_final: 0.0923 (tp) REVERT: o 216 GLU cc_start: 0.6666 (mp0) cc_final: 0.6180 (mt-10) REVERT: o 236 GLU cc_start: 0.6812 (mp0) cc_final: 0.6479 (mp0) REVERT: o 275 TYR cc_start: 0.9124 (m-80) cc_final: 0.8504 (m-80) REVERT: o 300 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7188 (tptt) REVERT: o 321 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8334 (mm-30) REVERT: o 356 MET cc_start: 0.8294 (mmm) cc_final: 0.7744 (mmm) REVERT: o 366 LYS cc_start: 0.8162 (mptt) cc_final: 0.7450 (tppt) REVERT: o 410 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: p 50 MET cc_start: 0.3418 (mtt) cc_final: 0.2749 (ttm) REVERT: q 49 PHE cc_start: 0.5302 (OUTLIER) cc_final: 0.3447 (t80) REVERT: y 205 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7543 (tm-30) outliers start: 252 outliers final: 196 residues processed: 1191 average time/residue: 0.7360 time to fit residues: 1565.9961 Evaluate side-chains 1153 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 939 time to evaluate : 6.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1745 SER Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1875 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 474 THR Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 238 TRP Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 493 ILE Chi-restraints excluded: chain V residue 505 VAL Chi-restraints excluded: chain V residue 564 ILE Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 652 ILE Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 711 LEU Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 773 VAL Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 906 THR Chi-restraints excluded: chain V residue 911 LEU Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 953 PHE Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 989 HIS Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1081 SER Chi-restraints excluded: chain V residue 1084 THR Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 208 HIS Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 158 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 248 LEU Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain c residue 325 VAL Chi-restraints excluded: chain c residue 332 ASN Chi-restraints excluded: chain c residue 337 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 29 LEU Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 308 PHE Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain o residue 410 TRP Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 156 ASP Chi-restraints excluded: chain y residue 205 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 856 optimal weight: 3.9990 chunk 902 optimal weight: 20.0000 chunk 823 optimal weight: 8.9990 chunk 877 optimal weight: 9.9990 chunk 901 optimal weight: 10.0000 chunk 528 optimal weight: 5.9990 chunk 382 optimal weight: 2.9990 chunk 689 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 792 optimal weight: 0.7980 chunk 829 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 676 GLN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1763 ASN A1883 ASN A1990 ASN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 833 ASN ** V1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 52 HIS n 4 ASN n 12 ASN ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 82974 Z= 0.320 Angle : 0.678 15.935 114660 Z= 0.342 Chirality : 0.044 0.311 13674 Planarity : 0.005 0.103 12979 Dihedral : 17.547 179.787 17378 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 3.99 % Allowed : 20.24 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.09), residues: 9070 helix: 1.64 (0.08), residues: 4158 sheet: -1.30 (0.16), residues: 1066 loop : -1.37 (0.10), residues: 3846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP o 434 HIS 0.009 0.001 HIS S 117 PHE 0.025 0.002 PHE o 302 TYR 0.031 0.002 TYR S 105 ARG 0.009 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 951 time to evaluate : 6.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8216 (tpp) cc_final: 0.7896 (ttt) REVERT: A 372 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: A 594 ASP cc_start: 0.8331 (p0) cc_final: 0.7709 (p0) REVERT: A 754 TYR cc_start: 0.8329 (t80) cc_final: 0.8003 (t80) REVERT: A 764 ASP cc_start: 0.7495 (t0) cc_final: 0.6745 (t0) REVERT: A 912 LEU cc_start: 0.9105 (tp) cc_final: 0.8871 (tp) REVERT: A 917 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5420 (mm-30) REVERT: A 941 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 988 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 1067 ASN cc_start: 0.8832 (t0) cc_final: 0.8474 (t0) REVERT: A 1085 LYS cc_start: 0.9121 (tptp) cc_final: 0.8795 (tptp) REVERT: A 1261 SER cc_start: 0.9195 (t) cc_final: 0.8656 (p) REVERT: A 1291 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7464 (tp30) REVERT: A 1330 LYS cc_start: 0.8865 (tppp) cc_final: 0.8193 (mtpt) REVERT: A 1732 MET cc_start: 0.8120 (mtp) cc_final: 0.7856 (ttm) REVERT: A 1740 TYR cc_start: 0.8179 (t80) cc_final: 0.7426 (t80) REVERT: A 1844 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7757 (p90) REVERT: A 1908 LEU cc_start: 0.9254 (tp) cc_final: 0.8918 (mt) REVERT: A 1933 ILE cc_start: 0.9426 (mt) cc_final: 0.9174 (tt) REVERT: A 1938 LYS cc_start: 0.8457 (tptt) cc_final: 0.8131 (pttm) REVERT: A 2037 TYR cc_start: 0.7449 (p90) cc_final: 0.7219 (p90) REVERT: A 2062 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: A 2063 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7020 (t80) REVERT: C 111 LYS cc_start: 0.8554 (pttt) cc_final: 0.8063 (tptp) REVERT: C 166 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7570 (tppt) REVERT: C 276 ASP cc_start: 0.7627 (m-30) cc_final: 0.7105 (m-30) REVERT: C 804 LYS cc_start: 0.8911 (tppt) cc_final: 0.8180 (mtmm) REVERT: C 880 MET cc_start: 0.8853 (mmm) cc_final: 0.8474 (mmt) REVERT: C 910 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7264 (mm-30) REVERT: H 294 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8249 (tttt) REVERT: H 477 MET cc_start: 0.6569 (mmp) cc_final: 0.5980 (mmt) REVERT: J 203 ASP cc_start: 0.7271 (t0) cc_final: 0.7064 (t70) REVERT: J 329 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6782 (t70) REVERT: J 377 ASP cc_start: 0.8170 (t0) cc_final: 0.7740 (t0) REVERT: K 73 TYR cc_start: 0.8591 (t80) cc_final: 0.8376 (t80) REVERT: L 25 ASP cc_start: 0.8566 (t0) cc_final: 0.8263 (t0) REVERT: L 27 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7628 (tt0) REVERT: L 53 MET cc_start: 0.8325 (mmm) cc_final: 0.8107 (mmt) REVERT: L 58 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: L 128 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7426 (tp-100) REVERT: M 240 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: M 241 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6557 (tt0) REVERT: N 243 ASN cc_start: 0.7919 (t0) cc_final: 0.7708 (t0) REVERT: N 282 LEU cc_start: 0.7486 (mt) cc_final: 0.7004 (pt) REVERT: P 9 LEU cc_start: 0.8390 (mt) cc_final: 0.8067 (mt) REVERT: S 38 LEU cc_start: 0.8668 (pt) cc_final: 0.8231 (mt) REVERT: S 41 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6738 (tm-30) REVERT: S 53 GLU cc_start: 0.8367 (tt0) cc_final: 0.8122 (tm-30) REVERT: S 163 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7924 (pp20) REVERT: V 672 MET cc_start: 0.0402 (mmp) cc_final: -0.0010 (mmp) REVERT: V 711 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.3980 (tp) REVERT: V 872 MET cc_start: 0.4307 (mmm) cc_final: 0.3987 (mtp) REVERT: V 1064 TYR cc_start: 0.1836 (OUTLIER) cc_final: 0.0623 (t80) REVERT: a 119 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6939 (tp30) REVERT: a 141 LYS cc_start: 0.8366 (mttt) cc_final: 0.7832 (tptt) REVERT: a 190 ASN cc_start: 0.6234 (p0) cc_final: 0.5732 (t0) REVERT: b 51 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5455 (tm-30) REVERT: c 219 MET cc_start: 0.1144 (ttm) cc_final: -0.0311 (ptm) REVERT: c 287 MET cc_start: 0.4200 (pmm) cc_final: 0.3868 (pmm) REVERT: c 300 ASN cc_start: 0.8439 (m-40) cc_final: 0.7695 (m110) REVERT: c 304 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8510 (mm-40) REVERT: d 30 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7835 (ttp80) REVERT: d 35 GLU cc_start: 0.7010 (tp30) cc_final: 0.6714 (tp30) REVERT: d 40 MET cc_start: 0.8397 (mpp) cc_final: 0.7638 (mpp) REVERT: d 48 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7126 (tp) REVERT: e 90 ILE cc_start: 0.4922 (mm) cc_final: 0.4572 (mm) REVERT: g 35 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.5433 (t80) REVERT: h 5 ASN cc_start: 0.6003 (m-40) cc_final: 0.5103 (p0) REVERT: h 21 ASN cc_start: 0.3401 (OUTLIER) cc_final: 0.1882 (t0) REVERT: j 31 MET cc_start: 0.5161 (mpp) cc_final: 0.3649 (mtt) REVERT: j 50 ASN cc_start: 0.5495 (OUTLIER) cc_final: 0.4469 (m-40) REVERT: l 40 LEU cc_start: 0.1665 (tp) cc_final: 0.1442 (tp) REVERT: o 216 GLU cc_start: 0.6627 (mp0) cc_final: 0.6212 (mt-10) REVERT: o 236 GLU cc_start: 0.6822 (mp0) cc_final: 0.6520 (mp0) REVERT: o 275 TYR cc_start: 0.9190 (m-80) cc_final: 0.8504 (m-80) REVERT: o 300 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7374 (tptt) REVERT: o 321 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8290 (mm-30) REVERT: o 356 MET cc_start: 0.8253 (mmm) cc_final: 0.7652 (mmm) REVERT: o 410 TRP cc_start: 0.7503 (OUTLIER) cc_final: 0.7194 (m-10) REVERT: p 50 MET cc_start: 0.3049 (mtt) cc_final: 0.2461 (ttm) REVERT: q 49 PHE cc_start: 0.5339 (OUTLIER) cc_final: 0.3451 (t80) REVERT: y 205 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7668 (tm-30) outliers start: 270 outliers final: 214 residues processed: 1148 average time/residue: 0.7078 time to fit residues: 1452.2163 Evaluate side-chains 1136 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 904 time to evaluate : 6.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 GLN Chi-restraints excluded: chain A residue 1657 ILE Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1906 SER Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 474 THR Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 149 MET Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 238 TRP Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 493 ILE Chi-restraints excluded: chain V residue 505 VAL Chi-restraints excluded: chain V residue 517 THR Chi-restraints excluded: chain V residue 564 ILE Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 652 ILE Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 711 LEU Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 773 VAL Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 906 THR Chi-restraints excluded: chain V residue 911 LEU Chi-restraints excluded: chain V residue 915 VAL Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 953 PHE Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 989 HIS Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1081 SER Chi-restraints excluded: chain V residue 1084 THR Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 208 HIS Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 158 VAL Chi-restraints excluded: chain c residue 160 VAL Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain c residue 281 VAL Chi-restraints excluded: chain c residue 299 LEU Chi-restraints excluded: chain c residue 332 ASN Chi-restraints excluded: chain c residue 337 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 42 ASP Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 39 ILE Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 248 SER Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 308 PHE Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain o residue 410 TRP Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 874 optimal weight: 2.9990 chunk 576 optimal weight: 20.0000 chunk 927 optimal weight: 20.0000 chunk 566 optimal weight: 10.0000 chunk 440 optimal weight: 3.9990 chunk 645 optimal weight: 10.0000 chunk 973 optimal weight: 2.9990 chunk 895 optimal weight: 10.0000 chunk 775 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 598 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS A1763 ASN A1883 ASN A1953 ASN C 84 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN C 929 GLN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN K 87 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 200 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 833 ASN ** V1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 82974 Z= 0.248 Angle : 0.648 15.129 114660 Z= 0.323 Chirality : 0.042 0.297 13674 Planarity : 0.004 0.102 12979 Dihedral : 17.498 179.744 17378 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 3.61 % Allowed : 20.84 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.09), residues: 9070 helix: 1.75 (0.08), residues: 4160 sheet: -1.33 (0.16), residues: 1060 loop : -1.34 (0.10), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP o 434 HIS 0.008 0.001 HIS V 960 PHE 0.041 0.002 PHE A 557 TYR 0.042 0.002 TYR A 556 ARG 0.008 0.001 ARG P 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18140 Ramachandran restraints generated. 9070 Oldfield, 0 Emsley, 9070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 968 time to evaluate : 6.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8210 (tpp) cc_final: 0.7882 (ttt) REVERT: A 372 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7538 (mtp85) REVERT: A 593 LEU cc_start: 0.9550 (tm) cc_final: 0.9210 (tt) REVERT: A 594 ASP cc_start: 0.8315 (p0) cc_final: 0.7694 (p0) REVERT: A 754 TYR cc_start: 0.8193 (t80) cc_final: 0.7862 (t80) REVERT: A 912 LEU cc_start: 0.9071 (tp) cc_final: 0.8845 (tp) REVERT: A 917 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5334 (mm-30) REVERT: A 941 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6940 (mt-10) REVERT: A 988 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 1067 ASN cc_start: 0.8807 (t0) cc_final: 0.8409 (t0) REVERT: A 1261 SER cc_start: 0.9093 (t) cc_final: 0.8558 (p) REVERT: A 1291 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7455 (tp30) REVERT: A 1330 LYS cc_start: 0.8864 (tppp) cc_final: 0.8220 (mtpt) REVERT: A 1521 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.6737 (mtp85) REVERT: A 1659 GLU cc_start: 0.8336 (pt0) cc_final: 0.8109 (pt0) REVERT: A 1740 TYR cc_start: 0.8166 (t80) cc_final: 0.7472 (t80) REVERT: A 1844 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7682 (p90) REVERT: A 1908 LEU cc_start: 0.9208 (tp) cc_final: 0.8881 (mt) REVERT: A 1938 LYS cc_start: 0.8472 (tptt) cc_final: 0.8085 (pptt) REVERT: A 1979 MET cc_start: 0.8532 (mmm) cc_final: 0.7806 (mmp) REVERT: A 1993 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6721 (p0) REVERT: A 2062 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 2063 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.6678 (t80) REVERT: C 111 LYS cc_start: 0.8539 (pttt) cc_final: 0.8032 (mmtt) REVERT: C 166 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7514 (tppt) REVERT: C 198 LEU cc_start: 0.8888 (mt) cc_final: 0.8600 (mm) REVERT: C 276 ASP cc_start: 0.7558 (m-30) cc_final: 0.7030 (m-30) REVERT: C 804 LYS cc_start: 0.9017 (tppt) cc_final: 0.8280 (mtmm) REVERT: C 843 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7891 (ptmt) REVERT: C 880 MET cc_start: 0.8881 (mmm) cc_final: 0.8523 (mmt) REVERT: C 910 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7222 (mm-30) REVERT: H 294 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8198 (tttt) REVERT: H 400 MET cc_start: 0.6566 (tpp) cc_final: 0.6319 (tpp) REVERT: H 477 MET cc_start: 0.6408 (mmp) cc_final: 0.5938 (mmt) REVERT: J 329 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6582 (t70) REVERT: J 377 ASP cc_start: 0.8238 (t0) cc_final: 0.7782 (t0) REVERT: K 40 LEU cc_start: 0.8635 (tp) cc_final: 0.8426 (tp) REVERT: K 73 TYR cc_start: 0.8491 (t80) cc_final: 0.8265 (t80) REVERT: L 25 ASP cc_start: 0.8587 (t0) cc_final: 0.8270 (t0) REVERT: L 53 MET cc_start: 0.8341 (mmm) cc_final: 0.8132 (mmt) REVERT: L 58 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: L 128 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7434 (tp-100) REVERT: M 199 MET cc_start: 0.7877 (mmm) cc_final: 0.7619 (mmm) REVERT: M 240 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: M 241 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6513 (tt0) REVERT: N 74 CYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7373 (p) REVERT: N 108 MET cc_start: 0.8050 (mmm) cc_final: 0.7825 (mmt) REVERT: N 221 ASP cc_start: 0.7911 (t0) cc_final: 0.7265 (t0) REVERT: N 282 LEU cc_start: 0.7384 (mt) cc_final: 0.6946 (pt) REVERT: P 9 LEU cc_start: 0.8305 (mt) cc_final: 0.7991 (mt) REVERT: S 38 LEU cc_start: 0.8630 (pt) cc_final: 0.8171 (mt) REVERT: S 41 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6637 (tm-30) REVERT: S 53 GLU cc_start: 0.8361 (tt0) cc_final: 0.8108 (tm-30) REVERT: S 163 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: V 647 PHE cc_start: 0.2032 (t80) cc_final: 0.0889 (t80) REVERT: V 672 MET cc_start: 0.0576 (mmp) cc_final: 0.0114 (mmp) REVERT: V 711 LEU cc_start: 0.4741 (OUTLIER) cc_final: 0.3974 (tp) REVERT: V 872 MET cc_start: 0.4540 (mmm) cc_final: 0.3922 (mtp) REVERT: V 1064 TYR cc_start: 0.1983 (OUTLIER) cc_final: 0.0699 (t80) REVERT: V 1089 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7069 (tm-30) REVERT: a 119 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6915 (tp30) REVERT: a 141 LYS cc_start: 0.8314 (mttt) cc_final: 0.7775 (tptt) REVERT: a 190 ASN cc_start: 0.6186 (p0) cc_final: 0.5755 (t0) REVERT: c 219 MET cc_start: 0.1335 (ttm) cc_final: -0.0452 (ptm) REVERT: c 287 MET cc_start: 0.4207 (pmm) cc_final: 0.3754 (pmm) REVERT: c 300 ASN cc_start: 0.8422 (m-40) cc_final: 0.7633 (m110) REVERT: c 304 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8486 (mm-40) REVERT: d 30 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7869 (ttp80) REVERT: d 35 GLU cc_start: 0.6905 (tp30) cc_final: 0.6543 (tp30) REVERT: d 40 MET cc_start: 0.8364 (mpp) cc_final: 0.7601 (mpp) REVERT: d 48 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7050 (tp) REVERT: e 90 ILE cc_start: 0.4851 (mm) cc_final: 0.4517 (mm) REVERT: g 35 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5689 (t80) REVERT: h 5 ASN cc_start: 0.6004 (m-40) cc_final: 0.5105 (p0) REVERT: h 21 ASN cc_start: 0.3298 (OUTLIER) cc_final: 0.1769 (t0) REVERT: j 31 MET cc_start: 0.5601 (mpp) cc_final: 0.4100 (mtt) REVERT: j 50 ASN cc_start: 0.5276 (OUTLIER) cc_final: 0.4623 (m-40) REVERT: l 40 LEU cc_start: 0.1581 (tp) cc_final: 0.1337 (tp) REVERT: m 38 MET cc_start: 0.3287 (tpp) cc_final: 0.0888 (ptp) REVERT: o 216 GLU cc_start: 0.6486 (mp0) cc_final: 0.6146 (mt-10) REVERT: o 236 GLU cc_start: 0.6910 (mp0) cc_final: 0.6639 (mp0) REVERT: o 275 TYR cc_start: 0.9169 (m-80) cc_final: 0.8468 (m-80) REVERT: o 300 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7149 (tptt) REVERT: o 321 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8188 (mm-30) REVERT: o 356 MET cc_start: 0.8284 (mmm) cc_final: 0.7742 (mmm) REVERT: o 366 LYS cc_start: 0.8233 (mptt) cc_final: 0.7621 (tppt) REVERT: p 50 MET cc_start: 0.3002 (mtt) cc_final: 0.2434 (ttm) REVERT: q 49 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.3476 (t80) REVERT: y 205 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 244 outliers final: 198 residues processed: 1142 average time/residue: 0.7267 time to fit residues: 1476.8538 Evaluate side-chains 1149 residues out of total 8487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 932 time to evaluate : 6.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1433 ASP Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1621 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 THR Chi-restraints excluded: chain A residue 1728 ILE Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1834 PHE Chi-restraints excluded: chain A residue 1844 PHE Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2062 GLU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 474 THR Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 261 THR Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 372 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 446 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 87 ASN Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain N residue 74 CYS Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 LEU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain S residue 200 GLN Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 238 TRP Chi-restraints excluded: chain S residue 247 VAL Chi-restraints excluded: chain V residue 299 ILE Chi-restraints excluded: chain V residue 493 ILE Chi-restraints excluded: chain V residue 505 VAL Chi-restraints excluded: chain V residue 564 ILE Chi-restraints excluded: chain V residue 573 ASP Chi-restraints excluded: chain V residue 580 THR Chi-restraints excluded: chain V residue 581 ASP Chi-restraints excluded: chain V residue 652 ILE Chi-restraints excluded: chain V residue 654 ASN Chi-restraints excluded: chain V residue 696 VAL Chi-restraints excluded: chain V residue 711 LEU Chi-restraints excluded: chain V residue 727 ILE Chi-restraints excluded: chain V residue 754 VAL Chi-restraints excluded: chain V residue 773 VAL Chi-restraints excluded: chain V residue 865 ASP Chi-restraints excluded: chain V residue 906 THR Chi-restraints excluded: chain V residue 911 LEU Chi-restraints excluded: chain V residue 915 VAL Chi-restraints excluded: chain V residue 921 ASP Chi-restraints excluded: chain V residue 935 VAL Chi-restraints excluded: chain V residue 953 PHE Chi-restraints excluded: chain V residue 985 LEU Chi-restraints excluded: chain V residue 989 HIS Chi-restraints excluded: chain V residue 1064 TYR Chi-restraints excluded: chain V residue 1081 SER Chi-restraints excluded: chain V residue 1085 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain a residue 103 THR Chi-restraints excluded: chain a residue 158 ASP Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 208 HIS Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 158 VAL Chi-restraints excluded: chain c residue 160 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain c residue 275 THR Chi-restraints excluded: chain c residue 281 VAL Chi-restraints excluded: chain c residue 299 LEU Chi-restraints excluded: chain c residue 332 ASN Chi-restraints excluded: chain c residue 337 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain g residue 35 PHE Chi-restraints excluded: chain h residue 21 ASN Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 34 ILE Chi-restraints excluded: chain j residue 50 ASN Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain o residue 71 SER Chi-restraints excluded: chain o residue 174 THR Chi-restraints excluded: chain o residue 198 CYS Chi-restraints excluded: chain o residue 300 LYS Chi-restraints excluded: chain o residue 308 PHE Chi-restraints excluded: chain o residue 315 LYS Chi-restraints excluded: chain o residue 399 CYS Chi-restraints excluded: chain o residue 443 ILE Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain q residue 49 PHE Chi-restraints excluded: chain q residue 71 ILE Chi-restraints excluded: chain y residue 98 ASP Chi-restraints excluded: chain y residue 156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 475 optimal weight: 3.9990 chunk 615 optimal weight: 6.9990 chunk 825 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 714 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 776 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 797 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 ASN A1687 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN C 776 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 GLN K 87 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 120 ASN S 200 GLN ** V 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 12 ASN ** o 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.149400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.120417 restraints weight = 215891.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.119774 restraints weight = 177467.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120325 restraints weight = 141984.576| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 82974 Z= 0.209 Angle : 0.629 16.495 114660 Z= 0.314 Chirality : 0.042 0.290 13674 Planarity : 0.004 0.102 12979 Dihedral : 17.438 179.700 17378 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.40 % Favored : 94.53 % Rotamer: Outliers : 3.48 % Allowed : 20.99 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 9070 helix: 1.85 (0.08), residues: 4160 sheet: -1.32 (0.16), residues: 1074 loop : -1.30 (0.10), residues: 3836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP o 434 HIS 0.008 0.001 HIS V 960 PHE 0.028 0.002 PHE o 302 TYR 0.034 0.002 TYR A 556 ARG 0.008 0.000 ARG P 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24058.69 seconds wall clock time: 421 minutes 19.10 seconds (25279.10 seconds total)