Starting phenix.real_space_refine on Sun Dec 10 12:22:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xtd_6773/12_2023/5xtd_6773_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= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians Fe 28 7.16 5 P 29 5.49 5 S 432 5.16 5 C 43195 2.51 5 N 11160 2.21 5 O 11945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "I ARG 10": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 75": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J ARG 303": "NH1" <-> "NH2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J ARG 360": "NH1" <-> "NH2" Residue "L ARG 75": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 106": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M ARG 175": "NH1" <-> "NH2" Residue "M ARG 308": "NH1" <-> "NH2" Residue "M ARG 325": "NH1" <-> "NH2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "M ARG 382": "NH1" <-> "NH2" Residue "M ARG 417": "NH1" <-> "NH2" Residue "M ARG 557": "NH1" <-> "NH2" Residue "M ARG 645": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 142": "NH1" <-> "NH2" Residue "P ARG 168": "NH1" <-> "NH2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ARG 211": "NH1" <-> "NH2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "Q ARG 207": "NH1" <-> "NH2" Residue "Q ARG 221": "NH1" <-> "NH2" Residue "Q ARG 342": "NH1" <-> "NH2" Residue "Q ARG 368": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "T ARG 120": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 82": "NH1" <-> "NH2" Residue "W ARG 88": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 43": "NH1" <-> "NH2" Residue "Y ARG 72": "NH1" <-> "NH2" Residue "Y GLU 79": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z ARG 42": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "b ARG 58": "NH1" <-> "NH2" Residue "b GLU 92": "OE1" <-> "OE2" Residue "b ARG 103": "NH1" <-> "NH2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "c ARG 58": "NH1" <-> "NH2" Residue "d ARG 103": "NH1" <-> "NH2" Residue "d ARG 147": "NH1" <-> "NH2" Residue "d ARG 161": "NH1" <-> "NH2" Residue "e ARG 113": "NH1" <-> "NH2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 77": "NH1" <-> "NH2" Residue "g ARG 85": "NH1" <-> "NH2" Residue "h ARG 32": "NH1" <-> "NH2" Residue "h ARG 74": "NH1" <-> "NH2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i ARG 232": "NH1" <-> "NH2" Residue "k ARG 23": "NH1" <-> "NH2" Residue "l PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 357": "NH1" <-> "NH2" Residue "l ARG 425": "NH1" <-> "NH2" Residue "l ARG 456": "NH1" <-> "NH2" Residue "n ARG 29": "NH1" <-> "NH2" Residue "o ARG 72": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 45": "NH1" <-> "NH2" Residue "p ARG 173": "NH1" <-> "NH2" Residue "p ARG 175": "NH1" <-> "NH2" Residue "r ARG 82": "NH1" <-> "NH2" Residue "r ARG 135": "NH1" <-> "NH2" Residue "r ARG 432": "NH1" <-> "NH2" Residue "s ARG 34": "NH1" <-> "NH2" Residue "s PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 281": "NH1" <-> "NH2" Residue "u ARG 47": "NH1" <-> "NH2" Residue "u ARG 98": "NH1" <-> "NH2" Residue "u ARG 101": "NH1" <-> "NH2" Residue "u ARG 119": "NH1" <-> "NH2" Residue "u ARG 145": "NH1" <-> "NH2" Residue "u ARG 166": "NH1" <-> "NH2" Residue "v ARG 7": "NH1" <-> "NH2" Residue "v ARG 71": "NH1" <-> "NH2" Residue "v ARG 104": "NH1" <-> "NH2" Residue "w ARG 295": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 66789 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3322 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1420 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1249 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 968 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "G" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 672 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 769 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "J" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2712 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 20, 'TRANS': 316} Chain: "K" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 274 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "L" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "M" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5274 Classifications: {'peptide': 687} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 654} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1195 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 10, 'TRANS': 132} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 20, 'TRANS': 191} Chain: "P" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1730 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3460 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 28, 'TRANS': 401} Chain: "S" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 568 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "T" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "U" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 70} Chain: "V" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1038 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 132} Chain: "W" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1135 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "X" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 686 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 533 Classifications: {'peptide': 59} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 53} Chain: "Z" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1174 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "b" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1059 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 13, 'TRANS': 110} Chain: "c" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 133} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "d" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1418 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 161} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 88} Chain: "f" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 405 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "g" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1004 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 11, 'TRANS': 107} Chain: "h" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 863 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "i" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2735 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 323} Chain: "j" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 919 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} 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: "k" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 740 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "l" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4717 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 570} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1313 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain: "n" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 473 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1066 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1495 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 16, 'TRANS': 155} Chain: "r" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3629 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 436} Chain: "s" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "u" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1394 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 13, 'TRANS': 155} Chain: "v" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 921 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "w" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2474 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 15, 'TRANS': 304} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'PLX': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 166 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'PLX': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "l" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 228 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 74 Chain: "n" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "p" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'PLX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2695 SG CYS A 379 41.237 48.245 175.535 1.00 32.72 S ATOM 3979 SG CYS B 114 40.067 60.997 140.070 1.00 12.09 S ATOM 4030 SG CYS B 121 46.385 67.527 129.964 1.00 12.49 S ATOM 4256 SG CYS B 150 44.770 65.435 124.294 1.00 10.16 S ATOM 4282 SG CYS B 153 49.622 62.349 128.035 1.00 12.44 S ATOM 5725 SG CYS C 183 51.746 65.435 120.803 1.00 12.72 S ATOM 4996 SG CYS C 89 52.939 68.601 113.952 1.00 26.32 S ATOM 4990 SG CYS C 88 56.900 65.370 116.618 1.00 28.78 S ATOM 5494 SG CYS C 153 53.892 71.602 119.705 1.00 14.63 S ATOM 14700 SG CYS M 128 43.465 56.636 149.336 1.00 16.07 S ATOM 14760 SG CYS M 137 44.780 61.077 155.922 1.00 15.29 S ATOM 15071 SG CYS M 176 38.536 59.392 164.194 1.00 19.64 S ATOM 15094 SG CYS M 179 43.340 59.679 165.068 1.00 23.25 S ATOM 15448 SG CYS M 226 39.602 63.545 160.972 1.00 20.74 S ATOM 15118 SG CYS M 182 39.360 64.725 166.019 1.00 25.87 S ATOM 15071 SG CYS M 176 38.536 59.392 164.194 1.00 19.64 S ATOM 21531 SG CYS O 176 37.110 31.526 181.831 1.00 61.11 S ATOM 21554 SG CYS O 180 38.392 28.611 182.826 1.00 70.08 S Time building chain proxies: 25.72, per 1000 atoms: 0.39 Number of scatterers: 66789 At special positions: 0 Unit cell: (210.102, 232.845, 228.513, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 28 26.01 S 432 16.00 P 29 15.00 O 11945 8.00 N 11160 7.00 C 43195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS l 279 " distance=2.05 Simple disulfide: pdb=" SG CYS d 149 " - pdb=" SG CYS e 141 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.02 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.02 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=1.94 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.05 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 160 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 111 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 117 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 150 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 153 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 121 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 156 " pdb="FE3 SF4 B 302 " - pdb=" NE2 HIS B 99 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 89 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 88 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 153 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 183 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " Number of angles added : 68 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 23 sheets defined 51.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.40 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.752A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 4.000A pdb=" N ILE A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 256 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.836A pdb=" N ILE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.886A pdb=" N LYS A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.688A pdb=" N ILE A 409 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix removed outlier: 3.688A pdb=" N ARG A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.620A pdb=" N THR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 74 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 196 through 209 removed outlier: 6.281A pdb=" N LEU B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 76 removed outlier: 3.952A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 4.009A pdb=" N HIS C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'E' and resid 25 through 40 removed outlier: 3.982A pdb=" N ARG E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 56 through 66 Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.325A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.446A pdb=" N GLY F 32 " --> pdb=" O PRO F 28 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.960A pdb=" N ASN F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'H' and resid 20 through 35 Processing helix chain 'H' and resid 43 through 61 removed outlier: 4.228A pdb=" N TYR H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 3.815A pdb=" N GLU H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 57 No H-bonds generated for 'chain 'I' and resid 54 through 57' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.106A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 removed outlier: 4.920A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 141 through 145 removed outlier: 3.778A pdb=" N PHE J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 141 through 145' Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 removed outlier: 3.865A pdb=" N ALA J 185 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL J 186 " --> pdb=" O ARG J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 223 removed outlier: 3.863A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 295 through 305 Processing helix chain 'J' and resid 316 through 323 removed outlier: 3.887A pdb=" N GLU J 320 " --> pdb=" O ARG J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 337 No H-bonds generated for 'chain 'J' and resid 335 through 337' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 349 through 353 Processing helix chain 'J' and resid 359 through 362 No H-bonds generated for 'chain 'J' and resid 359 through 362' Processing helix chain 'J' and resid 367 through 369 No H-bonds generated for 'chain 'J' and resid 367 through 369' Processing helix chain 'K' and resid 83 through 94 removed outlier: 3.648A pdb=" N LEU K 91 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS K 93 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE K 94 " --> pdb=" O GLU K 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 Processing helix chain 'L' and resid 120 through 123 removed outlier: 4.449A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 123' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.819A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 removed outlier: 3.724A pdb=" N PHE M 119 " --> pdb=" O GLY M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 181 through 186 Processing helix chain 'M' and resid 220 through 225 Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 291 No H-bonds generated for 'chain 'M' and resid 288 through 291' Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'M' and resid 319 through 330 Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 394 through 396 No H-bonds generated for 'chain 'M' and resid 394 through 396' Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 412 through 423 Processing helix chain 'M' and resid 448 through 456 removed outlier: 4.248A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 537 No H-bonds generated for 'chain 'M' and resid 535 through 537' Processing helix chain 'M' and resid 576 through 579 No H-bonds generated for 'chain 'M' and resid 576 through 579' Processing helix chain 'M' and resid 619 through 629 removed outlier: 4.045A pdb=" N ILE M 623 " --> pdb=" O ASP M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 639 through 648 removed outlier: 3.564A pdb=" N GLU M 647 " --> pdb=" O ARG M 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU M 648 " --> pdb=" O ASN M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 652 through 654 No H-bonds generated for 'chain 'M' and resid 652 through 654' Processing helix chain 'M' and resid 666 through 673 removed outlier: 3.731A pdb=" N LEU M 671 " --> pdb=" O GLN M 667 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER M 672 " --> pdb=" O ALA M 668 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 695 removed outlier: 4.143A pdb=" N TYR M 695 " --> pdb=" O LYS M 692 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 703 Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 21 through 29 removed outlier: 3.753A pdb=" N ARG N 25 " --> pdb=" O ARG N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 70 No H-bonds generated for 'chain 'N' and resid 68 through 70' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 88 removed outlier: 4.324A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.510A pdb=" N ALA O 86 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 104 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 208 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 101 removed outlier: 5.397A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 4.002A pdb=" N THR P 98 " --> pdb=" O PRO P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 172 removed outlier: 4.034A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR P 166 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU P 169 " --> pdb=" O TYR P 166 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP P 171 " --> pdb=" O ARG P 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 48 removed outlier: 4.211A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 120 through 125 removed outlier: 3.763A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 137 Processing helix chain 'Q' and resid 145 through 158 removed outlier: 3.916A pdb=" N ALA Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU Q 158 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 193 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.236A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS Q 209 " --> pdb=" O GLU Q 205 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE Q 213 " --> pdb=" O LYS Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 248 removed outlier: 3.884A pdb=" N MET Q 241 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP Q 242 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE Q 244 " --> pdb=" O MET Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 251 through 259 removed outlier: 3.656A pdb=" N LEU Q 258 " --> pdb=" O ARG Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 removed outlier: 3.593A pdb=" N ASN Q 270 " --> pdb=" O ARG Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 286 Processing helix chain 'Q' and resid 290 through 294 Processing helix chain 'Q' and resid 310 through 312 No H-bonds generated for 'chain 'Q' and resid 310 through 312' Processing helix chain 'Q' and resid 326 through 348 removed outlier: 3.972A pdb=" N ALA Q 345 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN Q 346 " --> pdb=" O ARG Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 384 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 3.806A pdb=" N HIS Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET Q 438 " --> pdb=" O GLY Q 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 3.939A pdb=" N GLY Q 452 " --> pdb=" O VAL Q 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 30 Proline residue: S 7 - end of helix removed outlier: 3.716A pdb=" N VAL S 14 " --> pdb=" O VAL S 11 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU S 16 " --> pdb=" O GLY S 13 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.058A pdb=" N ALA S 24 " --> pdb=" O LEU S 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG S 28 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.648A pdb=" N ILE S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 69 Processing helix chain 'T' and resid 51 through 56 Processing helix chain 'T' and resid 68 through 74 removed outlier: 3.802A pdb=" N ALA T 73 " --> pdb=" O ILE T 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 14 removed outlier: 3.917A pdb=" N PHE U 8 " --> pdb=" O ARG U 4 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP U 14 " --> pdb=" O LYS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 37 through 48 removed outlier: 3.866A pdb=" N LYS U 40 " --> pdb=" O PRO U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 3 through 10 removed outlier: 3.908A pdb=" N TRP V 10 " --> pdb=" O PHE V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 43 removed outlier: 4.561A pdb=" N SER V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER V 27 " --> pdb=" O TYR V 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA V 29 " --> pdb=" O THR V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 removed outlier: 4.008A pdb=" N VAL V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 69 removed outlier: 3.673A pdb=" N THR W 42 " --> pdb=" O ILE W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 100 removed outlier: 5.217A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.277A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N MET W 141 " --> pdb=" O SER W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 removed outlier: 3.811A pdb=" N ASP X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 126 removed outlier: 3.529A pdb=" N VAL X 116 " --> pdb=" O SER X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 44 through 53 removed outlier: 4.492A pdb=" N ARG Z 47 " --> pdb=" O PRO Z 44 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ARG Z 52 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR Z 53 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'a' and resid 62 through 77 removed outlier: 3.781A pdb=" N LEU a 68 " --> pdb=" O ASP a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 92 Processing helix chain 'a' and resid 109 through 112 Processing helix chain 'a' and resid 116 through 124 Processing helix chain 'a' and resid 129 through 163 removed outlier: 3.702A pdb=" N MET a 137 " --> pdb=" O TYR a 133 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL a 151 " --> pdb=" O ALA a 147 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 40 through 47 Processing helix chain 'b' and resid 49 through 52 No H-bonds generated for 'chain 'b' and resid 49 through 52' Processing helix chain 'b' and resid 56 through 74 removed outlier: 3.882A pdb=" N VAL b 61 " --> pdb=" O TRP b 57 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL b 64 " --> pdb=" O MET b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 92 removed outlier: 4.748A pdb=" N SER b 91 " --> pdb=" O LYS b 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' Processing helix chain 'c' and resid 110 through 112 No H-bonds generated for 'chain 'c' and resid 110 through 112' Processing helix chain 'c' and resid 126 through 149 removed outlier: 3.540A pdb=" N ASP c 148 " --> pdb=" O CYS c 144 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL c 149 " --> pdb=" O TRP c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 169 removed outlier: 3.504A pdb=" N TYR c 167 " --> pdb=" O TYR c 163 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU c 169 " --> pdb=" O ASN c 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 6 Processing helix chain 'd' and resid 22 through 34 Processing helix chain 'd' and resid 36 through 52 removed outlier: 4.497A pdb=" N GLN d 49 " --> pdb=" O PHE d 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS d 50 " --> pdb=" O ILE d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 70 No H-bonds generated for 'chain 'd' and resid 68 through 70' Processing helix chain 'd' and resid 77 through 110 removed outlier: 3.774A pdb=" N LYS d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 136 removed outlier: 4.217A pdb=" N ILE d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS d 121 " --> pdb=" O GLN d 117 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU d 122 " --> pdb=" O ASN d 118 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL d 123 " --> pdb=" O CYS d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 170 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 93 Processing helix chain 'e' and resid 98 through 108 removed outlier: 3.877A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'f' and resid 29 through 38 Proline residue: f 34 - end of helix removed outlier: 4.008A pdb=" N ALA f 37 " --> pdb=" O GLU f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 72 removed outlier: 4.223A pdb=" N PHE f 46 " --> pdb=" O LEU f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 19 Processing helix chain 'g' and resid 28 through 47 Processing helix chain 'g' and resid 57 through 95 Processing helix chain 'g' and resid 97 through 99 No H-bonds generated for 'chain 'g' and resid 97 through 99' Processing helix chain 'h' and resid 6 through 9 No H-bonds generated for 'chain 'h' and resid 6 through 9' Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 35 through 43 Processing helix chain 'h' and resid 52 through 55 No H-bonds generated for 'chain 'h' and resid 52 through 55' Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 84 Processing helix chain 'h' and resid 94 through 96 No H-bonds generated for 'chain 'h' and resid 94 through 96' Processing helix chain 'i' and resid 3 through 22 Proline residue: i 7 - end of helix removed outlier: 3.559A pdb=" N THR i 12 " --> pdb=" O VAL i 8 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR i 20 " --> pdb=" O GLY i 16 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA i 21 " --> pdb=" O THR i 17 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.775A pdb=" N THR i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 80 removed outlier: 3.737A pdb=" N ALA i 56 " --> pdb=" O SER i 52 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE i 57 " --> pdb=" O THR i 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR i 62 " --> pdb=" O LYS i 58 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER i 67 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 105 Processing helix chain 'i' and resid 112 through 121 Proline residue: i 116 - end of helix removed outlier: 3.740A pdb=" N THR i 119 " --> pdb=" O PRO i 116 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY i 121 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 131 Processing helix chain 'i' and resid 133 through 144 removed outlier: 4.173A pdb=" N ALA i 137 " --> pdb=" O GLN i 134 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 170 removed outlier: 3.863A pdb=" N GLY i 169 " --> pdb=" O GLY i 165 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU i 170 " --> pdb=" O SER i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 removed outlier: 3.609A pdb=" N MET i 191 " --> pdb=" O MET i 187 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 222 removed outlier: 3.678A pdb=" N ILE i 207 " --> pdb=" O ASN i 204 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN i 222 " --> pdb=" O LEU i 219 " (cutoff:3.500A) Processing helix chain 'i' and resid 227 through 234 removed outlier: 4.217A pdb=" N ARG i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR i 233 " --> pdb=" O LEU i 229 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Proline residue: i 242 - end of helix Proline residue: i 245 - end of helix Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.288A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 299 removed outlier: 4.277A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU i 288 " --> pdb=" O THR i 284 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN i 289 " --> pdb=" O ILE i 285 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR i 293 " --> pdb=" O ASN i 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER i 299 " --> pdb=" O ARG i 295 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 314 Processing helix chain 'i' and resid 326 through 333 Processing helix chain 'i' and resid 335 through 346 Proline residue: i 338 - end of helix Proline residue: i 341 - end of helix removed outlier: 3.737A pdb=" N LEU i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET i 345 " --> pdb=" O PHE i 342 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 23 removed outlier: 4.184A pdb=" N ASN j 10 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP j 23 " --> pdb=" O ILE j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 80 removed outlier: 4.350A pdb=" N VAL j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU j 72 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.836A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 removed outlier: 3.781A pdb=" N MET j 89 " --> pdb=" O PRO j 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU j 105 " --> pdb=" O SER j 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 21 Processing helix chain 'k' and resid 27 through 50 removed outlier: 4.104A pdb=" N MET k 47 " --> pdb=" O MET k 43 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR k 48 " --> pdb=" O ALA k 44 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 84 Proline residue: k 60 - end of helix removed outlier: 3.676A pdb=" N MET k 63 " --> pdb=" O PRO k 60 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR k 84 " --> pdb=" O ILE k 81 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 24 removed outlier: 3.771A pdb=" N LEU l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) Proline residue: l 17 - end of helix Processing helix chain 'l' and resid 31 through 56 removed outlier: 3.741A pdb=" N LYS l 37 " --> pdb=" O PRO l 33 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE l 49 " --> pdb=" O ILE l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 removed outlier: 3.747A pdb=" N ILE l 90 " --> pdb=" O SER l 86 " (cutoff:3.500A) Proline residue: l 91 - end of helix removed outlier: 3.623A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 removed outlier: 4.196A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.737A pdb=" N ILE l 172 " --> pdb=" O ALA l 168 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 223 Processing helix chain 'l' and resid 227 through 236 Proline residue: l 231 - end of helix Proline residue: l 234 - end of helix Processing helix chain 'l' and resid 241 through 247 Processing helix chain 'l' and resid 253 through 262 removed outlier: 3.678A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.498A pdb=" N ASN l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 293 removed outlier: 3.679A pdb=" N LEU l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 removed outlier: 3.620A pdb=" N ILE l 317 " --> pdb=" O MET l 313 " (cutoff:3.500A) Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.736A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE l 335 " --> pdb=" O THR l 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS l 336 " --> pdb=" O HIS l 332 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE l 346 " --> pdb=" O CYS l 342 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 392 through 401 Processing helix chain 'l' and resid 407 through 430 removed outlier: 3.924A pdb=" N SER l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 452 through 471 removed outlier: 5.597A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE l 466 " --> pdb=" O LEU l 462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN l 470 " --> pdb=" O PHE l 466 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 508 removed outlier: 4.435A pdb=" N ALA l 490 " --> pdb=" O LEU l 486 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU l 491 " --> pdb=" O LYS l 487 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 529 through 546 removed outlier: 4.336A pdb=" N ARG l 535 " --> pdb=" O SER l 531 " (cutoff:3.500A) Proline residue: l 538 - end of helix removed outlier: 4.101A pdb=" N SER l 545 " --> pdb=" O GLY l 541 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 564 through 576 Processing helix chain 'l' and resid 584 through 599 removed outlier: 3.718A pdb=" N PHE l 588 " --> pdb=" O ILE l 584 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE l 592 " --> pdb=" O PHE l 588 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE l 593 " --> pdb=" O LEU l 589 " (cutoff:3.500A) Proline residue: l 594 - end of helix Processing helix chain 'm' and resid 4 through 21 removed outlier: 4.016A pdb=" N LEU m 8 " --> pdb=" O ALA m 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 46 removed outlier: 4.078A pdb=" N LEU m 30 " --> pdb=" O ILE m 26 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE m 46 " --> pdb=" O ILE m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 58 removed outlier: 3.651A pdb=" N VAL m 55 " --> pdb=" O MET m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 74 removed outlier: 3.534A pdb=" N ALA m 72 " --> pdb=" O GLY m 68 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET m 73 " --> pdb=" O TYR m 69 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA m 74 " --> pdb=" O THR m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 112 removed outlier: 6.925A pdb=" N GLY m 111 " --> pdb=" O LYS m 107 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL m 112 " --> pdb=" O GLU m 108 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 removed outlier: 4.040A pdb=" N LEU m 145 " --> pdb=" O GLY m 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 150 through 173 removed outlier: 4.034A pdb=" N TYR m 165 " --> pdb=" O PHE m 161 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY m 173 " --> pdb=" O GLU m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 9 removed outlier: 3.725A pdb=" N VAL n 8 " --> pdb=" O LEU n 4 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG n 9 " --> pdb=" O LEU n 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 4 through 9' Processing helix chain 'n' and resid 11 through 38 removed outlier: 3.682A pdb=" N HIS n 14 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL n 17 " --> pdb=" O HIS n 14 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.882A pdb=" N ILE n 23 " --> pdb=" O GLY n 20 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP n 28 " --> pdb=" O CYS n 25 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP n 32 " --> pdb=" O ARG n 29 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR n 36 " --> pdb=" O GLU n 33 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA n 37 " --> pdb=" O ARG n 34 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE n 38 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 52 removed outlier: 3.598A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 71 Processing helix chain 'o' and resid 74 through 79 Proline residue: o 78 - end of helix No H-bonds generated for 'chain 'o' and resid 74 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix removed outlier: 3.734A pdb=" N GLU o 108 " --> pdb=" O ILE o 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN o 117 " --> pdb=" O GLU o 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 12 through 31 Processing helix chain 'p' and resid 34 through 51 removed outlier: 3.623A pdb=" N GLU p 50 " --> pdb=" O ALA p 46 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 74 Processing helix chain 'p' and resid 101 through 106 removed outlier: 3.947A pdb=" N ASP p 105 " --> pdb=" O TRP p 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 112 No H-bonds generated for 'chain 'p' and resid 109 through 112' Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.403A pdb=" N GLU p 123 " --> pdb=" O PHE p 119 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN p 124 " --> pdb=" O ALA p 120 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP p 125 " --> pdb=" O LYS p 121 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix removed outlier: 4.366A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 41 removed outlier: 3.906A pdb=" N THR r 29 " --> pdb=" O ILE r 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE r 37 " --> pdb=" O ILE r 33 " (cutoff:3.500A) Proline residue: r 38 - end of helix Processing helix chain 'r' and resid 60 through 83 Proline residue: r 64 - end of helix Proline residue: r 74 - end of helix removed outlier: 3.640A pdb=" N GLN r 81 " --> pdb=" O ILE r 77 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 109 removed outlier: 4.052A pdb=" N LEU r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.859A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 148 removed outlier: 4.397A pdb=" N GLY r 146 " --> pdb=" O LEU r 143 " (cutoff:3.500A) Processing helix chain 'r' and resid 150 through 170 removed outlier: 3.564A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.606A pdb=" N ILE r 165 " --> pdb=" O LEU r 161 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 removed outlier: 3.530A pdb=" N LEU r 181 " --> pdb=" O LEU r 177 " (cutoff:3.500A) Processing helix chain 'r' and resid 189 through 206 removed outlier: 3.659A pdb=" N ASN r 193 " --> pdb=" O SER r 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU r 194 " --> pdb=" O TRP r 190 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE r 203 " --> pdb=" O TYR r 199 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 210 through 212 No H-bonds generated for 'chain 'r' and resid 210 through 212' Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.143A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 248 removed outlier: 4.119A pdb=" N MET r 229 " --> pdb=" O ILE r 225 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL r 230 " --> pdb=" O ALA r 226 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL r 234 " --> pdb=" O VAL r 230 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU r 236 " --> pdb=" O ALA r 232 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS r 237 " --> pdb=" O ALA r 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET r 243 " --> pdb=" O GLY r 239 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 278 removed outlier: 4.120A pdb=" N ILE r 270 " --> pdb=" O LEU r 266 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.726A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.570A pdb=" N THR r 310 " --> pdb=" O PRO r 306 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER r 332 " --> pdb=" O CYS r 328 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 342 through 344 No H-bonds generated for 'chain 'r' and resid 342 through 344' Processing helix chain 'r' and resid 348 through 350 No H-bonds generated for 'chain 'r' and resid 348 through 350' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 414 removed outlier: 3.744A pdb=" N LEU r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR r 406 " --> pdb=" O THR r 403 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER r 407 " --> pdb=" O ALA r 404 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR r 412 " --> pdb=" O TYR r 409 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 424 through 426 No H-bonds generated for 'chain 'r' and resid 424 through 426' Processing helix chain 'r' and resid 431 through 447 removed outlier: 3.706A pdb=" N HIS r 440 " --> pdb=" O LEU r 436 " (cutoff:3.500A) Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 455 removed outlier: 3.517A pdb=" N THR r 455 " --> pdb=" O ASP r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 4.007A pdb=" N ARG s 25 " --> pdb=" O MET s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 87 Proline residue: s 75 - end of helix removed outlier: 4.308A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR s 87 " --> pdb=" O LEU s 83 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.544A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 157 removed outlier: 4.416A pdb=" N LEU s 133 " --> pdb=" O LEU s 129 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG s 134 " --> pdb=" O ILE s 130 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 169 removed outlier: 3.601A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN s 169 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 179 through 193 removed outlier: 3.885A pdb=" N ILE s 187 " --> pdb=" O MET s 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR s 193 " --> pdb=" O THR s 189 " (cutoff:3.500A) Processing helix chain 's' and resid 196 through 198 No H-bonds generated for 'chain 's' and resid 196 through 198' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 removed outlier: 4.090A pdb=" N THR s 275 " --> pdb=" O LEU s 271 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA s 276 " --> pdb=" O TRP s 272 " (cutoff:3.500A) Processing helix chain 's' and resid 282 through 289 removed outlier: 4.317A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS s 287 " --> pdb=" O ASP s 283 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU s 288 " --> pdb=" O GLN s 284 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU s 289 " --> pdb=" O LEU s 285 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 282 through 289' Processing helix chain 's' and resid 294 through 310 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 35 removed outlier: 3.885A pdb=" N ALA u 27 " --> pdb=" O ALA u 23 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA u 34 " --> pdb=" O HIS u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 48 removed outlier: 3.610A pdb=" N CYS u 46 " --> pdb=" O GLU u 42 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 75 removed outlier: 3.836A pdb=" N LEU u 57 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU u 58 " --> pdb=" O ARG u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 80 through 90 removed outlier: 3.752A pdb=" N GLU u 84 " --> pdb=" O GLU u 80 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR u 85 " --> pdb=" O PRO u 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE u 89 " --> pdb=" O TYR u 85 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP u 90 " --> pdb=" O TRP u 86 " (cutoff:3.500A) Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 101 through 112 removed outlier: 3.800A pdb=" N LYS u 106 " --> pdb=" O GLN u 103 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU u 109 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 11 Processing helix chain 'v' and resid 44 through 49 Processing helix chain 'v' and resid 58 through 72 removed outlier: 4.421A pdb=" N HIS v 61 " --> pdb=" O TYR v 58 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS v 62 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 122 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 72 through 80 removed outlier: 3.625A pdb=" N GLU w 76 " --> pdb=" O LYS w 72 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU w 79 " --> pdb=" O LYS w 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS w 80 " --> pdb=" O GLU w 76 " (cutoff:3.500A) Processing helix chain 'w' and resid 93 through 97 Processing helix chain 'w' and resid 106 through 109 No H-bonds generated for 'chain 'w' and resid 106 through 109' Processing helix chain 'w' and resid 114 through 118 Processing helix chain 'w' and resid 129 through 136 Processing helix chain 'w' and resid 139 through 153 Processing helix chain 'w' and resid 163 through 165 No H-bonds generated for 'chain 'w' and resid 163 through 165' Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.538A pdb=" N CYS w 196 " --> pdb=" O SER w 192 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 removed outlier: 3.928A pdb=" N GLN w 219 " --> pdb=" O GLN w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 251 Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 263 through 269 removed outlier: 3.518A pdb=" N LYS w 268 " --> pdb=" O GLN w 264 " (cutoff:3.500A) Processing helix chain 'w' and resid 274 through 276 No H-bonds generated for 'chain 'w' and resid 274 through 276' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 323 through 333 removed outlier: 3.530A pdb=" N HIS w 329 " --> pdb=" O ASP w 325 " (cutoff:3.500A) Processing helix chain 'w' and resid 351 through 354 Processing sheet with id= A, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= B, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.301A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 286 through 291 removed outlier: 3.938A pdb=" N ALA A 316 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= E, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'B' and resid 144 through 146 Processing sheet with id= G, first strand: chain 'F' and resid 52 through 56 removed outlier: 4.264A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 103 through 107 removed outlier: 8.272A pdb=" N LEU J 104 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL J 80 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU J 106 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE J 82 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER J 52 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N ILE J 81 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE J 54 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N ALA J 56 " --> pdb=" O PRO J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 165 through 167 removed outlier: 5.920A pdb=" N ILE J 199 " --> pdb=" O HIS J 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'J' and resid 226 through 229 Processing sheet with id= K, first strand: chain 'L' and resid 77 through 80 Processing sheet with id= L, first strand: chain 'L' and resid 106 through 108 removed outlier: 3.637A pdb=" N TRP L 107 " --> pdb=" O SER L 116 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 32 through 35 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.025A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 305 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 399 through 401 Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'P' and resid 76 through 79 removed outlier: 3.573A pdb=" N SER P 79 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP P 113 " --> pdb=" O ASN P 131 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'P' and resid 209 through 213 Processing sheet with id= T, first strand: chain 'Q' and resid 96 through 100 removed outlier: 3.656A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= V, first strand: chain 'T' and resid 85 through 87 Processing sheet with id= W, first strand: chain 'w' and resid 61 through 63 removed outlier: 3.636A pdb=" N ILE w 205 " --> pdb=" O THR w 61 " (cutoff:3.500A) 2612 hydrogen bonds defined for protein. 7116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.57 Time building geometry restraints manager: 25.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.38: 26096 1.38 - 1.58: 41559 1.58 - 1.79: 342 1.79 - 1.99: 402 1.99 - 2.20: 80 Bond restraints: 68479 Sorted by residual: bond pdb=" CB7 CDL l 704 " pdb=" OB8 CDL l 704 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" CB7 CDL l 703 " pdb=" OB8 CDL l 703 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CB7 CDL V 201 " pdb=" OB8 CDL V 201 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" CA7 CDL l 704 " pdb=" OA8 CDL l 704 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" CB7 CDL n 101 " pdb=" OB8 CDL n 101 " ideal model delta sigma weight residual 1.334 1.449 -0.115 1.10e-02 8.26e+03 1.09e+02 ... (remaining 68474 not shown) Histogram of bond angle deviations from ideal: 87.34 - 99.35: 183 99.35 - 111.37: 30394 111.37 - 123.39: 58646 123.39 - 135.40: 3553 135.40 - 147.42: 12 Bond angle restraints: 92788 Sorted by residual: angle pdb=" S1 FES M 803 " pdb="FE2 FES M 803 " pdb=" S2 FES M 803 " ideal model delta sigma weight residual 104.33 89.24 15.09 1.14e+00 7.69e-01 1.75e+02 angle pdb=" S1 FES M 803 " pdb="FE1 FES M 803 " pdb=" S2 FES M 803 " ideal model delta sigma weight residual 104.33 89.20 15.13 1.20e+00 6.94e-01 1.59e+02 angle pdb="FE2 SF4 M 801 " pdb=" S3 SF4 M 801 " pdb="FE4 SF4 M 801 " ideal model delta sigma weight residual 73.70 92.46 -18.76 1.50e+00 4.44e-01 1.56e+02 angle pdb="FE2 SF4 M 801 " pdb=" S1 SF4 M 801 " pdb="FE4 SF4 M 801 " ideal model delta sigma weight residual 73.70 92.41 -18.71 1.50e+00 4.44e-01 1.56e+02 angle pdb=" S1 FES O 301 " pdb="FE2 FES O 301 " pdb=" S2 FES O 301 " ideal model delta sigma weight residual 104.33 90.50 13.83 1.14e+00 7.69e-01 1.47e+02 ... (remaining 92783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 40744 35.66 - 71.31: 612 71.31 - 106.97: 61 106.97 - 142.62: 18 142.62 - 178.28: 15 Dihedral angle restraints: 41450 sinusoidal: 17575 harmonic: 23875 Sorted by residual: dihedral pdb=" CA LYS w 338 " pdb=" C LYS w 338 " pdb=" N TYR w 339 " pdb=" CA TYR w 339 " ideal model delta harmonic sigma weight residual -180.00 -142.74 -37.26 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" CA PHE Y 84 " pdb=" C PHE Y 84 " pdb=" N PRO Y 85 " pdb=" CA PRO Y 85 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA MET l 383 " pdb=" C MET l 383 " pdb=" N PRO l 384 " pdb=" CA PRO l 384 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 41447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 10097 0.222 - 0.445: 29 0.445 - 0.667: 1 0.667 - 0.890: 0 0.890 - 1.112: 4 Chirality restraints: 10131 Sorted by residual: chirality pdb="FE4 SF4 M 801 " pdb=" S1 SF4 M 801 " pdb=" S2 SF4 M 801 " pdb=" S3 SF4 M 801 " both_signs ideal model delta sigma weight residual False 10.55 9.44 1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb="FE3 SF4 M 801 " pdb=" S1 SF4 M 801 " pdb=" S2 SF4 M 801 " pdb=" S4 SF4 M 801 " both_signs ideal model delta sigma weight residual False -10.55 -9.46 -1.09 2.00e-01 2.50e+01 2.97e+01 chirality pdb="FE1 SF4 M 801 " pdb=" S2 SF4 M 801 " pdb=" S3 SF4 M 801 " pdb=" S4 SF4 M 801 " both_signs ideal model delta sigma weight residual False -10.55 -9.52 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 10128 not shown) Planarity restraints: 11619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP r 307 " -0.034 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP r 307 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP r 307 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP r 307 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP r 307 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP r 307 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP r 307 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP r 307 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP r 307 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP r 307 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN l 446 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.73e+01 pdb=" C ASN l 446 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN l 446 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN l 447 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 264 " 0.022 2.00e-02 2.50e+03 2.62e-02 1.72e+01 pdb=" CG TRP i 264 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP i 264 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP i 264 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP i 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP i 264 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP i 264 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 264 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 264 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP i 264 " 0.001 2.00e-02 2.50e+03 ... (remaining 11616 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 8 1.82 - 2.59: 1210 2.59 - 3.36: 98220 3.36 - 4.13: 160048 4.13 - 4.90: 297651 Nonbonded interactions: 557137 Sorted by model distance: nonbonded pdb=" OD2 ASP b 108 " pdb=" CG1 VAL d 19 " model vdw 1.049 3.460 nonbonded pdb=" CE MET k 1 " pdb=" ND2 ASN k 50 " model vdw 1.336 3.540 nonbonded pdb=" O LEU l 186 " pdb=" CD1 ILE l 190 " model vdw 1.374 3.460 nonbonded pdb=" OD2 ASP b 108 " pdb=" CB VAL d 19 " model vdw 1.459 3.470 nonbonded pdb=" O ILE M 177 " pdb=" N CYS M 179 " model vdw 1.482 2.520 ... (remaining 557132 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 'G' selection = (chain 'X' and (resid 72 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156)) } 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 22.630 Check model and map are aligned: 0.720 Set scattering table: 0.480 Process input model: 145.090 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.012 0.225 68479 Z= 0.800 Angle : 1.582 20.417 92788 Z= 1.047 Chirality : 0.069 1.112 10131 Planarity : 0.007 0.101 11619 Dihedral : 12.913 178.278 26035 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 27.86 Ramachandran Plot: Outliers : 2.88 % Allowed : 6.50 % Favored : 90.63 % Rotamer: Outliers : 0.83 % Allowed : 1.42 % Favored : 97.74 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.09), residues: 8097 helix: -1.91 (0.06), residues: 4076 sheet: -3.49 (0.21), residues: 353 loop : 0.43 (0.12), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP r 307 HIS 0.022 0.002 HIS l 534 PHE 0.046 0.003 PHE C 106 TYR 0.044 0.003 TYR w 339 ARG 0.016 0.001 ARG c 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1902 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1843 time to evaluate : 6.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 26 residues processed: 1884 average time/residue: 0.7260 time to fit residues: 2243.5623 Evaluate side-chains 1027 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1001 time to evaluate : 5.802 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.5681 time to fit residues: 34.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 673 optimal weight: 0.7980 chunk 604 optimal weight: 0.8980 chunk 335 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 407 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 625 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 380 optimal weight: 0.7980 chunk 465 optimal weight: 0.9990 chunk 724 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 313 ASN A 393 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS B 184 ASN B 191 ASN C 95 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS E 49 GLN ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN G 80 GLN G 101 ASN G 115 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 HIS L 86 ASN ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 384 ASN M 444 HIS M 460 HIS M 498 GLN M 514 ASN ** M 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 688 GLN N 91 HIS ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN O 41 HIS O 69 ASN ** O 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN ** O 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN P 236 ASN ** P 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 60 HIS ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 183 HIS ** Q 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 380 HIS ** Q 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 HIS T 64 ASN W 8 GLN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 112 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN ** b 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 83 HIS ** b 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN c 84 HIS d 61 GLN d 85 GLN ** d 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 GLN i 150 ASN i 204 ASN i 222 ASN ** i 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 94 ASN l 25 ASN l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 GLN l 205 ASN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 348 HIS ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 569 HIS ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN n 40 ASN o 52 ASN ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 HIS p 75 GLN p 124 GLN r 30 HIS r 48 ASN r 139 GLN r 168 HIS ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN r 319 HIS r 366 ASN r 390 ASN r 415 GLN s 93 ASN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 169 GLN s 171 HIS s 235 ASN ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN u 95 GLN u 99 HIS u 104 GLN u 143 HIS v 61 HIS v 85 HIS w 85 HIS w 111 ASN w 132 GLN w 182 GLN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 68479 Z= 0.286 Angle : 0.818 11.799 92788 Z= 0.420 Chirality : 0.047 0.286 10131 Planarity : 0.006 0.084 11619 Dihedral : 14.418 177.200 10007 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.99 % Allowed : 6.26 % Favored : 92.75 % Rotamer: Outliers : 2.54 % Allowed : 9.39 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.08 % 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: -1.00 (0.09), residues: 8097 helix: -0.38 (0.07), residues: 4070 sheet: -3.18 (0.21), residues: 376 loop : -0.52 (0.11), residues: 3651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP s 272 HIS 0.018 0.002 HIS O 41 PHE 0.028 0.002 PHE l 326 TYR 0.041 0.002 TYR w 339 ARG 0.015 0.001 ARG L 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1506 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1326 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 85 residues processed: 1435 average time/residue: 0.6523 time to fit residues: 1590.1083 Evaluate side-chains 1113 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1028 time to evaluate : 5.824 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.5329 time to fit residues: 92.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 402 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 603 optimal weight: 5.9990 chunk 493 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 725 optimal weight: 3.9990 chunk 784 optimal weight: 0.0570 chunk 646 optimal weight: 0.5980 chunk 719 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 582 optimal weight: 0.5980 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 185 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN N 31 ASN N 113 HIS N 123 GLN ** O 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN ** P 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 62 HIS ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 HIS ** g 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 88 ASN i 222 ASN ** i 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 296 ASN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN l 524 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 45 ASN ** m 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 26 ASN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 GLN r 304 GLN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 68479 Z= 0.250 Angle : 0.737 15.244 92788 Z= 0.374 Chirality : 0.045 0.252 10131 Planarity : 0.005 0.069 11619 Dihedral : 13.443 176.299 10007 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.78 % Favored : 92.38 % Rotamer: Outliers : 1.93 % Allowed : 12.11 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.04 % 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: -0.68 (0.09), residues: 8097 helix: 0.16 (0.08), residues: 4094 sheet: -2.82 (0.22), residues: 374 loop : -0.78 (0.11), residues: 3629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP u 86 HIS 0.009 0.001 HIS w 225 PHE 0.031 0.002 PHE C 106 TYR 0.035 0.002 TYR S 61 ARG 0.012 0.001 ARG L 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1163 time to evaluate : 7.123 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 outliers start: 137 outliers final: 50 residues processed: 1247 average time/residue: 0.6629 time to fit residues: 1428.4130 Evaluate side-chains 1051 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1001 time to evaluate : 5.850 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.5171 time to fit residues: 56.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 717 optimal weight: 0.9980 chunk 545 optimal weight: 3.9990 chunk 376 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 487 optimal weight: 4.9990 chunk 728 optimal weight: 1.9990 chunk 771 optimal weight: 0.9990 chunk 380 optimal weight: 2.9990 chunk 690 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN N 123 GLN ** O 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN ** P 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 GLN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 264 HIS ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 86 ASN ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN r 192 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 330 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 68479 Z= 0.236 Angle : 0.705 13.664 92788 Z= 0.354 Chirality : 0.044 0.218 10131 Planarity : 0.005 0.065 11619 Dihedral : 12.866 175.466 10007 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.43 % Favored : 92.75 % Rotamer: Outliers : 1.89 % Allowed : 13.58 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.51 (0.09), residues: 8097 helix: 0.44 (0.08), residues: 4077 sheet: -2.74 (0.21), residues: 382 loop : -0.89 (0.11), residues: 3638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP u 86 HIS 0.009 0.001 HIS T 41 PHE 0.031 0.002 PHE l 495 TYR 0.044 0.002 TYR S 61 ARG 0.009 0.000 ARG O 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1100 time to evaluate : 5.892 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 outliers start: 134 outliers final: 58 residues processed: 1180 average time/residue: 0.6419 time to fit residues: 1304.6644 Evaluate side-chains 1042 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 984 time to evaluate : 5.737 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4981 time to fit residues: 62.6998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 642 optimal weight: 6.9990 chunk 437 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 574 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 658 optimal weight: 5.9990 chunk 533 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 393 optimal weight: 0.8980 chunk 692 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** O 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 44 GLN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 116 HIS h 13 ASN i 63 GLN ** i 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 7 ASN l 30 ASN l 328 HIS ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 HIS ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 186 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 68479 Z= 0.348 Angle : 0.752 12.970 92788 Z= 0.378 Chirality : 0.046 0.226 10131 Planarity : 0.006 0.067 11619 Dihedral : 12.568 178.907 10007 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.20 % Favored : 92.05 % Rotamer: Outliers : 1.79 % Allowed : 15.54 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.58 (0.09), residues: 8097 helix: 0.48 (0.08), residues: 4075 sheet: -2.63 (0.22), residues: 382 loop : -1.06 (0.11), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP u 86 HIS 0.010 0.001 HIS d 50 PHE 0.032 0.002 PHE i 342 TYR 0.034 0.002 TYR b 88 ARG 0.009 0.001 ARG O 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1036 time to evaluate : 5.905 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 outliers start: 127 outliers final: 61 residues processed: 1116 average time/residue: 0.6531 time to fit residues: 1254.0479 Evaluate side-chains 998 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 937 time to evaluate : 5.859 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5146 time to fit residues: 67.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 259 optimal weight: 5.9990 chunk 694 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 452 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 772 optimal weight: 7.9990 chunk 640 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** O 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 431 HIS Q 442 HIS T 41 HIS T 44 GLN ** T 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN h 13 ASN ** i 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN ** o 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 104 GLN ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 68479 Z= 0.313 Angle : 0.734 14.079 92788 Z= 0.367 Chirality : 0.045 0.424 10131 Planarity : 0.005 0.067 11619 Dihedral : 12.346 175.170 10007 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.93 % Favored : 92.31 % Rotamer: Outliers : 1.79 % Allowed : 16.11 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.57 (0.09), residues: 8097 helix: 0.55 (0.08), residues: 4076 sheet: -2.54 (0.22), residues: 383 loop : -1.16 (0.11), residues: 3638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP s 185 HIS 0.007 0.001 HIS l 534 PHE 0.034 0.002 PHE P 61 TYR 0.042 0.002 TYR S 61 ARG 0.009 0.001 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 992 time to evaluate : 5.851 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 outliers start: 127 outliers final: 56 residues processed: 1081 average time/residue: 0.6589 time to fit residues: 1227.0667 Evaluate side-chains 1006 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 950 time to evaluate : 5.938 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5406 time to fit residues: 65.2722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 744 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 439 optimal weight: 2.9990 chunk 563 optimal weight: 0.7980 chunk 436 optimal weight: 0.8980 chunk 649 optimal weight: 0.9990 chunk 431 optimal weight: 0.5980 chunk 769 optimal weight: 0.0570 chunk 481 optimal weight: 3.9990 chunk 468 optimal weight: 2.9990 chunk 355 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 234 GLN T 41 HIS W 135 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 ASN k 7 ASN l 30 ASN ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 138 GLN ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 104 GLN ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68479 Z= 0.196 Angle : 0.697 14.153 92788 Z= 0.345 Chirality : 0.043 0.305 10131 Planarity : 0.005 0.075 11619 Dihedral : 11.895 169.842 10007 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.73 % Rotamer: Outliers : 1.03 % Allowed : 16.92 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.40 (0.09), residues: 8097 helix: 0.75 (0.08), residues: 4073 sheet: -2.24 (0.23), residues: 388 loop : -1.17 (0.11), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP Q 268 HIS 0.006 0.001 HIS i 25 PHE 0.055 0.002 PHE P 61 TYR 0.023 0.002 TYR l 422 ARG 0.011 0.000 ARG c 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1099 time to evaluate : 5.852 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 outliers start: 73 outliers final: 28 residues processed: 1146 average time/residue: 0.6561 time to fit residues: 1294.6268 Evaluate side-chains 1021 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 993 time to evaluate : 5.776 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5076 time to fit residues: 34.6973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 475 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 459 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 488 optimal weight: 2.9990 chunk 524 optimal weight: 0.8980 chunk 380 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 604 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 59 ASN ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 HIS ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 ASN l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 329 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68479 Z= 0.238 Angle : 0.719 14.209 92788 Z= 0.356 Chirality : 0.044 0.306 10131 Planarity : 0.005 0.112 11619 Dihedral : 11.732 167.796 10007 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.63 % Favored : 92.64 % Rotamer: Outliers : 1.04 % Allowed : 17.61 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.38 (0.09), residues: 8097 helix: 0.76 (0.08), residues: 4089 sheet: -2.05 (0.23), residues: 390 loop : -1.20 (0.11), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP i 167 HIS 0.007 0.001 HIS Q 442 PHE 0.046 0.002 PHE P 61 TYR 0.032 0.002 TYR S 61 ARG 0.012 0.000 ARG L 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1026 time to evaluate : 5.891 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 outliers start: 74 outliers final: 40 residues processed: 1064 average time/residue: 0.6680 time to fit residues: 1226.6951 Evaluate side-chains 1004 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 964 time to evaluate : 5.991 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5455 time to fit residues: 48.3940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 699 optimal weight: 1.9990 chunk 736 optimal weight: 0.6980 chunk 672 optimal weight: 1.9990 chunk 716 optimal weight: 0.8980 chunk 431 optimal weight: 0.5980 chunk 312 optimal weight: 0.4980 chunk 562 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 647 optimal weight: 4.9990 chunk 677 optimal weight: 0.0370 chunk 714 optimal weight: 0.0870 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS T 121 GLN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN h 13 ASN j 108 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 HIS ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 31 HIS ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 68479 Z= 0.190 Angle : 0.702 14.966 92788 Z= 0.349 Chirality : 0.043 0.310 10131 Planarity : 0.005 0.069 11619 Dihedral : 11.403 167.574 10007 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.42 % Favored : 92.89 % Rotamer: Outliers : 0.65 % Allowed : 17.71 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.32 (0.09), residues: 8097 helix: 0.84 (0.08), residues: 4085 sheet: -1.76 (0.24), residues: 384 loop : -1.23 (0.11), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP i 167 HIS 0.030 0.001 HIS G 103 PHE 0.047 0.002 PHE P 61 TYR 0.066 0.002 TYR H 44 ARG 0.013 0.000 ARG O 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1089 time to evaluate : 5.739 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 outliers start: 46 outliers final: 16 residues processed: 1106 average time/residue: 0.6587 time to fit residues: 1259.9095 Evaluate side-chains 1019 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1003 time to evaluate : 6.870 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5712 time to fit residues: 25.7314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 470 optimal weight: 3.9990 chunk 757 optimal weight: 4.9990 chunk 462 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 526 optimal weight: 2.9990 chunk 795 optimal weight: 3.9990 chunk 731 optimal weight: 0.4980 chunk 633 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 489 optimal weight: 3.9990 chunk 388 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 HIS ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN ** j 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 505 ASN ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN p 12 HIS ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 68479 Z= 0.319 Angle : 0.763 16.468 92788 Z= 0.378 Chirality : 0.046 0.287 10131 Planarity : 0.005 0.070 11619 Dihedral : 11.482 172.607 10007 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.88 % Favored : 92.45 % Rotamer: Outliers : 0.61 % Allowed : 18.50 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.41 (0.09), residues: 8097 helix: 0.75 (0.08), residues: 4087 sheet: -1.78 (0.24), residues: 390 loop : -1.28 (0.11), residues: 3620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP i 167 HIS 0.013 0.001 HIS G 103 PHE 0.046 0.002 PHE P 61 TYR 0.039 0.002 TYR H 44 ARG 0.011 0.001 ARG O 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 982 time to evaluate : 6.729 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 outliers start: 43 outliers final: 19 residues processed: 997 average time/residue: 0.6511 time to fit residues: 1122.6247 Evaluate side-chains 967 residues out of total 7176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 948 time to evaluate : 5.778 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5505 time to fit residues: 27.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 502 optimal weight: 0.0070 chunk 674 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 chunk 583 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 175 optimal weight: 5.9990 chunk 634 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 651 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 116 optimal weight: 0.6980 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN O 59 ASN P 236 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 285 ASN T 41 HIS ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN i 204 ASN j 108 GLN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN ** l 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 ASN ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 169 ASN ** r 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 GLN r 425 ASN ** s 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 140 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.119806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094706 restraints weight = 192755.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094117 restraints weight = 158546.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094375 restraints weight = 126464.607| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 68479 Z= 0.197 Angle : 0.726 15.890 92788 Z= 0.358 Chirality : 0.044 0.322 10131 Planarity : 0.005 0.065 11619 Dihedral : 11.208 177.022 10007 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.19 % Favored : 93.18 % Rotamer: Outliers : 0.44 % Allowed : 19.06 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.30 (0.10), residues: 8097 helix: 0.86 (0.08), residues: 4090 sheet: -1.55 (0.25), residues: 376 loop : -1.27 (0.11), residues: 3631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP i 167 HIS 0.011 0.001 HIS G 103 PHE 0.044 0.002 PHE P 61 TYR 0.048 0.002 TYR j 37 ARG 0.014 0.000 ARG F 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19564.76 seconds wall clock time: 343 minutes 24.01 seconds (20604.01 seconds total)