Starting phenix.real_space_refine on Sat Jan 20 07:26:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1o_32253/01_2024/7w1o_32253_updated.pdb" } resolution = 3.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 473 5.16 5 C 43003 2.51 5 N 11068 2.21 5 O 11925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 279": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 175": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "P GLU 229": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 335": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 105": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 268": "OE1" <-> "OE2" Residue "l TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "p GLU 28": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 92": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "u GLU 49": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 189": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66536 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3315 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1405 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 959 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2337 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1731 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 192} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3362 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, '2MR:plan-2': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 560 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1311 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} 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: "d" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1441 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "e" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 889 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2707 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4784 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1045 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 116} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3628 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 158} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "v" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1012 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "w" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2583 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 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: "G" 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 202 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "g" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 149 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "j" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 104 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "l" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 291 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2703 SG CYS A 382 48.897 48.505 178.368 1.00 23.88 S ATOM 3045 SG CYS A 425 48.330 44.969 183.864 1.00 27.94 S ATOM 2723 SG CYS A 385 45.505 44.548 178.241 1.00 25.02 S ATOM 2684 SG CYS A 379 43.790 49.468 182.244 1.00 29.99 S ATOM 3939 SG CYS B 113 38.196 65.039 143.602 1.00 32.94 S ATOM 3958 SG CYS B 116 43.332 62.122 147.094 1.00 24.63 S ATOM 3981 SG CYS B 119 44.156 64.904 141.739 1.00 34.73 S ATOM 4310 SG CYS B 162 41.238 59.155 142.658 1.00 29.40 S ATOM 4008 SG CYS B 123 50.553 67.235 136.949 1.00 31.98 S ATOM 4234 SG CYS B 152 48.302 65.564 131.191 1.00 24.73 S ATOM 4281 SG CYS B 158 46.334 61.879 135.822 1.00 43.59 S ATOM 4260 SG CYS B 155 52.401 61.939 134.454 1.00 20.83 S ATOM 5699 SG CYS C 166 54.825 65.327 126.719 1.00 28.79 S ATOM 4965 SG CYS C 71 59.718 64.513 123.001 1.00 20.68 S ATOM 4971 SG CYS C 72 56.189 66.568 120.905 1.00 20.66 S ATOM 4965 SG CYS C 71 59.718 64.513 123.001 1.00 20.68 S ATOM 5469 SG CYS C 136 57.696 69.269 125.414 1.00 33.56 S ATOM 14485 SG CYS M 131 42.836 61.947 159.042 1.00 17.92 S ATOM 14464 SG CYS M 128 46.048 57.849 156.026 1.00 17.85 S ATOM 14525 SG CYS M 137 48.280 60.933 161.440 1.00 18.25 S ATOM 14857 SG CYS M 179 46.731 61.382 172.324 1.00 18.69 S ATOM 15211 SG CYS M 226 43.837 63.946 168.129 1.00 18.56 S ATOM 14881 SG CYS M 182 41.504 64.232 174.420 1.00 18.03 S ATOM 14834 SG CYS M 176 40.818 58.905 170.910 1.00 18.35 S ATOM 14082 SG CYS M 78 58.184 56.037 175.755 1.00 21.61 S ATOM 14183 SG CYS M 92 56.515 58.084 178.309 1.00 22.45 S ATOM 13971 SG CYS M 64 52.269 58.223 176.167 1.00 20.47 S ATOM 14057 SG CYS M 75 52.939 56.256 173.044 1.00 21.53 S ATOM 21020 SG CYS O 135 31.918 32.212 186.290 1.00 57.67 S ATOM 21054 SG CYS O 140 31.558 29.009 187.664 1.00 60.61 S ATOM 21331 SG CYS O 176 36.335 33.972 189.087 1.00 56.95 S ATOM 21354 SG CYS O 180 36.144 30.272 189.386 1.00 62.87 S ATOM 27983 SG CYS T 86 30.069 52.247 151.401 1.00 25.02 S ATOM 28161 SG CYS T 111 31.404 55.541 152.431 1.00 26.30 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.70 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.70 Time building chain proxies: 26.92, per 1000 atoms: 0.40 Number of scatterers: 66536 At special positions: 0 Unit cell: (216.988, 215.914, 234.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 473 16.00 P 37 15.00 Mg 1 11.99 O 11925 8.00 N 11068 7.00 C 43003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 36 " - pdb=" SG CYS u 66 " distance=2.29 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=1.92 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.08 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.02 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.56 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb=" SF4 M 801 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " 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="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 330 helices and 29 sheets defined 52.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.10 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 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 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 302 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 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.037A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.142A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.614A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 111 through 123 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.333A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.605A 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: 4.892A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL F 42 " --> 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 96 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 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.067A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 66 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.181A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.699A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix 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 Processing helix chain 'J' and resid 214 through 218 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 322 Processing helix chain 'J' and resid 335 through 338 No H-bonds generated for 'chain 'J' and resid 335 through 338' Processing helix chain 'J' and resid 345 through 353 removed outlier: 3.692A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.742A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.834A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 69 through 73 removed outlier: 4.074A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 123 removed outlier: 4.512A 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 160 through 164 Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.857A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 4.709A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.637A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 395 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 467 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 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.731A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' 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 90 removed outlier: 4.812A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 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 146 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 53 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.651A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.001A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 59 No H-bonds generated for 'chain 'Q' and resid 56 through 59' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 4.306A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.135A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 4.288A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 286 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.489A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.475A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.234A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix removed outlier: 3.952A pdb=" N ALA S 14 " --> pdb=" O VAL S 11 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 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 Processing helix chain 'W' and resid 32 through 97 removed outlier: 3.609A pdb=" N THR W 42 " --> pdb=" O VAL W 38 " (cutoff:3.500A) Proline residue: W 73 - end of helix 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: 6.273A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 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 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 29 through 37 Processing helix chain 'Z' and resid 48 through 52 removed outlier: 4.357A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 removed outlier: 4.456A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 116 through 124 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.750A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 83 through 124 removed outlier: 6.549A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 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 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 No H-bonds generated for 'chain 'h' and resid 96 through 99' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.629A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.415A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 4.070A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.791A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.079A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.824A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.598A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 27 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.960A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 54 through 85 removed outlier: 4.087A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 4.233A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.838A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.264A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.889A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 112 through 132 removed outlier: 4.638A pdb=" N ASN l 115 " --> pdb=" O PRO l 112 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG l 116 " --> pdb=" O PHE l 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 137 through 157 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.981A 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 211 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 3.939A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.498A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.806A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.496A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.713A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 4.351A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 547 Proline residue: l 530 - end of helix removed outlier: 4.192A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG l 535 " --> pdb=" O ILE l 532 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 3.789A pdb=" N LYS l 547 " --> pdb=" O MET l 544 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.709A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 148 removed outlier: 4.458A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.930A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.516A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.997A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 93 through 97 removed outlier: 4.347A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.837A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (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 16 Proline residue: r 7 - end of helix removed outlier: 4.038A 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 42 removed outlier: 4.174A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.960A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.627A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.647A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 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 171 removed outlier: 3.754A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.108A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 3.951A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.177A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 248 removed outlier: 3.542A pdb=" N TYR r 241 " --> pdb=" O LEU r 238 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.063A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.605A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.706A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.270A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.964A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.465A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 4.283A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 4.029A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 168 removed outlier: 3.962A pdb=" N ILE s 166 " --> pdb=" O LEU s 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 253 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.048A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 removed outlier: 3.544A pdb=" N THR u 87 " --> pdb=" O THR u 83 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 49 through 52 removed outlier: 3.597A pdb=" N LYS w 52 " --> pdb=" O THR w 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 49 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 176 removed outlier: 3.649A pdb=" N PHE w 169 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.083A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 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 244 Processing helix chain 'w' and resid 246 through 251 removed outlier: 3.795A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 4.000A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 6.276A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.768A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.168A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 3.823A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.471A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.466A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 472 through 476 removed outlier: 6.593A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.218A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.817A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.688A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.622A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 401 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.122A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.675A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2913 hydrogen bonds defined for protein. 8076 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: 22.15 Time building geometry restraints manager: 23.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27210 1.40 - 1.62: 40046 1.62 - 1.84: 845 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 68181 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.290 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.634 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.297 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.26e+02 ... (remaining 68176 not shown) Histogram of bond angle deviations from ideal: 73.52 - 85.92: 76 85.92 - 98.33: 9 98.33 - 110.73: 22418 110.73 - 123.13: 66548 123.13 - 135.54: 3199 Bond angle restraints: 92250 Sorted by residual: angle pdb=" N ASN r 48 " pdb=" CA ASN r 48 " pdb=" C ASN r 48 " ideal model delta sigma weight residual 111.07 121.46 -10.39 1.07e+00 8.73e-01 9.42e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 122.44 -14.70 1.95e+00 2.62e-01 5.66e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.23 -14.39 1.91e+00 2.73e-01 5.64e+01 angle pdb=" C51 CDL l 701 " pdb=" CB5 CDL l 701 " pdb=" OB6 CDL l 701 " ideal model delta sigma weight residual 111.33 120.90 -9.57 1.32e+00 5.72e-01 5.24e+01 angle pdb=" C11 CDL V 202 " pdb=" CA5 CDL V 202 " pdb=" OA6 CDL V 202 " ideal model delta sigma weight residual 111.33 120.66 -9.33 1.32e+00 5.72e-01 4.98e+01 ... (remaining 92245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 39657 35.24 - 70.48: 1619 70.48 - 105.72: 107 105.72 - 140.96: 22 140.96 - 176.20: 14 Dihedral angle restraints: 41419 sinusoidal: 17721 harmonic: 23698 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 86.52 171.07 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -145.59 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 82.62 -142.61 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 41416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 9272 0.085 - 0.170: 712 0.170 - 0.255: 37 0.255 - 0.339: 9 0.339 - 0.424: 3 Chirality restraints: 10033 Sorted by residual: chirality pdb=" CA TRP u 86 " pdb=" N TRP u 86 " pdb=" C TRP u 86 " pdb=" CB TRP u 86 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.35 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CG LEU A 169 " pdb=" CB LEU A 169 " pdb=" CD1 LEU A 169 " pdb=" CD2 LEU A 169 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 10030 not shown) Planarity restraints: 11533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " 0.431 2.00e-02 2.50e+03 4.67e-01 2.73e+03 pdb=" C11 UQ s 401 " 0.085 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " 0.553 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " -0.636 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.433 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.411 2.00e-02 2.50e+03 3.67e-01 1.68e+03 pdb=" C18 UQ s 401 " 0.422 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.402 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.007 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.406 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.179 2.00e-02 2.50e+03 2.14e-01 5.74e+02 pdb=" C13 UQ s 401 " -0.118 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.349 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.043 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.245 2.00e-02 2.50e+03 ... (remaining 11530 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 1020 2.65 - 3.21: 62431 3.21 - 3.77: 104520 3.77 - 4.34: 146940 4.34 - 4.90: 241095 Nonbonded interactions: 556006 Sorted by model distance: nonbonded pdb=" OE1 GLN M 133 " pdb="MG MG M 804 " model vdw 2.081 2.170 nonbonded pdb=" O HIS J 356 " pdb=" O ARG J 357 " model vdw 2.148 3.040 nonbonded pdb=" O27 8Q1 X 201 " pdb=" O33 8Q1 X 201 " model vdw 2.178 3.040 nonbonded pdb=" O LYS E 57 " pdb=" NZ LYS E 57 " model vdw 2.183 2.520 nonbonded pdb=" OH TYR X 90 " pdb=" OD2 ASP X 114 " model vdw 2.195 2.440 ... (remaining 556001 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' and (resid 69 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 96 or (resid 97 through 98 and (na \ me N or name CA or name C or name O or name CB )) or resid 99 through 101 or (re \ sid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 th \ rough 156 or resid 201)) selection = (chain 'X' and (resid 69 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 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.500 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 157.830 Find NCS groups from input model: 2.340 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.312 68181 Z= 0.465 Angle : 0.878 17.410 92250 Z= 0.459 Chirality : 0.047 0.424 10033 Planarity : 0.009 0.467 11533 Dihedral : 18.362 176.197 26106 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 0.58 % Allowed : 17.68 % Favored : 81.74 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 8027 helix: 1.09 (0.08), residues: 4274 sheet: -0.31 (0.26), residues: 408 loop : -0.79 (0.11), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 433 HIS 0.010 0.001 HIS r 30 PHE 0.055 0.002 PHE k 12 TYR 0.038 0.002 TYR E 123 ARG 0.014 0.001 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1236 time to evaluate : 5.827 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: I 62 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: J 278 GLN cc_start: 0.7902 (mm110) cc_final: 0.7680 (mm110) REVERT: M 647 GLU cc_start: 0.6817 (tp30) cc_final: 0.6514 (tm-30) REVERT: N 9 ARG cc_start: 0.5304 (mtm180) cc_final: 0.4822 (ttp-170) REVERT: Q 52 MET cc_start: 0.8035 (mmt) cc_final: 0.7604 (mmt) REVERT: Y 43 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7552 (mtm-85) REVERT: Z 62 SER cc_start: 0.8167 (t) cc_final: 0.7585 (p) REVERT: b 16 ARG cc_start: 0.7556 (ptp-110) cc_final: 0.7243 (ptp-110) REVERT: l 317 ILE cc_start: 0.8935 (mm) cc_final: 0.8717 (mm) REVERT: l 411 MET cc_start: 0.8420 (mmp) cc_final: 0.8031 (mmp) REVERT: l 544 MET cc_start: 0.8243 (mmp) cc_final: 0.7842 (mmp) REVERT: o 29 THR cc_start: 0.8934 (m) cc_final: 0.8659 (p) REVERT: s 134 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8091 (mtm180) REVERT: v 44 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6758 (mt0) REVERT: w 143 TYR cc_start: 0.8606 (t80) cc_final: 0.8375 (t80) REVERT: w 196 CYS cc_start: 0.7839 (m) cc_final: 0.7393 (p) outliers start: 41 outliers final: 25 residues processed: 1260 average time/residue: 0.6657 time to fit residues: 1439.9520 Evaluate side-chains 1217 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1191 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain M residue 471 LYS Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain X residue 117 GLU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 139 MET Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 52 THR Chi-restraints excluded: chain i residue 190 MET Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 50 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 0.8980 chunk 601 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 405 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 621 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 0.0000 chunk 462 optimal weight: 10.0000 chunk 720 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 115 GLN I 25 GLN L 86 ASN ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN O 187 GLN ** P 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 GLN i 144 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 580 GLN n 11 HIS p 62 GLN p 78 GLN p 124 GLN p 141 GLN s 5 ASN s 124 ASN u 65 GLN u 95 GLN w 306 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68181 Z= 0.177 Angle : 0.562 10.627 92250 Z= 0.282 Chirality : 0.041 0.205 10033 Planarity : 0.005 0.067 11533 Dihedral : 14.079 170.006 10262 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 2.35 % Allowed : 16.81 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8027 helix: 1.35 (0.08), residues: 4275 sheet: -0.15 (0.26), residues: 406 loop : -0.57 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 433 HIS 0.007 0.001 HIS T 123 PHE 0.028 0.001 PHE l 335 TYR 0.028 0.001 TYR E 123 ARG 0.005 0.000 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1314 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7867 (ptp-170) REVERT: B 208 ASP cc_start: 0.8826 (t70) cc_final: 0.8502 (t0) REVERT: E 61 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: G 115 GLN cc_start: 0.8834 (tm130) cc_final: 0.8478 (tm-30) REVERT: H 82 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (tt) REVERT: I 62 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: L 98 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8130 (mmtt) REVERT: M 647 GLU cc_start: 0.6774 (tp30) cc_final: 0.6466 (tm-30) REVERT: N 9 ARG cc_start: 0.5186 (mtm180) cc_final: 0.4405 (ttt-90) REVERT: P 146 TYR cc_start: 0.8907 (p90) cc_final: 0.8252 (p90) REVERT: Q 52 MET cc_start: 0.8267 (mmt) cc_final: 0.7889 (mmt) REVERT: Q 82 LEU cc_start: 0.7594 (tt) cc_final: 0.7364 (tp) REVERT: Q 351 MET cc_start: 0.8851 (mmt) cc_final: 0.8596 (tpt) REVERT: T 46 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8038 (p0) REVERT: U 16 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8089 (tp30) REVERT: W 138 TYR cc_start: 0.8700 (m-80) cc_final: 0.8467 (m-80) REVERT: X 117 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: X 136 GLU cc_start: 0.7803 (pp20) cc_final: 0.7508 (pp20) REVERT: X 155 TYR cc_start: 0.5790 (m-10) cc_final: 0.5542 (m-80) REVERT: Y 43 ARG cc_start: 0.7909 (mmm-85) cc_final: 0.7416 (mtm-85) REVERT: b 16 ARG cc_start: 0.7513 (ptp-110) cc_final: 0.7306 (ptp-110) REVERT: b 116 VAL cc_start: 0.7110 (m) cc_final: 0.6812 (m) REVERT: e 83 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.6453 (t0) REVERT: l 419 THR cc_start: 0.8698 (m) cc_final: 0.8451 (p) REVERT: o 29 THR cc_start: 0.8822 (m) cc_final: 0.8549 (p) REVERT: o 70 TYR cc_start: 0.9060 (t80) cc_final: 0.8682 (t80) REVERT: r 243 MET cc_start: 0.8951 (mtm) cc_final: 0.8724 (mtp) REVERT: r 410 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7308 (ttm) REVERT: s 113 VAL cc_start: 0.9281 (m) cc_final: 0.9024 (t) REVERT: v 44 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6989 (mm-40) REVERT: v 54 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8386 (pm20) outliers start: 165 outliers final: 94 residues processed: 1407 average time/residue: 0.6226 time to fit residues: 1501.0039 Evaluate side-chains 1307 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1204 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain V residue 7 HIS Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 20 ASP Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 117 GLU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 153 ASP Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 118 ASP Chi-restraints excluded: chain c residue 166 LEU Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain g residue 72 PHE Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 170 LEU Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 306 THR Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 79 ASN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 31 MET Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 124 ASN Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 36 CYS Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 129 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 55 GLU Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 599 optimal weight: 0.5980 chunk 490 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 721 optimal weight: 7.9990 chunk 779 optimal weight: 0.2980 chunk 642 optimal weight: 0.9980 chunk 715 optimal weight: 8.9990 chunk 245 optimal weight: 0.3980 chunk 578 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 86 ASN ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN V 79 GLN ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 GLN n 11 HIS p 78 GLN p 124 GLN p 141 GLN ** r 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 5 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 68181 Z= 0.172 Angle : 0.535 10.717 92250 Z= 0.268 Chirality : 0.040 0.210 10033 Planarity : 0.004 0.057 11533 Dihedral : 13.166 170.174 10225 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.47 % Favored : 95.52 % Rotamer: Outliers : 2.72 % Allowed : 17.50 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.10), residues: 8027 helix: 1.47 (0.08), residues: 4263 sheet: -0.15 (0.26), residues: 407 loop : -0.50 (0.11), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS T 123 PHE 0.029 0.001 PHE l 335 TYR 0.038 0.001 TYR E 123 ARG 0.006 0.000 ARG n 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1291 time to evaluate : 5.790 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: B 208 ASP cc_start: 0.8803 (t70) cc_final: 0.8350 (t0) REVERT: C 55 ASN cc_start: 0.8409 (m-40) cc_final: 0.8092 (m110) REVERT: E 66 MET cc_start: 0.8725 (mmp) cc_final: 0.8219 (mmm) REVERT: G 115 GLN cc_start: 0.8795 (tm130) cc_final: 0.8361 (tm-30) REVERT: G 120 MET cc_start: 0.7953 (mtm) cc_final: 0.7480 (ttm) REVERT: H 82 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8036 (tt) REVERT: I 62 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: J 327 MET cc_start: 0.7992 (ptt) cc_final: 0.7769 (ptt) REVERT: M 647 GLU cc_start: 0.6710 (tp30) cc_final: 0.6374 (tm-30) REVERT: N 3 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5436 (tt) REVERT: N 8 ARG cc_start: 0.6577 (ptm160) cc_final: 0.6353 (mtp-110) REVERT: N 9 ARG cc_start: 0.5230 (mtm180) cc_final: 0.4553 (ttp-170) REVERT: N 73 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (m) REVERT: P 146 TYR cc_start: 0.8881 (p90) cc_final: 0.8304 (p90) REVERT: Q 52 MET cc_start: 0.8297 (mmt) cc_final: 0.7931 (mmt) REVERT: Q 351 MET cc_start: 0.8875 (mmt) cc_final: 0.8626 (tpt) REVERT: T 46 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7981 (p0) REVERT: X 136 GLU cc_start: 0.7779 (pp20) cc_final: 0.7539 (pp20) REVERT: X 155 TYR cc_start: 0.5740 (m-10) cc_final: 0.5501 (m-80) REVERT: b 16 ARG cc_start: 0.7352 (ptp-110) cc_final: 0.7051 (ptp-110) REVERT: b 116 VAL cc_start: 0.7068 (m) cc_final: 0.6754 (m) REVERT: e 83 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.6371 (t0) REVERT: i 268 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7717 (tt0) REVERT: j 68 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7204 (mt-10) REVERT: l 317 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8567 (mm) REVERT: l 419 THR cc_start: 0.8644 (m) cc_final: 0.8412 (p) REVERT: o 29 THR cc_start: 0.8752 (m) cc_final: 0.8497 (p) REVERT: o 70 TYR cc_start: 0.9025 (t80) cc_final: 0.8634 (t80) REVERT: p 179 MET cc_start: 0.6768 (mtp) cc_final: 0.6497 (mtp) REVERT: r 135 ARG cc_start: 0.8571 (tpt170) cc_final: 0.8354 (tpt90) REVERT: r 243 MET cc_start: 0.8828 (mtm) cc_final: 0.8420 (mtp) REVERT: s 113 VAL cc_start: 0.9300 (m) cc_final: 0.8970 (t) REVERT: v 44 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7047 (mm-40) REVERT: v 54 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: v 105 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7640 (tt0) outliers start: 191 outliers final: 124 residues processed: 1398 average time/residue: 0.6586 time to fit residues: 1587.7943 Evaluate side-chains 1338 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1205 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 303 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 619 ASP Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 195 ASP Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain Q residue 53 TYR Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain V residue 7 HIS Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 117 GLU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 153 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 60 ASN Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 118 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 170 LEU Chi-restraints excluded: chain i residue 190 MET Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 235 SER Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 306 THR Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 540 HIS Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 79 ASN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 178 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 129 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 237 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 6.9990 chunk 542 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 484 optimal weight: 6.9990 chunk 724 optimal weight: 0.9990 chunk 766 optimal weight: 0.0020 chunk 378 optimal weight: 8.9990 chunk 686 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 182 ASN O 187 GLN ** P 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN Y 54 GLN ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 GLN l 205 ASN p 78 GLN p 124 GLN p 141 GLN r 44 GLN s 5 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 68181 Z= 0.263 Angle : 0.567 10.825 92250 Z= 0.283 Chirality : 0.042 0.215 10033 Planarity : 0.005 0.054 11533 Dihedral : 12.724 168.396 10218 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.67 % Favored : 95.32 % Rotamer: Outliers : 3.49 % Allowed : 17.82 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.10), residues: 8027 helix: 1.43 (0.08), residues: 4270 sheet: -0.19 (0.26), residues: 405 loop : -0.52 (0.11), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS T 123 PHE 0.030 0.001 PHE k 12 TYR 0.026 0.001 TYR E 123 ARG 0.007 0.000 ARG n 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1233 time to evaluate : 5.758 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: B 208 ASP cc_start: 0.8836 (t70) cc_final: 0.8336 (t0) REVERT: C 55 ASN cc_start: 0.8357 (m-40) cc_final: 0.8045 (m110) REVERT: C 98 ARG cc_start: 0.5950 (tmm-80) cc_final: 0.5641 (tmm-80) REVERT: E 66 MET cc_start: 0.8729 (mmp) cc_final: 0.8283 (mmm) REVERT: G 115 GLN cc_start: 0.8758 (tm130) cc_final: 0.8552 (tm-30) REVERT: H 18 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: I 13 ASN cc_start: 0.8148 (m-40) cc_final: 0.7713 (m-40) REVERT: I 62 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: M 647 GLU cc_start: 0.6876 (tp30) cc_final: 0.6517 (tm-30) REVERT: N 3 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5465 (tt) REVERT: N 9 ARG cc_start: 0.5225 (mtm180) cc_final: 0.4589 (ttp-170) REVERT: N 73 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8421 (m) REVERT: O 185 MET cc_start: 0.8117 (ppp) cc_final: 0.7814 (tmm) REVERT: Q 52 MET cc_start: 0.8410 (mmt) cc_final: 0.7987 (mmt) REVERT: Q 139 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8753 (mp) REVERT: Q 351 MET cc_start: 0.8869 (mmt) cc_final: 0.8457 (tpt) REVERT: T 46 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (p0) REVERT: V 126 LYS cc_start: 0.8730 (tptt) cc_final: 0.8520 (tptt) REVERT: W 138 TYR cc_start: 0.8691 (m-80) cc_final: 0.8481 (m-80) REVERT: X 155 TYR cc_start: 0.5806 (m-10) cc_final: 0.5533 (m-80) REVERT: a 188 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6475 (m-30) REVERT: b 16 ARG cc_start: 0.7357 (ptp-110) cc_final: 0.7124 (ptp-110) REVERT: b 116 VAL cc_start: 0.7152 (m) cc_final: 0.6905 (m) REVERT: e 83 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.6408 (t70) REVERT: g 51 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7916 (mmt180) REVERT: i 268 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7776 (tt0) REVERT: j 2 ASN cc_start: 0.6652 (m-40) cc_final: 0.6408 (m110) REVERT: j 68 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7179 (mt-10) REVERT: l 317 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (mm) REVERT: l 397 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6662 (mp0) REVERT: l 419 THR cc_start: 0.8719 (m) cc_final: 0.8441 (p) REVERT: o 29 THR cc_start: 0.8770 (m) cc_final: 0.8516 (p) REVERT: o 70 TYR cc_start: 0.9051 (t80) cc_final: 0.8648 (t80) REVERT: p 124 GLN cc_start: 0.8115 (mt0) cc_final: 0.7895 (mt0) REVERT: p 179 MET cc_start: 0.6905 (mtp) cc_final: 0.6539 (mtp) REVERT: r 243 MET cc_start: 0.8679 (mtm) cc_final: 0.8472 (mtp) REVERT: v 54 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: v 105 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: w 160 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6599 (mp0) outliers start: 245 outliers final: 170 residues processed: 1381 average time/residue: 0.6562 time to fit residues: 1568.8832 Evaluate side-chains 1372 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1190 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 303 THR Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain Q residue 53 TYR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain V residue 7 HIS Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 117 GLU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 153 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 60 ASN Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 118 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 170 LEU Chi-restraints excluded: chain i residue 190 MET Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 65 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 162 THR Chi-restraints excluded: chain l residue 235 SER Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 306 THR Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 432 LEU Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain o residue 79 ASN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 72 LEU Chi-restraints excluded: chain r residue 178 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain u residue 36 CYS Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 129 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 196 CYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 237 ILE Chi-restraints excluded: chain w residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 570 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 654 optimal weight: 0.9980 chunk 529 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 9.9990 chunk 688 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN ** P 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 GLN ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 GLN i 152 ASN i 172 GLN ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 99 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 68181 Z= 0.357 Angle : 0.628 10.911 92250 Z= 0.314 Chirality : 0.044 0.233 10033 Planarity : 0.005 0.054 11533 Dihedral : 12.626 170.458 10218 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 4.22 % Allowed : 17.96 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.09), residues: 8027 helix: 1.23 (0.08), residues: 4292 sheet: -0.33 (0.26), residues: 405 loop : -0.66 (0.11), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS T 123 PHE 0.031 0.002 PHE i 292 TYR 0.022 0.002 TYR Y 44 ARG 0.008 0.001 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1513 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1217 time to evaluate : 5.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7357 (mt) REVERT: A 296 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 79 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8035 (ptp-170) REVERT: B 208 ASP cc_start: 0.8832 (t70) cc_final: 0.8339 (t0) REVERT: C 117 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9062 (tt) REVERT: G 115 GLN cc_start: 0.8760 (tm130) cc_final: 0.8538 (tm-30) REVERT: G 120 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7498 (ttm) REVERT: G 134 ASP cc_start: 0.5458 (p0) cc_final: 0.5188 (p0) REVERT: H 18 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: I 29 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7851 (mm110) REVERT: I 62 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: M 142 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: M 277 MET cc_start: 0.8462 (tmm) cc_final: 0.8123 (tpp) REVERT: N 3 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5485 (tt) REVERT: N 9 ARG cc_start: 0.5391 (mtm180) cc_final: 0.4665 (ttp-170) REVERT: N 73 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8532 (m) REVERT: O 185 MET cc_start: 0.8121 (ppp) cc_final: 0.7823 (tmm) REVERT: P 128 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9090 (mm) REVERT: Q 52 MET cc_start: 0.8526 (mmt) cc_final: 0.8060 (mmt) REVERT: Q 139 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8825 (mp) REVERT: Q 308 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8170 (p90) REVERT: Q 351 MET cc_start: 0.8914 (mmt) cc_final: 0.8532 (tpt) REVERT: T 46 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7988 (p0) REVERT: W 138 TYR cc_start: 0.8732 (m-10) cc_final: 0.8483 (m-80) REVERT: Y 43 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7695 (mtm-85) REVERT: Z 14 MET cc_start: 0.3741 (ppp) cc_final: 0.3101 (ptm) REVERT: Z 62 SER cc_start: 0.8293 (t) cc_final: 0.7693 (p) REVERT: a 188 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: b 16 ARG cc_start: 0.7662 (ptp-110) cc_final: 0.7418 (ptp-110) REVERT: e 83 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.6530 (t70) REVERT: e 148 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: g 51 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7990 (mmt180) REVERT: g 122 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7679 (mtm-85) REVERT: i 268 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7807 (tt0) REVERT: j 22 PHE cc_start: 0.7394 (t80) cc_final: 0.7054 (t80) REVERT: j 23 TRP cc_start: 0.5318 (m-10) cc_final: 0.5027 (m-10) REVERT: j 68 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7207 (mt-10) REVERT: l 397 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6652 (mp0) REVERT: o 18 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9018 (tt) REVERT: o 29 THR cc_start: 0.8770 (m) cc_final: 0.8508 (p) REVERT: o 70 TYR cc_start: 0.9102 (t80) cc_final: 0.8732 (t80) REVERT: p 179 MET cc_start: 0.7047 (mtp) cc_final: 0.6387 (mtp) REVERT: r 229 MET cc_start: 0.9134 (mtp) cc_final: 0.8770 (mtp) REVERT: s 3 MET cc_start: 0.8037 (tpp) cc_final: 0.7739 (tpt) REVERT: s 43 TYR cc_start: 0.8116 (m-80) cc_final: 0.7635 (m-80) REVERT: v 54 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8462 (pm20) outliers start: 296 outliers final: 204 residues processed: 1409 average time/residue: 0.6154 time to fit residues: 1489.1240 Evaluate side-chains 1389 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1165 time to evaluate : 5.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 172 VAL Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 142 GLN Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 303 THR Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 600 GLU Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 50 GLU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain Q residue 53 TYR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 356 ILE Chi-restraints excluded: chain Q residue 439 SER Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 122 HIS Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain V residue 7 HIS Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 82 GLU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 134 GLN Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 117 GLU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 153 ASP Chi-restraints excluded: chain Y residue 39 HIS Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 60 ASN Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 80 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 118 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 114 MET Chi-restraints excluded: chain e residue 148 GLN Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 43 SER Chi-restraints excluded: chain g residue 72 PHE Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain h residue 22 SER Chi-restraints excluded: chain h residue 50 ILE Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 170 LEU Chi-restraints excluded: chain i residue 190 MET Chi-restraints excluded: chain i residue 193 VAL Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 4 MET Chi-restraints excluded: chain j residue 9 THR Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 65 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 162 THR Chi-restraints excluded: chain l residue 235 SER Chi-restraints excluded: chain l residue 306 THR Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 432 LEU Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain m residue 172 THR Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 72 LEU Chi-restraints excluded: chain r residue 85 SER Chi-restraints excluded: chain r residue 178 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 269 MET Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 31 MET Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain u residue 36 CYS Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 129 THR Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 159 LEU Chi-restraints excluded: chain w residue 196 CYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 237 ILE Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 5.9990 chunk 690 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 767 optimal weight: 8.9990 chunk 636 optimal weight: 2.9990 chunk 355 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 402 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: