Starting phenix.real_space_refine on Sat Feb 17 02:57:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2y_32267/02_2024/7w2y_32267_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44196 2.51 5 N 11237 2.21 5 O 12239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J GLU 365": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "j PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68232 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 690 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 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: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2748 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 319} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} 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: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1277 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 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: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} 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: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'DCQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' 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: 30 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: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 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: "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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 334 Unusual residues: {'CDL': 3, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "W" 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: "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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 87 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "j" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "l" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 288 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 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 2718 SG CYS A 382 47.560 49.602 172.998 1.00 29.86 S ATOM 3060 SG CYS A 425 46.816 46.672 178.945 1.00 27.18 S ATOM 2738 SG CYS A 385 44.265 45.431 173.329 1.00 28.07 S ATOM 2699 SG CYS A 379 42.176 50.495 177.030 1.00 16.10 S ATOM 3961 SG CYS B 113 36.858 64.173 137.602 1.00 25.89 S ATOM 3980 SG CYS B 116 41.827 62.037 141.628 1.00 17.00 S ATOM 4003 SG CYS B 119 43.033 64.401 136.023 1.00 3.35 S ATOM 4332 SG CYS B 162 40.403 58.636 136.823 1.00 7.19 S ATOM 4030 SG CYS B 123 49.216 66.969 131.394 1.00 3.34 S ATOM 4256 SG CYS B 152 47.346 65.065 125.606 1.00 7.89 S ATOM 4303 SG CYS B 158 45.457 61.399 130.605 1.00 10.52 S ATOM 4282 SG CYS B 155 51.440 61.590 129.136 1.00 6.19 S ATOM 5724 SG CYS C 166 54.017 64.770 121.486 1.00 13.79 S ATOM 4996 SG CYS C 72 54.510 65.961 115.134 1.00 21.38 S ATOM 4990 SG CYS C 71 59.708 64.339 118.101 1.00 15.47 S ATOM 5494 SG CYS C 136 56.539 69.666 119.959 1.00 5.67 S ATOM 14943 SG CYS M 131 40.950 62.577 153.642 1.00 10.86 S ATOM 14922 SG CYS M 128 44.696 57.884 150.753 1.00 18.02 S ATOM 14983 SG CYS M 137 46.745 61.512 155.766 1.00 7.54 S ATOM 15315 SG CYS M 179 45.023 62.071 166.828 1.00 18.43 S ATOM 15669 SG CYS M 226 41.896 64.651 162.455 1.00 15.69 S ATOM 15339 SG CYS M 182 39.480 64.822 168.544 1.00 21.03 S ATOM 15292 SG CYS M 176 39.266 59.334 165.294 1.00 9.82 S ATOM 14540 SG CYS M 78 56.302 57.214 171.118 1.00 22.06 S ATOM 14641 SG CYS M 92 54.697 59.700 173.037 1.00 17.05 S ATOM 14429 SG CYS M 64 50.249 59.457 170.817 1.00 9.89 S ATOM 14515 SG CYS M 75 51.321 57.547 167.824 1.00 11.95 S ATOM 21478 SG CYS O 135 31.297 32.767 181.672 1.00 43.09 S ATOM 21512 SG CYS O 140 31.130 29.548 182.949 1.00 52.85 S ATOM 21792 SG CYS O 176 36.001 34.501 183.902 1.00 56.08 S ATOM 21815 SG CYS O 180 36.147 31.175 185.129 1.00 51.26 S ATOM 28554 SG CYS T 86 29.095 51.313 146.078 1.00 28.82 S ATOM 28732 SG CYS T 111 30.691 54.749 146.882 1.00 30.91 S ATOM 28754 SG CYS T 114 28.640 54.231 143.836 1.00 33.03 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.63 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.63 Time building chain proxies: 26.92, per 1000 atoms: 0.39 Number of scatterers: 68232 At special positions: 0 Unit cell: (219.137, 214.84, 229.879, 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 482 16.00 P 48 15.00 Mg 1 11.99 O 12239 8.00 N 11237 7.00 C 44196 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=2.04 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.93 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " 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="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " 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 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 114 " Number of angles added : 3 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 358 helices and 29 sheets defined 53.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.77 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.698A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 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 removed outlier: 3.669A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 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: 4.310A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.044A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.626A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 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: 5.829A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.207A 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 80 removed outlier: 3.629A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 135 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 185 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.152A 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: 4.391A 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 39 removed outlier: 5.316A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 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 94 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 3.954A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.912A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 65 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 75 removed outlier: 4.057A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.597A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 4.040A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.939A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 323 removed outlier: 3.513A pdb=" N HIS J 323 " --> pdb=" O VAL J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.640A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.521A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 4.226A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.921A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) 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 146 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: 3.688A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 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 396 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 425 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.761A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 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 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 577 through 579 No H-bonds generated for 'chain 'M' and resid 577 through 579' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' 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 654 Processing helix chain 'M' and resid 665 through 674 removed outlier: 3.963A pdb=" N LEU M 674 " --> pdb=" O GLU M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 695 removed outlier: 3.837A pdb=" N TYR M 695 " --> pdb=" O LYS M 692 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 703 Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.755A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 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 removed outlier: 3.817A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.627A 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 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 44 through 46 No H-bonds generated for 'chain 'P' and resid 44 through 46' Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.576A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 3.637A pdb=" N ASP P 102 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.999A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) 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: 4.101A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.748A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.155A 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: 3.969A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (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: 3.825A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.737A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.639A 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 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 3.637A pdb=" N LEU Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 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 Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 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 54 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 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' 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 99 Proline residue: W 73 - end of helix removed outlier: 3.896A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 138 Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.611A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.740A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.904A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.920A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.650A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' 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 129 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.928A 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 82 through 124 removed outlier: 3.913A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.520A 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 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 100 through 107 Processing helix chain 'e' and resid 116 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 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.855A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' 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 48 through 55 removed outlier: 3.870A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 88 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.670A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) 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: 4.256A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.825A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.870A 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 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.995A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.750A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.659A 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 removed outlier: 3.593A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.637A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.552A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.513A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.925A 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: 3.675A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.698A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.471A 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: 3.822A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 4.061A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 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: 4.142A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.315A 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 269 removed outlier: 4.046A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.452A 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: 4.048A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 362 through 365 No H-bonds generated for 'chain 'l' and resid 362 through 365' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.776A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.719A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 5.782A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.480A 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: 3.877A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.405A 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 533 Proline residue: l 530 - end of helix removed outlier: 4.145A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 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 46 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.187A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 removed outlier: 3.546A pdb=" N ARG m 173 " --> pdb=" O MET m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 33 removed outlier: 6.267A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.718A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 117 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: 4.477A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' 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: 4.865A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.185A 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: 4.227A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 Proline residue: r 74 - end of helix removed outlier: 4.420A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.680A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.751A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.340A 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 170 removed outlier: 3.892A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.779A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.203A 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: 4.328A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.901A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.646A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.598A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.660A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (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 Processing helix chain 'r' and resid 431 through 448 Proline residue: r 443 - end of helix removed outlier: 3.732A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (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: 3.757A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.387A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.900A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.193A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.537A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 192 removed outlier: 5.299A pdb=" N TRP s 179 " --> pdb=" O PHE s 176 " (cutoff:3.500A) Proline residue: s 180 - end of helix Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.859A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 11 through 13 No H-bonds generated for 'chain 'u' and resid 11 through 13' Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.908A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) 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 80 through 91 Processing helix chain 'u' and resid 102 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 50 through 52 No H-bonds generated for 'chain 'w' and resid 50 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.710A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' 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 175 removed outlier: 3.625A pdb=" N PHE w 169 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.314A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.556A 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 251 removed outlier: 5.155A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.884A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.119A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' 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: 6.461A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.082A 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: 5.956A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.711A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.314A 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 Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.601A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 229 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 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 removed outlier: 6.272A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) 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 365 through 368 removed outlier: 4.648A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.340A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.532A 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: 6.157A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.515A 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: 6.567A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.770A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.781A 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: 6.221A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.356A 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 402 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: 6.512A 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: 6.760A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.619A 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 2948 hydrogen bonds defined for protein. 8286 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: 22.97 Time building geometry restraints manager: 24.05 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: 27783 1.40 - 1.62: 41172 1.62 - 1.84: 882 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69917 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.288 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 69912 not shown) Histogram of bond angle deviations from ideal: 73.58 - 85.99: 76 85.99 - 98.39: 0 98.39 - 110.80: 24087 110.80 - 123.20: 67463 123.20 - 135.60: 2877 Bond angle restraints: 94503 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.35 -16.61 1.95e+00 2.62e-01 7.22e+01 angle pdb=" C11 CDL s 401 " pdb=" CA5 CDL s 401 " pdb=" OA6 CDL s 401 " ideal model delta sigma weight residual 111.33 120.96 -9.63 1.32e+00 5.72e-01 5.31e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.27 8.19 1.17e+00 7.36e-01 4.93e+01 angle pdb=" C51 CDL V 201 " pdb=" CB5 CDL V 201 " pdb=" OB6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.48 -9.15 1.32e+00 5.72e-01 4.79e+01 angle pdb=" C51 CDL N 201 " pdb=" CB5 CDL N 201 " pdb=" OB6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.37 -9.04 1.32e+00 5.72e-01 4.67e+01 ... (remaining 94498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 40657 35.05 - 70.10: 1801 70.10 - 105.15: 139 105.15 - 140.20: 23 140.20 - 175.25: 9 Dihedral angle restraints: 42629 sinusoidal: 18536 harmonic: 24093 Sorted by residual: dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -150.97 64.97 1 1.00e+01 1.00e-02 5.54e+01 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 -102.41 72.84 -175.25 1 2.00e+01 2.50e-03 4.79e+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 84.96 -144.96 1 2.00e+01 2.50e-03 4.36e+01 ... (remaining 42626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 10005 0.109 - 0.218: 179 0.218 - 0.326: 6 0.326 - 0.435: 2 0.435 - 0.544: 1 Chirality restraints: 10193 Sorted by residual: chirality pdb=" CA ARG P 44 " pdb=" N ARG P 44 " pdb=" C ARG P 44 " pdb=" CB ARG P 44 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA PHE s 19 " pdb=" N PHE s 19 " pdb=" C PHE s 19 " pdb=" CB PHE s 19 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+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 -2.39 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 10190 not shown) Planarity restraints: 11767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ J 402 " -0.520 2.00e-02 2.50e+03 4.46e-01 2.48e+03 pdb=" C23 UQ J 402 " 0.611 2.00e-02 2.50e+03 pdb=" C24 UQ J 402 " 0.414 2.00e-02 2.50e+03 pdb=" C25 UQ J 402 " -0.092 2.00e-02 2.50e+03 pdb=" C26 UQ J 402 " -0.413 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.338 2.00e-02 2.50e+03 3.14e-01 1.24e+03 pdb=" C18 UQ s 402 " -0.324 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.381 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.005 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.361 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.307 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C13 UQ J 402 " -0.575 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.230 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.041 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.004 2.00e-02 2.50e+03 ... (remaining 11764 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4759 2.74 - 3.28: 67044 3.28 - 3.82: 118641 3.82 - 4.36: 148950 4.36 - 4.90: 245713 Nonbonded interactions: 585107 Sorted by model distance: nonbonded pdb=" O ILE Q 184 " pdb=" OG1 THR Q 188 " model vdw 2.196 2.440 nonbonded pdb=" OG SER s 109 " pdb=" OE2 GLU s 192 " model vdw 2.204 2.440 nonbonded pdb=" OG SER l 545 " pdb=" O SER r 274 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.209 2.440 nonbonded pdb=" OD2 ASP l 554 " pdb=" OH TYR r 288 " model vdw 2.212 2.440 ... (remaining 585102 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 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 156 or \ resid 201)) selection = (chain 'X' and (resid 69 through 110 or (resid 111 through 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 149 or (resid 150 t \ hrough 153 and (name N or name 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.040 Extract box with map and model: 9.540 Check model and map are aligned: 0.770 Set scattering table: 0.530 Process input model: 162.490 Find NCS groups from input model: 2.130 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: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.317 69917 Z= 0.485 Angle : 0.798 17.328 94503 Z= 0.400 Chirality : 0.043 0.544 10193 Planarity : 0.009 0.446 11767 Dihedral : 18.488 175.251 27070 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 1.05 % Allowed : 13.98 % Favored : 84.97 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.19 % 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: 0.97 (0.09), residues: 8173 helix: 1.46 (0.08), residues: 4332 sheet: 0.32 (0.25), residues: 411 loop : -0.31 (0.11), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP l 144 HIS 0.007 0.001 HIS J 37 PHE 0.029 0.001 PHE i 292 TYR 0.025 0.001 TYR Z 19 ARG 0.016 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1050 time to evaluate : 6.080 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: F 89 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.7121 (ttm-80) REVERT: L 70 GLU cc_start: 0.8295 (tt0) cc_final: 0.7971 (tt0) REVERT: Q 182 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8824 (t0) REVERT: T 52 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8370 (mtp180) REVERT: X 123 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8604 (mt-10) REVERT: f 51 SER cc_start: 0.8929 (t) cc_final: 0.8721 (m) REVERT: h 53 GLU cc_start: 0.8442 (tt0) cc_final: 0.8210 (tt0) REVERT: i 47 ASN cc_start: 0.8004 (m110) cc_final: 0.7582 (p0) REVERT: l 207 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7782 (tp30) REVERT: m 1 MET cc_start: 0.4501 (OUTLIER) cc_final: 0.1488 (tpt) REVERT: r 243 MET cc_start: 0.9160 (mtt) cc_final: 0.8872 (mmm) REVERT: s 24 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8919 (tp30) REVERT: w 289 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7789 (ttp80) outliers start: 75 outliers final: 51 residues processed: 1108 average time/residue: 1.6138 time to fit residues: 2285.7061 Evaluate side-chains 1052 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 998 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 484 SER Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 229 SER Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 85 SER Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 152 SER Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 10.0000 chunk 610 optimal weight: 0.4980 chunk 338 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 411 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 630 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 383 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 chunk 731 optimal weight: 3.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 164 ASN E 48 HIS F 93 ASN J 154 GLN J 341 GLN K 75 ASN K 78 HIS M 498 GLN N 113 HIS N 116 ASN O 106 GLN T 74 GLN V 129 GLN b 14 GLN i 147 GLN i 322 GLN l 109 HIS l 580 GLN m 86 ASN n 11 HIS p 66 GLN p 78 GLN r 139 GLN r 192 ASN w 223 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 69917 Z= 0.349 Angle : 0.619 12.406 94503 Z= 0.312 Chirality : 0.045 0.203 10193 Planarity : 0.005 0.075 11767 Dihedral : 15.540 173.540 10981 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 2.84 % Allowed : 13.22 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 8173 helix: 1.39 (0.08), residues: 4316 sheet: 0.40 (0.26), residues: 390 loop : -0.35 (0.10), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 86 HIS 0.009 0.001 HIS J 37 PHE 0.038 0.002 PHE i 292 TYR 0.026 0.002 TYR J 180 ARG 0.011 0.001 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1019 time to evaluate : 6.253 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.8816 (mtm180) REVERT: E 42 GLU cc_start: 0.8910 (tp30) cc_final: 0.8450 (tp30) REVERT: F 25 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: F 38 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: G 98 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7746 (tt) REVERT: L 154 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8453 (ptmm) REVERT: M 94 MET cc_start: 0.9390 (tpt) cc_final: 0.8908 (tpp) REVERT: M 473 MET cc_start: 0.9044 (ttt) cc_final: 0.8801 (mtp) REVERT: M 485 ASP cc_start: 0.8581 (p0) cc_final: 0.8337 (p0) REVERT: N 41 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: N 132 LYS cc_start: 0.8821 (ttpp) cc_final: 0.8594 (tttt) REVERT: Q 57 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: T 52 ARG cc_start: 0.8573 (mtp180) cc_final: 0.8371 (mtp180) REVERT: U 79 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: X 151 LYS cc_start: 0.8436 (tppt) cc_final: 0.8069 (tmtt) REVERT: Y 41 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: a 72 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: d 62 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: h 53 GLU cc_start: 0.8460 (tt0) cc_final: 0.8234 (tt0) REVERT: h 55 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: h 71 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8777 (mtpt) REVERT: i 97 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8605 (mmp) REVERT: i 321 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7432 (tttm) REVERT: l 496 MET cc_start: 0.7778 (tpt) cc_final: 0.7399 (ttm) REVERT: l 500 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8178 (tp) REVERT: m 1 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.1646 (tpt) REVERT: p 114 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7699 (mtp) REVERT: r 91 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7949 (mtp180) REVERT: r 222 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: u 80 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: v 45 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: v 81 LYS cc_start: 0.8558 (mttp) cc_final: 0.8197 (mmpt) REVERT: w 102 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (mptt) outliers start: 203 outliers final: 110 residues processed: 1129 average time/residue: 1.6471 time to fit residues: 2378.2548 Evaluate side-chains 1126 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 993 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 220 MET Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 248 SER Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 82 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 43 ARG Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 51 SER Chi-restraints excluded: chain f residue 59 ILE Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 229 SER Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 233 LEU Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 507 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 95 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 343 ILE Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 608 optimal weight: 0.9990 chunk 497 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 732 optimal weight: 0.0020 chunk 791 optimal weight: 7.9990 chunk 652 optimal weight: 6.9990 chunk 726 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 587 optimal weight: 3.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 93 ASN J 154 GLN J 341 GLN K 75 ASN M 498 GLN M 663 ASN N 113 HIS N 116 ASN O 106 GLN T 74 GLN V 129 GLN a 141 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 160 GLN i 147 GLN i 322 GLN l 109 HIS p 78 GLN r 139 GLN w 37 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 69917 Z= 0.155 Angle : 0.504 10.485 94503 Z= 0.256 Chirality : 0.040 0.171 10193 Planarity : 0.004 0.075 11767 Dihedral : 14.432 175.583 10947 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 2.06 % Allowed : 14.41 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.09), residues: 8173 helix: 1.70 (0.08), residues: 4314 sheet: 0.25 (0.24), residues: 434 loop : -0.21 (0.11), residues: 3425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 PHE 0.031 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.009 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1060 time to evaluate : 6.184 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: E 34 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7798 (mm-30) REVERT: E 42 GLU cc_start: 0.8862 (tp30) cc_final: 0.8308 (tp30) REVERT: G 84 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7678 (mt) REVERT: G 98 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7748 (tp) REVERT: M 427 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.9004 (tp) REVERT: M 473 MET cc_start: 0.8961 (ttt) cc_final: 0.8687 (mtp) REVERT: M 485 ASP cc_start: 0.8581 (p0) cc_final: 0.8267 (p0) REVERT: Q 57 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: Q 100 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8385 (mt-10) REVERT: U 79 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: W 121 MET cc_start: 0.8061 (tpp) cc_final: 0.7784 (tpp) REVERT: Z 39 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7711 (ttt90) REVERT: a 160 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9050 (mtt) REVERT: d 97 LYS cc_start: 0.8353 (mttp) cc_final: 0.8108 (mttp) REVERT: h 53 GLU cc_start: 0.8442 (tt0) cc_final: 0.8224 (tt0) REVERT: h 55 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: i 47 ASN cc_start: 0.7980 (m110) cc_final: 0.7602 (p0) REVERT: j 109 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8490 (mptt) REVERT: l 500 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8176 (tp) REVERT: m 1 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.1729 (tpt) REVERT: r 91 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7865 (mtp180) REVERT: u 80 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: v 81 LYS cc_start: 0.8465 (mttp) cc_final: 0.8185 (mmpt) REVERT: v 88 ASP cc_start: 0.8892 (m-30) cc_final: 0.8381 (m-30) REVERT: w 45 LEU cc_start: 0.8143 (pp) cc_final: 0.7936 (pp) outliers start: 147 outliers final: 65 residues processed: 1140 average time/residue: 1.6066 time to fit residues: 2352.1723 Evaluate side-chains 1090 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1013 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 1.9990 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 349 optimal weight: 6.9990 chunk 491 optimal weight: 0.4980 chunk 734 optimal weight: 8.9990 chunk 778 optimal weight: 1.9990 chunk 383 optimal weight: 8.9990 chunk 696 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN J 154 GLN J 341 GLN M 498 GLN M 663 ASN M 676 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN i 147 GLN i 322 GLN l 109 HIS m 86 ASN n 11 HIS p 78 GLN r 139 GLN v 65 GLN w 149 HIS w 300 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 69917 Z= 0.260 Angle : 0.557 10.819 94503 Z= 0.282 Chirality : 0.043 0.194 10193 Planarity : 0.005 0.072 11767 Dihedral : 14.111 174.796 10923 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 2.98 % Allowed : 14.28 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4313 sheet: 0.32 (0.25), residues: 416 loop : -0.22 (0.11), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS J 37 PHE 0.035 0.002 PHE i 292 TYR 0.021 0.002 TYR J 180 ARG 0.009 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1039 time to evaluate : 6.137 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.8750 (mtm180) REVERT: C 49 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8197 (mmtt) REVERT: E 34 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7828 (mm-30) REVERT: E 42 GLU cc_start: 0.8864 (tp30) cc_final: 0.8292 (tp30) REVERT: E 119 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8579 (mm) REVERT: K 106 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: L 154 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8454 (ptmm) REVERT: M 464 GLN cc_start: 0.8079 (tp40) cc_final: 0.7471 (tm130) REVERT: M 473 MET cc_start: 0.9053 (ttt) cc_final: 0.8792 (mtp) REVERT: M 485 ASP cc_start: 0.8573 (p0) cc_final: 0.8256 (p0) REVERT: N 41 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: Q 57 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: Q 100 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8444 (mt-10) REVERT: U 79 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: W 52 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8615 (mtpt) REVERT: W 120 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7169 (ttt) REVERT: X 147 TYR cc_start: 0.8932 (t80) cc_final: 0.8719 (t80) REVERT: Y 41 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: Z 39 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7716 (ttt90) REVERT: a 160 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.9077 (mtt) REVERT: d 62 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: h 53 GLU cc_start: 0.8443 (tt0) cc_final: 0.8223 (tt0) REVERT: h 55 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: h 71 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8788 (mtpt) REVERT: i 47 ASN cc_start: 0.8076 (m110) cc_final: 0.7752 (p0) REVERT: i 97 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8506 (mmp) REVERT: i 321 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7422 (tttm) REVERT: l 500 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8158 (tp) REVERT: m 1 MET cc_start: 0.4493 (OUTLIER) cc_final: 0.1644 (tmt) REVERT: m 98 MET cc_start: 0.7557 (mtt) cc_final: 0.7315 (mtp) REVERT: o 85 LYS cc_start: 0.8858 (tttp) cc_final: 0.8572 (tttp) REVERT: p 114 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7700 (mtp) REVERT: r 91 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7901 (mtp180) REVERT: r 222 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: u 80 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: v 45 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: v 81 LYS cc_start: 0.8574 (mttp) cc_final: 0.8284 (mmpt) REVERT: v 88 ASP cc_start: 0.8902 (m-30) cc_final: 0.8370 (m-30) REVERT: w 45 LEU cc_start: 0.8256 (pp) cc_final: 0.8053 (pp) outliers start: 213 outliers final: 104 residues processed: 1145 average time/residue: 1.6326 time to fit residues: 2395.1830 Evaluate side-chains 1142 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1014 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 82 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 30 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain n residue 56 THR Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 45 GLU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 3.9990 chunk 441 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 579 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 664 optimal weight: 8.9990 chunk 537 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 8.9990 chunk 698 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN J 154 GLN J 341 GLN M 498 GLN M 663 ASN M 676 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN a 141 GLN ** b 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 160 GLN h 21 GLN i 147 GLN i 319 HIS i 322 GLN l 109 HIS n 11 HIS p 78 GLN r 139 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 69917 Z= 0.258 Angle : 0.554 10.828 94503 Z= 0.281 Chirality : 0.043 0.193 10193 Planarity : 0.005 0.072 11767 Dihedral : 13.843 177.762 10923 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 2.92 % Allowed : 14.72 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 8173 helix: 1.59 (0.08), residues: 4312 sheet: 0.25 (0.25), residues: 425 loop : -0.22 (0.11), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS J 37 PHE 0.034 0.002 PHE i 292 TYR 0.023 0.002 TYR J 180 ARG 0.010 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1039 time to evaluate : 6.238 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: A 224 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8766 (mtm180) REVERT: A 241 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8678 (m) REVERT: C 49 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8197 (mmtt) REVERT: C 195 ARG cc_start: 0.8299 (mtt90) cc_final: 0.8004 (mtt-85) REVERT: E 42 GLU cc_start: 0.8862 (tp30) cc_final: 0.8289 (tp30) REVERT: E 119 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8567 (mm) REVERT: H 7 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8123 (mptp) REVERT: J 179 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7915 (mtm-85) REVERT: L 154 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8440 (ptmm) REVERT: M 464 GLN cc_start: 0.8021 (tp40) cc_final: 0.7413 (tm130) REVERT: M 473 MET cc_start: 0.9100 (ttt) cc_final: 0.8818 (mtp) REVERT: N 41 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: Q 57 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: Q 100 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8448 (mt-10) REVERT: U 79 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: W 52 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8595 (mtpt) REVERT: W 120 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7213 (ttt) REVERT: X 147 TYR cc_start: 0.8959 (t80) cc_final: 0.8715 (t80) REVERT: Y 41 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: Z 39 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7705 (ttt90) REVERT: a 160 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.9092 (mtt) REVERT: d 62 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: h 53 GLU cc_start: 0.8447 (tt0) cc_final: 0.8223 (tt0) REVERT: h 55 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: h 71 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8772 (mtpt) REVERT: i 47 ASN cc_start: 0.8094 (m110) cc_final: 0.7776 (p0) REVERT: i 97 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8504 (mmp) REVERT: i 281 LEU cc_start: 0.8849 (mt) cc_final: 0.8627 (mm) REVERT: i 321 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7437 (tttm) REVERT: l 500 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8206 (tp) REVERT: m 1 MET cc_start: 0.4567 (OUTLIER) cc_final: 0.3958 (mpp) REVERT: m 86 ASN cc_start: 0.8638 (t0) cc_final: 0.8403 (t0) REVERT: m 98 MET cc_start: 0.7560 (mtt) cc_final: 0.7305 (mtp) REVERT: p 114 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7702 (mtp) REVERT: r 91 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7912 (mtp180) REVERT: r 222 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: u 80 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: v 54 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: v 81 LYS cc_start: 0.8556 (mttp) cc_final: 0.8267 (mmpt) REVERT: v 88 ASP cc_start: 0.8902 (m-30) cc_final: 0.8390 (m-30) REVERT: v 115 ARG cc_start: 0.7358 (ppp80) cc_final: 0.6730 (ttp80) REVERT: w 45 LEU cc_start: 0.8285 (pp) cc_final: 0.8071 (pp) outliers start: 209 outliers final: 114 residues processed: 1152 average time/residue: 1.6202 time to fit residues: 2396.4101 Evaluate side-chains 1155 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1014 time to evaluate : 5.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 179 ARG Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 120 MET Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 82 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 30 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 0.9990 chunk 700 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 456 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 778 optimal weight: 0.9980 chunk 646 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 408 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 80 ASN F 93 ASN J 154 GLN J 341 GLN M 498 GLN M 663 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN a 189 ASN c 160 GLN h 21 GLN i 147 GLN i 322 GLN l 109 HIS p 78 GLN r 139 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69917 Z= 0.180 Angle : 0.512 10.763 94503 Z= 0.259 Chirality : 0.041 0.198 10193 Planarity : 0.004 0.073 11767 Dihedral : 13.354 175.439 10922 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 2.62 % Allowed : 15.35 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 8173 helix: 1.74 (0.08), residues: 4312 sheet: 0.23 (0.24), residues: 434 loop : -0.15 (0.11), residues: 3427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.011 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1042 time to evaluate : 6.258 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: A 224 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.8657 (mtm180) REVERT: A 241 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8659 (m) REVERT: C 195 ARG cc_start: 0.8278 (mtt90) cc_final: 0.8010 (mtt-85) REVERT: E 34 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 42 GLU cc_start: 0.8839 (tp30) cc_final: 0.8330 (tp30) REVERT: E 119 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8531 (mm) REVERT: H 7 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8132 (mptp) REVERT: L 154 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8441 (ptmm) REVERT: M 464 GLN cc_start: 0.8050 (tp40) cc_final: 0.7431 (tm130) REVERT: M 473 MET cc_start: 0.9057 (ttt) cc_final: 0.8807 (mtp) REVERT: M 485 ASP cc_start: 0.8557 (p0) cc_final: 0.8266 (p0) REVERT: N 41 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: P 161 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8617 (mppt) REVERT: Q 57 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: Q 315 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: U 79 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: X 147 TYR cc_start: 0.8978 (t80) cc_final: 0.8740 (t80) REVERT: Y 56 ILE cc_start: 0.8484 (mm) cc_final: 0.8252 (mt) REVERT: Z 39 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7669 (ttt90) REVERT: a 72 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7699 (ttm170) REVERT: a 160 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9082 (mtt) REVERT: b 21 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7439 (ttm170) REVERT: b 27 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8538 (mt-10) REVERT: d 62 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: h 55 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: h 71 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8750 (mtpt) REVERT: i 47 ASN cc_start: 0.8048 (m110) cc_final: 0.7840 (p0) REVERT: i 97 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8595 (mmp) REVERT: i 321 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7405 (tttm) REVERT: j 16 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8615 (tp) REVERT: j 109 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8476 (mptt) REVERT: l 500 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8203 (tp) REVERT: m 1 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4076 (mpp) REVERT: m 86 ASN cc_start: 0.8651 (t0) cc_final: 0.8438 (t160) REVERT: m 98 MET cc_start: 0.7576 (mtt) cc_final: 0.7302 (mtp) REVERT: p 114 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: r 91 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7868 (mtp180) REVERT: r 222 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: u 80 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5890 (mp0) REVERT: v 54 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: v 81 LYS cc_start: 0.8542 (mttp) cc_final: 0.8234 (mmpt) REVERT: v 88 ASP cc_start: 0.8878 (m-30) cc_final: 0.8367 (m-30) REVERT: v 115 ARG cc_start: 0.7378 (ppp80) cc_final: 0.6745 (ttp80) outliers start: 187 outliers final: 92 residues processed: 1146 average time/residue: 1.6072 time to fit residues: 2369.6093 Evaluate side-chains 1130 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1011 time to evaluate : 6.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 693 ASP Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 30 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 443 optimal weight: 1.9990 chunk 568 optimal weight: 5.9990 chunk 440 optimal weight: 0.3980 chunk 655 optimal weight: 9.9990 chunk 434 optimal weight: 9.9990 chunk 775 optimal weight: 2.9990 chunk 485 optimal weight: 8.9990 chunk 473 optimal weight: 4.9990 chunk 358 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN G 101 ASN J 154 GLN J 341 GLN M 498 GLN M 663 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN a 141 GLN c 160 GLN h 21 GLN i 147 GLN i 322 GLN l 109 HIS p 78 GLN r 139 GLN r 251 ASN r 304 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 69917 Z= 0.239 Angle : 0.545 13.057 94503 Z= 0.275 Chirality : 0.042 0.210 10193 Planarity : 0.005 0.071 11767 Dihedral : 13.306 174.946 10921 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 2.77 % Allowed : 15.32 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.09), residues: 8173 helix: 1.67 (0.08), residues: 4308 sheet: 0.29 (0.25), residues: 427 loop : -0.17 (0.11), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS J 37 PHE 0.034 0.002 PHE i 292 TYR 0.021 0.001 TYR J 180 ARG 0.011 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1015 time to evaluate : 6.220 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7393 (pp20) REVERT: A 224 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8744 (mtm180) REVERT: A 241 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8679 (m) REVERT: C 49 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8165 (mmtt) REVERT: C 195 ARG cc_start: 0.8276 (mtt90) cc_final: 0.8010 (mtt-85) REVERT: E 42 GLU cc_start: 0.8859 (tp30) cc_final: 0.8355 (tp30) REVERT: E 119 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (mm) REVERT: F 25 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: H 7 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8138 (mptp) REVERT: K 106 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: L 154 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8441 (ptmm) REVERT: M 464 GLN cc_start: 0.8037 (tp40) cc_final: 0.7413 (tm130) REVERT: M 473 MET cc_start: 0.9100 (ttt) cc_final: 0.8841 (mtp) REVERT: M 485 ASP cc_start: 0.8584 (p0) cc_final: 0.8298 (p0) REVERT: N 41 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: P 161 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8622 (mppt) REVERT: Q 57 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: Q 100 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8373 (mt-10) REVERT: Q 315 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: T 105 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6585 (mm-30) REVERT: U 79 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: X 147 TYR cc_start: 0.8991 (t80) cc_final: 0.8750 (t80) REVERT: Y 41 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: Z 39 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7680 (ttt90) REVERT: a 72 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: a 160 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9090 (mtt) REVERT: b 21 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7437 (ttm170) REVERT: d 15 ARG cc_start: 0.7296 (tpp-160) cc_final: 0.7073 (tpp80) REVERT: d 62 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: h 55 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: h 71 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8765 (mtpt) REVERT: i 47 ASN cc_start: 0.8162 (m110) cc_final: 0.7865 (p0) REVERT: i 97 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8585 (mmp) REVERT: i 321 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7453 (tttm) REVERT: j 16 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8583 (tp) REVERT: l 491 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7555 (tt) REVERT: l 500 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8216 (tp) REVERT: m 1 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.4150 (mpp) REVERT: m 86 ASN cc_start: 0.8673 (t0) cc_final: 0.8451 (t160) REVERT: m 98 MET cc_start: 0.7601 (mtt) cc_final: 0.7312 (mtp) REVERT: p 114 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7680 (mtp) REVERT: r 91 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.7917 (mtp180) REVERT: r 222 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: u 80 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: v 54 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: v 65 GLN cc_start: 0.8516 (tt0) cc_final: 0.8160 (tt0) REVERT: v 81 LYS cc_start: 0.8559 (mttp) cc_final: 0.8264 (mmpt) REVERT: v 88 ASP cc_start: 0.8896 (m-30) cc_final: 0.8380 (m-30) REVERT: v 115 ARG cc_start: 0.7357 (ppp80) cc_final: 0.6736 (ttp80) REVERT: w 95 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.9019 (m-30) outliers start: 198 outliers final: 121 residues processed: 1130 average time/residue: 1.6390 time to fit residues: 2382.1175 Evaluate side-chains 1162 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1008 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 498 GLN Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 693 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 30 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 5.9990 chunk 309 optimal weight: 0.7980 chunk 463 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 chunk 493 optimal weight: 7.9990 chunk 528 optimal weight: 0.0010 chunk 383 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 609 optimal weight: 10.0000 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 GLN F 93 ASN G 101 ASN J 154 GLN J 341 GLN M 663 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN c 160 GLN i 147 GLN i 322 GLN l 109 HIS p 78 GLN r 139 GLN r 304 GLN w 132 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69917 Z= 0.189 Angle : 0.524 12.450 94503 Z= 0.265 Chirality : 0.041 0.217 10193 Planarity : 0.004 0.072 11767 Dihedral : 13.080 175.312 10921 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 2.60 % Allowed : 15.57 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 8173 helix: 1.74 (0.08), residues: 4311 sheet: 0.24 (0.24), residues: 434 loop : -0.13 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.013 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1026 time to evaluate : 6.146 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7384 (pp20) REVERT: A 224 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8668 (mtm180) REVERT: A 241 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8670 (m) REVERT: C 49 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8122 (mmtt) REVERT: C 195 ARG cc_start: 0.8272 (mtt90) cc_final: 0.8006 (mtt-85) REVERT: E 34 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 42 GLU cc_start: 0.8842 (tp30) cc_final: 0.8342 (tp30) REVERT: E 119 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8539 (mm) REVERT: H 7 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8155 (mptp) REVERT: J 175 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8383 (mtpt) REVERT: K 94 SER cc_start: 0.8533 (t) cc_final: 0.8168 (p) REVERT: K 106 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: L 154 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8445 (ptmm) REVERT: M 77 MET cc_start: 0.9431 (tpt) cc_final: 0.9165 (tpt) REVERT: M 464 GLN cc_start: 0.8019 (tp40) cc_final: 0.7409 (tm130) REVERT: M 473 MET cc_start: 0.9087 (ttt) cc_final: 0.8819 (mtp) REVERT: M 485 ASP cc_start: 0.8574 (p0) cc_final: 0.8290 (p0) REVERT: N 41 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: P 161 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8598 (mppt) REVERT: Q 57 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: Q 100 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8368 (mt-10) REVERT: Q 315 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8467 (mt-10) REVERT: T 105 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6579 (mm-30) REVERT: U 79 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: X 147 TYR cc_start: 0.8985 (t80) cc_final: 0.8735 (t80) REVERT: Y 41 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: Y 56 ILE cc_start: 0.8504 (mm) cc_final: 0.8283 (mt) REVERT: Z 39 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7684 (ttt90) REVERT: a 72 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7675 (ttm170) REVERT: a 160 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9087 (mtt) REVERT: b 21 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7443 (ttm170) REVERT: d 62 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: h 55 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: h 71 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8756 (mtpt) REVERT: i 47 ASN cc_start: 0.8146 (m110) cc_final: 0.7853 (p0) REVERT: i 321 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7450 (tttm) REVERT: j 16 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8577 (tp) REVERT: j 109 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8499 (mptt) REVERT: l 491 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7552 (tt) REVERT: l 500 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8205 (tp) REVERT: m 1 MET cc_start: 0.4680 (OUTLIER) cc_final: 0.3721 (mpt) REVERT: m 86 ASN cc_start: 0.8645 (t0) cc_final: 0.8428 (t160) REVERT: m 98 MET cc_start: 0.7597 (mtt) cc_final: 0.7306 (mtp) REVERT: p 114 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: r 91 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7884 (mtp180) REVERT: r 222 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: u 80 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5892 (mp0) REVERT: v 54 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: v 65 GLN cc_start: 0.8506 (tt0) cc_final: 0.8155 (tt0) REVERT: v 81 LYS cc_start: 0.8543 (mttp) cc_final: 0.8231 (mmpt) REVERT: v 88 ASP cc_start: 0.8881 (m-30) cc_final: 0.8371 (m-30) REVERT: v 115 ARG cc_start: 0.7365 (ppp80) cc_final: 0.6700 (ttp80) REVERT: w 95 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.9003 (m-30) REVERT: w 303 GLU cc_start: 0.8104 (tp30) cc_final: 0.7866 (tp30) outliers start: 186 outliers final: 113 residues processed: 1137 average time/residue: 1.6279 time to fit residues: 2382.1317 Evaluate side-chains 1159 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1014 time to evaluate : 6.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 693 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 30 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.7980 chunk 743 optimal weight: 1.9990 chunk 678 optimal weight: 1.9990 chunk 723 optimal weight: 5.9990 chunk 435 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 567 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 653 optimal weight: 7.9990 chunk 683 optimal weight: 0.9990 chunk 720 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 GLN F 93 ASN G 101 ASN J 154 GLN J 341 GLN M 663 ASN M 669 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN c 160 GLN i 147 GLN i 322 GLN l 109 HIS p 78 GLN r 139 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 69917 Z= 0.193 Angle : 0.524 12.105 94503 Z= 0.264 Chirality : 0.041 0.213 10193 Planarity : 0.004 0.072 11767 Dihedral : 12.786 175.282 10920 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 2.52 % Allowed : 15.63 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 8173 helix: 1.76 (0.08), residues: 4301 sheet: 0.24 (0.24), residues: 434 loop : -0.14 (0.11), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.033 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.019 0.000 ARG h 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1033 time to evaluate : 6.194 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7387 (pp20) REVERT: A 224 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8680 (mtm180) REVERT: A 241 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8670 (m) REVERT: C 49 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8119 (mmtt) REVERT: C 195 ARG cc_start: 0.8266 (mtt90) cc_final: 0.8003 (mtt-85) REVERT: E 42 GLU cc_start: 0.8842 (tp30) cc_final: 0.8350 (tp30) REVERT: E 119 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8541 (mm) REVERT: F 25 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: G 81 ASP cc_start: 0.7474 (m-30) cc_final: 0.6930 (OUTLIER) REVERT: G 84 LEU cc_start: 0.8029 (mp) cc_final: 0.7823 (mt) REVERT: H 7 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8149 (mptp) REVERT: J 175 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8399 (mtpt) REVERT: K 94 SER cc_start: 0.8486 (t) cc_final: 0.8121 (p) REVERT: K 106 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: L 154 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8452 (ptmm) REVERT: M 473 MET cc_start: 0.9087 (ttt) cc_final: 0.8823 (mtp) REVERT: M 485 ASP cc_start: 0.8537 (p0) cc_final: 0.8270 (p0) REVERT: N 41 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: N 131 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7454 (ptp90) REVERT: P 161 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8591 (mppt) REVERT: Q 57 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: Q 100 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8343 (mt-10) REVERT: Q 315 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: U 79 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: X 147 TYR cc_start: 0.8988 (t80) cc_final: 0.8738 (t80) REVERT: Y 41 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: Y 56 ILE cc_start: 0.8485 (mm) cc_final: 0.8258 (mt) REVERT: Z 39 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7632 (ttt90) REVERT: a 72 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: a 160 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.9079 (mtt) REVERT: b 21 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7444 (ttm170) REVERT: d 62 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: h 55 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: h 71 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8761 (mtpt) REVERT: h 81 ARG cc_start: 0.6566 (mtm110) cc_final: 0.6351 (ptp-110) REVERT: i 47 ASN cc_start: 0.8142 (m110) cc_final: 0.7853 (p0) REVERT: i 321 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7450 (tttm) REVERT: j 16 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8564 (tp) REVERT: j 109 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8427 (mptt) REVERT: m 1 MET cc_start: 0.4497 (OUTLIER) cc_final: 0.3713 (mpt) REVERT: m 86 ASN cc_start: 0.8648 (t0) cc_final: 0.8429 (t160) REVERT: m 98 MET cc_start: 0.7724 (mtt) cc_final: 0.7407 (mtp) REVERT: p 114 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7644 (mtp) REVERT: r 91 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7869 (mtp180) REVERT: r 222 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: u 80 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: v 54 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: v 65 GLN cc_start: 0.8495 (tt0) cc_final: 0.8155 (tt0) REVERT: v 81 LYS cc_start: 0.8526 (mttp) cc_final: 0.8231 (mmpt) REVERT: v 88 ASP cc_start: 0.8880 (m-30) cc_final: 0.8374 (m-30) REVERT: v 115 ARG cc_start: 0.7347 (ppp80) cc_final: 0.6736 (ttp80) REVERT: w 95 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.9008 (m-30) REVERT: w 254 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6946 (mt-10) outliers start: 180 outliers final: 112 residues processed: 1139 average time/residue: 1.6480 time to fit residues: 2412.3273 Evaluate side-chains 1157 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1014 time to evaluate : 6.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 693 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 315 GLU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain g residue 30 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 6.9990 chunk 764 optimal weight: 5.9990 chunk 466 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 531 optimal weight: 4.9990 chunk 801 optimal weight: 3.9990 chunk 738 optimal weight: 6.9990 chunk 638 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 493 optimal weight: 7.9990 chunk 391 optimal weight: 0.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 GLN F 93 ASN G 101 ASN J 154 GLN J 341 GLN M 464 GLN M 569 GLN M 663 ASN N 116 ASN O 106 GLN T 74 GLN V 129 GLN Z 33 GLN c 160 GLN i 147 GLN i 322 GLN l 109 HIS m 46 ASN p 78 GLN r 139 GLN w 300 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 69917 Z= 0.374 Angle : 0.626 12.262 94503 Z= 0.316 Chirality : 0.046 0.280 10193 Planarity : 0.005 0.070 11767 Dihedral : 13.159 173.524 10919 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 2.52 % Allowed : 15.91 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.09), residues: 8173 helix: 1.46 (0.08), residues: 4303 sheet: 0.31 (0.26), residues: 392 loop : -0.28 (0.10), residues: 3478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP m 125 HIS 0.010 0.001 HIS J 37 PHE 0.036 0.002 PHE i 292 TYR 0.025 0.002 TYR J 180 ARG 0.017 0.001 ARG h 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1020 time to evaluate : 6.271 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: A 224 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.8801 (mtm180) REVERT: A 241 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8692 (m) REVERT: C 49 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8202 (mmtt) REVERT: C 195 ARG cc_start: 0.8321 (mtt90) cc_final: 0.8007 (mtt-85) REVERT: E 42 GLU cc_start: 0.8890 (tp30) cc_final: 0.8338 (tp30) REVERT: E 119 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8581 (mm) REVERT: F 25 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: F 38 GLU cc_start: 0.7802 (tt0) cc_final: 0.7495 (tt0) REVERT: G 81 ASP cc_start: 0.7463 (m-30) cc_final: 0.6919 (OUTLIER) REVERT: G 134 ASP cc_start: 0.7927 (m-30) cc_final: 0.7655 (m-30) REVERT: H 7 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8173 (mptp) REVERT: J 175 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8391 (mtpt) REVERT: J 303 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7465 (tpt170) REVERT: K 106 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: L 154 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8502 (ptmm) REVERT: M 473 MET cc_start: 0.9166 (ttt) cc_final: 0.8870 (mtp) REVERT: M 485 ASP cc_start: 0.8590 (p0) cc_final: 0.8328 (p0) REVERT: N 8 ARG cc_start: 0.5806 (mtt-85) cc_final: 0.5525 (mpp80) REVERT: N 41 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: P 161 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8670 (mppt) REVERT: Q 57 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: U 16 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7945 (mm-30) REVERT: U 79 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: Y 41 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: Z 39 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7762 (ttt90) REVERT: a 53 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7982 (mtm110) REVERT: a 72 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7652 (ttm170) REVERT: a 160 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.9087 (mtt) REVERT: d 62 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: h 55 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: h 71 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8778 (mtpt) REVERT: h 81 ARG cc_start: 0.6706 (mtm110) cc_final: 0.5773 (ptp90) REVERT: i 47 ASN cc_start: 0.8185 (m110) cc_final: 0.7897 (p0) REVERT: i 149 ILE cc_start: 0.7846 (pp) cc_final: 0.7419 (mt) REVERT: i 179 MET cc_start: 0.9207 (mmm) cc_final: 0.8964 (mmm) REVERT: i 321 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7428 (tttm) REVERT: j 16 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (tp) REVERT: l 491 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7497 (tt) REVERT: m 1 MET cc_start: 0.4511 (OUTLIER) cc_final: 0.3825 (mpt) REVERT: m 86 ASN cc_start: 0.8736 (t0) cc_final: 0.8474 (t160) REVERT: m 98 MET cc_start: 0.7578 (mtt) cc_final: 0.7276 (mtp) REVERT: n 34 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8158 (mttp) REVERT: p 49 ASP cc_start: 0.7859 (m-30) cc_final: 0.7609 (m-30) REVERT: p 114 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7689 (mtp) REVERT: r 91 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: r 222 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: r 398 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7891 (mmt) REVERT: u 80 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: v 54 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: v 65 GLN cc_start: 0.8523 (tt0) cc_final: 0.8072 (tt0) REVERT: v 81 LYS cc_start: 0.8577 (mttp) cc_final: 0.8219 (mmpt) REVERT: v 88 ASP cc_start: 0.8919 (m-30) cc_final: 0.8503 (m-30) REVERT: w 95 ASP cc_start: 0.9264 (OUTLIER) cc_final: 0.9025 (m-30) REVERT: w 254 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6746 (mm-30) outliers start: 180 outliers final: 107 residues processed: 1119 average time/residue: 1.6542 time to fit residues: 2372.5263 Evaluate side-chains 1153 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1012 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 7 LYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 175 LYS Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 220 MET Chi-restraints excluded: chain J residue 303 ARG Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 538 ARG Chi-restraints excluded: chain M residue 540 ASN Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 693 ASP Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 186 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 161 LYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 36 LEU Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 72 LYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain f residue 56 ILE Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 8 THR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 87 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 198 LEU Chi-restraints excluded: chain l residue 317 ILE Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 52 ASN Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 15 THR Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 222 GLU Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 398 MET Chi-restraints excluded: chain s residue 9 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 80 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 133 SER Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.7980 chunk 680 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 588 optimal weight: 0.9990 chunk 94 optimal weight: 0.0170 chunk 177 optimal weight: 4.9990 chunk 639 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 656 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 GLN F 93 ASN G 101 ASN J 154 GLN J 341 GLN M 464 GLN M 663 ASN N 116 ASN O 106 GLN P 196 HIS T 74 GLN V 129 GLN Z 33 GLN c 160 GLN i 147 GLN i 171 ASN i 322 GLN l 109 HIS m 46 ASN p 12 HIS p 78 GLN r 30 HIS r 139 GLN w 300 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099481 restraints weight = 87614.822| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.20 r_work: 0.2914 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 69917 Z= 0.146 Angle : 0.502 12.763 94503 Z= 0.254 Chirality : 0.040 0.229 10193 Planarity : 0.004 0.073 11767 Dihedral : 12.397 176.112 10919 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 1.43 % Allowed : 16.98 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 8173 helix: 1.80 (0.08), residues: 4304 sheet: 0.23 (0.24), residues: 433 loop : -0.13 (0.11), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP m 125 HIS 0.005 0.001 HIS J 37 PHE 0.029 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.018 0.000 ARG h 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31113.47 seconds wall clock time: 538 minutes 7.74 seconds (32287.74 seconds total)