Starting phenix.real_space_refine on Sat Jan 20 08:31:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w00_32232/01_2024/7w00_32232_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 39 5.49 5 Mg 1 5.21 5 S 474 5.16 5 C 43189 2.51 5 N 11086 2.21 5 O 11957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 600": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 215": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 387": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 151": "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 "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 53": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 28": "OE1" <-> "OE2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 262": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66775 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3315 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 967 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: "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: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 678 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 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: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2348 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5293 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 657} 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: "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: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1661 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 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: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3377 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 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: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} 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: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 875 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 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: "c" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1299 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 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: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 797 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "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: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4783 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 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: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3630 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2390 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 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: "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: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2581 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 285 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "o" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "r" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 250 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2703 SG CYS A 382 48.707 49.420 175.823 1.00 37.32 S ATOM 3045 SG CYS A 425 47.800 46.015 181.612 1.00 43.79 S ATOM 2723 SG CYS A 385 45.319 45.293 175.840 1.00 37.01 S ATOM 2684 SG CYS A 379 43.724 50.571 179.728 1.00 42.64 S ATOM 3946 SG CYS B 113 38.451 66.342 141.085 1.00 32.56 S ATOM 3965 SG CYS B 116 43.534 63.367 144.754 1.00 28.92 S ATOM 3988 SG CYS B 119 44.606 66.139 139.454 1.00 29.23 S ATOM 4317 SG CYS B 162 41.462 60.525 140.203 1.00 31.76 S ATOM 4015 SG CYS B 123 51.111 68.414 134.715 1.00 30.10 S ATOM 4241 SG CYS B 152 48.981 66.883 128.913 1.00 33.29 S ATOM 4288 SG CYS B 158 46.663 63.328 133.701 1.00 33.47 S ATOM 4267 SG CYS B 155 52.867 63.129 132.296 1.00 36.79 S ATOM 5709 SG CYS C 166 55.125 66.396 124.678 1.00 37.39 S ATOM 4975 SG CYS C 71 60.317 66.134 120.953 1.00 36.97 S ATOM 4981 SG CYS C 72 56.933 68.137 118.710 1.00 35.96 S ATOM 4975 SG CYS C 71 60.317 66.134 120.953 1.00 36.97 S ATOM 5479 SG CYS C 136 58.149 70.684 123.486 1.00 33.94 S ATOM 14501 SG CYS M 131 42.661 63.419 157.117 1.00 33.03 S ATOM 14480 SG CYS M 128 46.143 58.824 153.831 1.00 30.01 S ATOM 14541 SG CYS M 137 48.346 61.986 159.176 1.00 33.39 S ATOM 14873 SG CYS M 179 46.743 62.058 170.197 1.00 35.53 S ATOM 15227 SG CYS M 226 43.833 65.106 165.936 1.00 33.19 S ATOM 14897 SG CYS M 182 41.587 65.419 171.976 1.00 32.19 S ATOM 14850 SG CYS M 176 40.905 59.869 168.416 1.00 33.58 S ATOM 14098 SG CYS M 78 58.017 56.855 173.571 1.00 35.55 S ATOM 14199 SG CYS M 92 56.492 58.828 176.340 1.00 37.23 S ATOM 13987 SG CYS M 64 52.090 59.137 173.884 1.00 33.90 S ATOM 14073 SG CYS M 75 52.988 57.082 170.944 1.00 35.07 S ATOM 21030 SG CYS O 135 31.437 32.956 184.179 1.00 67.22 S ATOM 21064 SG CYS O 140 30.935 29.638 184.757 1.00 68.93 S ATOM 21344 SG CYS O 176 35.782 34.741 186.474 1.00 65.71 S ATOM 21367 SG CYS O 180 35.653 31.194 186.438 1.00 74.20 S ATOM 28018 SG CYS T 86 30.364 53.549 149.159 1.00 41.19 S ATOM 28196 SG CYS T 111 31.501 56.546 150.032 1.00 42.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.60 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.60 Time building chain proxies: 25.67, per 1000 atoms: 0.38 Number of scatterers: 66775 At special positions: 0 Unit cell: (218.063, 216.988, 232.027, 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 474 16.00 P 39 15.00 Mg 1 11.99 O 11957 8.00 N 11086 7.00 C 43189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.02 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 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " 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: 20.45 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " 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 180 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " 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="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " 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="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 85 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 331 helices and 28 sheets defined 52.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.20 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: 3.590A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 164 through 179 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 217 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.704A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.650A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 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 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.639A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 111 through 123 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.216A 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: 4.617A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.822A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 78 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.963A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 66 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.142A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 97 Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 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 212 through 218 removed outlier: 3.743A pdb=" N PHE J 217 " --> pdb=" O PHE J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 317 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.480A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.644A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 182 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 220 through 225 removed outlier: 3.984A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 4.901A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) 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 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' Processing helix chain 'M' and resid 382 through 384 No H-bonds generated for 'chain 'M' and resid 382 through 384' Processing helix chain 'M' and resid 392 through 396 removed outlier: 3.698A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 479 through 482 No H-bonds generated for 'chain 'M' and resid 479 through 482' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 521 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.409A 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 removed outlier: 3.625A pdb=" N LEU O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'P' and resid 53 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.785A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.599A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR P 166 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (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: 4.336A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 4.274A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.295A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.587A 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: 4.303A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 241 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.368A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 4.397A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.196A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 31 Proline residue: S 7 - end of helix removed outlier: 4.375A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.698A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 69 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 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 48 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 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 removed outlier: 3.723A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 99 removed outlier: 3.672A pdb=" N GLY W 39 " --> pdb=" O MET W 35 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR W 42 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) Proline residue: W 73 - end of helix removed outlier: 3.987A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.234A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 removed outlier: 3.504A pdb=" N LEU X 89 " --> pdb=" O TYR X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Z' and resid 29 through 39 removed outlier: 3.622A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 52 removed outlier: 4.721A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 58 No H-bonds generated for 'chain 'Z' and resid 56 through 58' Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 77 Processing helix chain 'a' and resid 80 through 92 removed outlier: 3.837A pdb=" N THR a 87 " --> pdb=" O ALA a 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU a 88 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 116 through 124 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 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.443A 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: 3.814A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.669A 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 175 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.869A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.594A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.253A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 145 removed outlier: 3.751A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix removed outlier: 3.713A pdb=" N VAL i 141 " --> pdb=" O ALA i 137 " (cutoff:3.500A) Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.932A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 4.338A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.915A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.294A 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 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.416A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 315 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.876A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.975A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 4.060A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.830A 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: 4.321A 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: 3.831A 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: 3.901A 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: 4.317A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.728A 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 252 through 262 removed outlier: 4.509A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL l 257 " --> pdb=" O VAL l 254 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.367A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.711A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 387 through 400 removed outlier: 4.087A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.575A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE l 462 " --> pdb=" O LEU l 458 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE l 463 " --> pdb=" O ILE l 459 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.127A 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: 3.732A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.807A 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 534 Proline residue: l 530 - end of helix removed outlier: 4.212A 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 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 4.112A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 148 removed outlier: 4.212A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 7.006A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.695A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 51 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 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 5.292A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 93 through 96 removed outlier: 4.320A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 93 through 96' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.813A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.187A 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: 4.365A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.895A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.867A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.606A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 171 removed outlier: 4.267A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.516A pdb=" N THR r 170 " --> pdb=" O ILE r 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.027A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.197A 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 237 through 250 removed outlier: 4.512A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.449A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 283 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.727A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.962A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.507A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 3 through 32 Proline residue: s 12 - end of helix removed outlier: 3.976A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.404A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 4.389A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.887A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.811A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 274 Processing helix chain 's' and resid 282 through 291 Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 12 No H-bonds generated for 'chain 'u' and resid 10 through 12' Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 97 No H-bonds generated for 'chain 'w' and resid 94 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 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.037A 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 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.958A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.270A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 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: 6.112A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.434A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.909A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.517A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= I, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= J, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= K, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= L, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= N, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= O, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.851A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'M' and resid 513 through 516 removed outlier: 6.237A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= R, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.445A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 169 through 174 removed outlier: 7.026A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.643A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= V, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.749A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= X, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Y, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= Z, first strand: chain 'l' and resid 62 through 67 removed outlier: 3.819A pdb=" N ASN l 65 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.656A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'w' and resid 84 through 86 2883 hydrogen bonds defined for protein. 8010 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: 22.47 Time building geometry restraints manager: 22.58 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: 27250 1.40 - 1.62: 40240 1.62 - 1.84: 848 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 68418 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C18 UQ s 401 " pdb=" C19 UQ s 401 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C13 UQ s 401 " pdb=" C14 UQ s 401 " ideal model delta sigma weight residual 1.335 1.549 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C8 UQ s 401 " pdb=" C9 UQ s 401 " ideal model delta sigma weight residual 1.334 1.541 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.617 -0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 68413 not shown) Histogram of bond angle deviations from ideal: 73.60 - 86.29: 76 86.29 - 98.98: 4 98.98 - 111.67: 32808 111.67 - 124.36: 57961 124.36 - 137.05: 1665 Bond angle restraints: 92514 Sorted by residual: angle pdb=" C GLU C 126 " pdb=" N PRO C 127 " pdb=" CA PRO C 127 " ideal model delta sigma weight residual 119.84 137.05 -17.21 1.25e+00 6.40e-01 1.90e+02 angle pdb=" C MET C 124 " pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 120.21 130.53 -10.32 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N LEU r 250 " pdb=" CA LEU r 250 " pdb=" C LEU r 250 " ideal model delta sigma weight residual 111.28 121.14 -9.86 1.09e+00 8.42e-01 8.18e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.94 -16.20 1.95e+00 2.62e-01 6.88e+01 angle pdb=" C GLU C 126 " pdb=" N PRO C 127 " pdb=" CD PRO C 127 " ideal model delta sigma weight residual 125.00 94.15 30.85 4.10e+00 5.95e-02 5.66e+01 ... (remaining 92509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 39884 35.92 - 71.84: 1583 71.84 - 107.76: 100 107.76 - 143.68: 26 143.68 - 179.60: 13 Dihedral angle restraints: 41606 sinusoidal: 17905 harmonic: 23701 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+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 -60.00 116.36 -176.35 1 2.00e+01 2.50e-03 4.80e+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 257.59 88.55 169.05 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 41603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 8924 0.066 - 0.132: 1056 0.132 - 0.199: 39 0.199 - 0.265: 7 0.265 - 0.331: 5 Chirality restraints: 10031 Sorted by residual: 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 -2.42 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA HIS p 169 " pdb=" N HIS p 169 " pdb=" C HIS p 169 " pdb=" CB HIS p 169 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL E 96 " pdb=" CA VAL E 96 " pdb=" CG1 VAL E 96 " pdb=" CG2 VAL E 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 10028 not shown) Planarity restraints: 11549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.216 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" C3N NDP J 401 " 0.435 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.032 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.342 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " -0.044 2.00e-02 2.50e+03 2.28e-01 6.48e+02 pdb=" C11 UQ s 401 " 0.134 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " -0.193 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " 0.365 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.135 2.00e-02 2.50e+03 1.94e-01 4.72e+02 pdb=" C13 UQ s 401 " -0.061 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.344 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.058 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.212 2.00e-02 2.50e+03 ... (remaining 11546 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5393 2.74 - 3.28: 66519 3.28 - 3.82: 111473 3.82 - 4.36: 132744 4.36 - 4.90: 232828 Nonbonded interactions: 548957 Sorted by model distance: nonbonded pdb=" O SER Q 439 " pdb=" OG SER Q 439 " model vdw 2.199 2.440 nonbonded pdb=" O2' FMN A 502 " pdb=" O4' FMN A 502 " model vdw 2.201 2.440 nonbonded pdb=" O TYR B 38 " pdb=" OG SER I 107 " model vdw 2.203 2.440 nonbonded pdb=" OE2 GLU Q 176 " pdb=" OH TYR Q 311 " model vdw 2.207 2.440 nonbonded pdb=" OG SER C 146 " pdb=" O 2MR Q 118 " model vdw 2.211 2.440 ... (remaining 548952 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 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 156 or resid 201)) selection = (chain 'X' and ((resid 69 through 71 and (name N or name CA or name C or name O \ or name CB )) or resid 72 through 149 or (resid 150 through 153 and (name N or n \ ame CA or name C or name O or name CB )) or resid 154 or (resid 155 through 156 \ and (name N or name CA or name C or name O or name CB )) 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=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 9.790 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 153.720 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.006 0.318 68418 Z= 0.433 Angle : 0.776 30.845 92514 Z= 0.392 Chirality : 0.042 0.331 10031 Planarity : 0.007 0.293 11549 Dihedral : 18.626 179.596 26299 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 0.37 % Allowed : 18.28 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 1.04 (0.10), residues: 8027 helix: 1.73 (0.08), residues: 4241 sheet: 0.28 (0.26), residues: 419 loop : -0.59 (0.11), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS Q 223 PHE 0.030 0.001 PHE l 335 TYR 0.029 0.001 TYR l 422 ARG 0.013 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1190 time to evaluate : 5.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7985 (t0) REVERT: G 81 ASP cc_start: 0.7588 (m-30) cc_final: 0.7248 (t0) REVERT: N 44 TYR cc_start: 0.8916 (m-80) cc_final: 0.8673 (m-80) REVERT: O 144 ASN cc_start: 0.9101 (t0) cc_final: 0.8862 (t0) REVERT: Q 197 MET cc_start: 0.8408 (ptt) cc_final: 0.7942 (ptm) REVERT: X 125 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8088 (tm-30) REVERT: Z 59 ASN cc_start: 0.8247 (t0) cc_final: 0.8007 (t0) REVERT: c 103 GLU cc_start: 0.7859 (pt0) cc_final: 0.7560 (mt-10) REVERT: e 143 ASP cc_start: 0.8701 (p0) cc_final: 0.8449 (p0) REVERT: i 179 MET cc_start: 0.7934 (mmt) cc_final: 0.7699 (mmt) REVERT: k 27 MET cc_start: 0.8744 (mmm) cc_final: 0.8438 (tpt) REVERT: k 91 GLN cc_start: 0.8368 (pp30) cc_final: 0.7922 (pp30) REVERT: l 338 MET cc_start: 0.7943 (tpp) cc_final: 0.7391 (ttm) REVERT: m 1 MET cc_start: 0.3598 (tmm) cc_final: 0.3189 (mmm) REVERT: r 207 MET cc_start: 0.8664 (mtp) cc_final: 0.8354 (mtp) REVERT: r 256 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7443 (p90) REVERT: s 222 MET cc_start: 0.8245 (mmp) cc_final: 0.7962 (mmp) REVERT: s 274 ARG cc_start: 0.8651 (ttt180) cc_final: 0.8315 (ttt180) REVERT: u 36 CYS cc_start: 0.8309 (m) cc_final: 0.8103 (m) REVERT: v 43 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8427 (mm-40) REVERT: v 52 MET cc_start: 0.7493 (mtp) cc_final: 0.7258 (mtp) REVERT: w 259 SER cc_start: 0.8227 (t) cc_final: 0.8026 (m) outliers start: 26 outliers final: 14 residues processed: 1202 average time/residue: 0.6571 time to fit residues: 1344.4196 Evaluate side-chains 1155 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1139 time to evaluate : 5.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain P residue 236 ASN Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 84 ILE Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 126 GLN Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 256 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 0.9980 chunk 601 optimal weight: 4.9990 chunk 333 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 621 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 462 optimal weight: 9.9990 chunk 720 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS K 75 ASN K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN c 56 ASN c 94 HIS l 524 ASN l 541 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 44 GLN u 16 GLN u 99 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 68418 Z= 0.205 Angle : 0.528 11.707 92514 Z= 0.261 Chirality : 0.041 0.274 10031 Planarity : 0.005 0.160 11549 Dihedral : 14.876 177.240 10375 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 2.10 % Allowed : 17.87 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 1.07 (0.10), residues: 8027 helix: 1.75 (0.08), residues: 4238 sheet: 0.18 (0.25), residues: 439 loop : -0.55 (0.11), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS Q 223 PHE 0.029 0.001 PHE i 292 TYR 0.020 0.001 TYR l 422 ARG 0.007 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1183 time to evaluate : 6.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7903 (t0) cc_final: 0.7641 (t0) REVERT: A 338 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8343 (p0) REVERT: C 126 GLU cc_start: 0.8622 (tp30) cc_final: 0.8316 (mm-30) REVERT: E 24 ASP cc_start: 0.8288 (t0) cc_final: 0.7937 (t0) REVERT: F 69 TYR cc_start: 0.8660 (m-80) cc_final: 0.8266 (m-80) REVERT: G 81 ASP cc_start: 0.7705 (m-30) cc_final: 0.7342 (t0) REVERT: G 118 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7355 (mp) REVERT: G 120 MET cc_start: 0.8641 (mtp) cc_final: 0.8280 (mtp) REVERT: G 147 TYR cc_start: 0.8340 (t80) cc_final: 0.8097 (t80) REVERT: I 13 ASN cc_start: 0.8614 (m-40) cc_final: 0.8393 (m110) REVERT: I 30 GLU cc_start: 0.8175 (pm20) cc_final: 0.7738 (pm20) REVERT: M 117 MET cc_start: 0.9014 (tpp) cc_final: 0.8651 (tpt) REVERT: O 144 ASN cc_start: 0.9097 (t0) cc_final: 0.8854 (t0) REVERT: O 206 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: W 86 MET cc_start: 0.8686 (mtp) cc_final: 0.8288 (mtt) REVERT: X 125 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8149 (tm-30) REVERT: c 81 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8490 (ttm-80) REVERT: c 103 GLU cc_start: 0.8001 (pt0) cc_final: 0.7681 (pt0) REVERT: e 143 ASP cc_start: 0.8704 (p0) cc_final: 0.8435 (p0) REVERT: f 65 ASP cc_start: 0.8069 (m-30) cc_final: 0.7737 (m-30) REVERT: g 47 ASP cc_start: 0.8846 (t0) cc_final: 0.8643 (t0) REVERT: h 83 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8002 (ttt180) REVERT: i 179 MET cc_start: 0.8012 (mmt) cc_final: 0.7751 (mmt) REVERT: j 68 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: k 43 MET cc_start: 0.8368 (tpp) cc_final: 0.8123 (ttm) REVERT: k 91 GLN cc_start: 0.8394 (pp30) cc_final: 0.7876 (pp30) REVERT: l 1 MET cc_start: 0.5489 (ppp) cc_final: 0.5250 (ppp) REVERT: l 338 MET cc_start: 0.8017 (tpp) cc_final: 0.7513 (ttm) REVERT: l 445 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7943 (mt-10) REVERT: l 503 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6714 (mt-10) REVERT: m 1 MET cc_start: 0.3467 (OUTLIER) cc_final: 0.3226 (mmm) REVERT: m 46 ASN cc_start: 0.8989 (m-40) cc_final: 0.8174 (m110) REVERT: r 207 MET cc_start: 0.8802 (mtp) cc_final: 0.8544 (mtp) REVERT: r 256 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7339 (p90) REVERT: s 43 TYR cc_start: 0.8465 (m-80) cc_final: 0.8220 (m-80) REVERT: s 274 ARG cc_start: 0.8736 (ttt180) cc_final: 0.8293 (ttt180) REVERT: u 66 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7221 (t) REVERT: v 48 ASP cc_start: 0.8225 (m-30) cc_final: 0.8009 (m-30) REVERT: v 101 GLU cc_start: 0.8620 (tp30) cc_final: 0.8293 (tp30) REVERT: w 259 SER cc_start: 0.8250 (t) cc_final: 0.8030 (m) REVERT: w 264 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8121 (mp0) outliers start: 148 outliers final: 84 residues processed: 1268 average time/residue: 0.6266 time to fit residues: 1353.1448 Evaluate side-chains 1236 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1143 time to evaluate : 5.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 236 ASN Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 284 GLN Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 264 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 599 optimal weight: 0.9980 chunk 490 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 721 optimal weight: 1.9990 chunk 779 optimal weight: 9.9990 chunk 642 optimal weight: 10.0000 chunk 715 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 578 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 182 ASN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN b 126 GLN c 56 ASN i 221 HIS k 7 ASN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 16 GLN u 99 HIS ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 68418 Z= 0.298 Angle : 0.556 12.421 92514 Z= 0.275 Chirality : 0.042 0.231 10031 Planarity : 0.005 0.156 11549 Dihedral : 14.084 171.106 10359 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 2.94 % Allowed : 17.93 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 0.99 (0.10), residues: 8027 helix: 1.68 (0.08), residues: 4237 sheet: 0.08 (0.25), residues: 444 loop : -0.58 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS Q 223 PHE 0.031 0.001 PHE i 292 TYR 0.020 0.001 TYR P 64 ARG 0.009 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1160 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7988 (t0) cc_final: 0.7604 (t0) REVERT: A 338 ASP cc_start: 0.8765 (OUTLIER------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 68418 Z= 0.203 Angle : 0.523 12.647 92514 Z= 0.258 Chirality : 0.041 0.239 10031 Planarity : 0.004 0.153 11549 Dihedral : 13.394 168.962 10356 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.95 % Allowed : 18.58 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 1.08 (0.10), residues: 8027 helix: 1.77 (0.08), residues: 4235 sheet: 0.14 (0.25), residues: 443 loop : -0.55 (0.11), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS Q 223 PHE 0.029 0.001 PHE i 292 TYR 0.020 0.001 TYR l 422 ARG 0.009 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1182 time to evaluate : 6.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7976 (t0) cc_final: 0.7523 (t0) REVERT: B 76 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7969 (t80) REVERT: E 18 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (ttpt) REVERT: E 24 ASP cc_start: 0.8229 (t0) cc_final: 0.7870 (t0) REVERT: E 68 MET cc_start: 0.8413 (mmm) cc_final: 0.8201 (mmm) REVERT: F 69 TYR cc_start: 0.8641 (m-80) cc_final: 0.8215 (m-80) REVERT: F 73 GLN cc_start: 0.7249 (mp10) cc_final: 0.6877 (mp10) REVERT: G 81 ASP cc_start: 0.7713 (m-30) cc_final: 0.7291 (t0) REVERT: H 27 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8341 (mm) REVERT: I 13 ASN cc_start: 0.8507 (m-40) cc_final: 0.8271 (m110) REVERT: I 30 GLU cc_start: 0.8150 (pm20) cc_final: 0.7564 (pm20) REVERT: J 140 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7533 (p0) REVERT: M 58 MET cc_start: 0.7165 (ttt) cc_final: 0.6958 (ttt) REVERT: M 370 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: M 479 SER cc_start: 0.9257 (m) cc_final: 0.9018 (t) REVERT: N 9 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.4680 (ttp-170) REVERT: N 44 TYR cc_start: 0.8966 (m-80) cc_final: 0.8716 (m-80) REVERT: O 144 ASN cc_start: 0.9129 (t0) cc_final: 0.8824 (t0) REVERT: P 93 VAL cc_start: 0.9333 (t) cc_final: 0.9057 (p) REVERT: S 59 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8359 (mtm-85) REVERT: V 120 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8050 (mm) REVERT: W 86 MET cc_start: 0.8736 (mtp) cc_final: 0.8494 (mtt) REVERT: X 125 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8138 (tm-30) REVERT: d 143 TYR cc_start: 0.8889 (m-80) cc_final: 0.8558 (m-80) REVERT: e 143 ASP cc_start: 0.8720 (p0) cc_final: 0.8448 (p0) REVERT: f 65 ASP cc_start: 0.8175 (m-30) cc_final: 0.7855 (m-30) REVERT: f 68 GLU cc_start: 0.8783 (tp30) cc_final: 0.8515 (tp30) REVERT: g 47 ASP cc_start: 0.8903 (t0) cc_final: 0.8567 (t0) REVERT: h 83 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7978 (ttt180) REVERT: i 179 MET cc_start: 0.8165 (mmp) cc_final: 0.7865 (mmt) REVERT: j 68 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: k 91 GLN cc_start: 0.8411 (pp30) cc_final: 0.7845 (pp30) REVERT: l 338 MET cc_start: 0.7983 (tpp) cc_final: 0.7751 (ttm) REVERT: l 445 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: m 46 ASN cc_start: 0.9051 (m-40) cc_final: 0.8521 (m110) REVERT: o 126 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8325 (m-40) REVERT: p 14 GLN cc_start: 0.8160 (mp10) cc_final: 0.7855 (mp10) REVERT: r 207 MET cc_start: 0.8902 (mtp) cc_final: 0.8639 (mtp) REVERT: r 256 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7289 (p90) REVERT: r 282 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8096 (tt) REVERT: r 437 MET cc_start: 0.8654 (mpp) cc_final: 0.8036 (mpp) REVERT: u 66 CYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7254 (t) REVERT: u 90 ASP cc_start: 0.8933 (t70) cc_final: 0.8720 (t0) REVERT: v 15 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8019 (tptm) REVERT: v 16 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6990 (mm-30) REVERT: v 101 GLU cc_start: 0.8582 (tp30) cc_final: 0.8083 (tp30) REVERT: w 259 SER cc_start: 0.8265 (t) cc_final: 0.8027 (m) REVERT: w 264 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8078 (mp0) outliers start: 208 outliers final: 130 residues processed: 1307 average time/residue: 0.6004 time to fit residues: 1339.9035 Evaluate side-chains 1285 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1140 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 236 ASN Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 282 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain r residue 357 THR Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 264 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 3.9990 chunk 435 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 570 optimal weight: 6.9990 chunk 316 optimal weight: 0.1980 chunk 654 optimal weight: 0.9980 chunk 529 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 391 optimal weight: 7.9990 chunk 688 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN ** b 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN i 172 GLN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN r 349 GLN u 16 GLN u 99 HIS ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 68418 Z= 0.303 Angle : 0.565 12.570 92514 Z= 0.278 Chirality : 0.043 0.258 10031 Planarity : 0.005 0.152 11549 Dihedral : 12.935 170.143 10354 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 3.29 % Allowed : 18.74 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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 (0.10), residues: 8027 helix: 1.68 (0.08), residues: 4236 sheet: 0.07 (0.25), residues: 445 loop : -0.61 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS Q 223 PHE 0.031 0.001 PHE i 292 TYR 0.022 0.001 TYR b 88 ARG 0.010 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1160 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7937 (t0) cc_final: 0.7460 (t0) REVERT: B 76 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8139 (t80) REVERT: E 18 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8282 (ttpt) REVERT: E 24 ASP cc_start: 0.8285 (t0) cc_final: 0.7883 (t0) REVERT: F 69 TYR cc_start: 0.8659 (m-80) cc_final: 0.8249 (m-80) REVERT: F 73 GLN cc_start: 0.7282 (mp10) cc_final: 0.6900 (mp10) REVERT: G 81 ASP cc_start: 0.7709 (m-30) cc_final: 0.7286 (t0) REVERT: H 27 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8343 (mm) REVERT: I 13 ASN cc_start: 0.8553 (m-40) cc_final: 0.8314 (m110) REVERT: I 30 GLU cc_start: 0.8185 (pm20) cc_final: 0.7626 (pm20) REVERT: M 58 MET cc_start: 0.7231 (ttt) cc_final: 0.7014 (ttt) REVERT: M 277 MET cc_start: 0.9055 (tmm) cc_final: 0.8724 (tpp) REVERT: M 370 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: M 479 SER cc_start: 0.9283 (m) cc_final: 0.9083 (t) REVERT: M 546 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7693 (t80) REVERT: N 9 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.4588 (ttp-170) REVERT: N 44 TYR cc_start: 0.9029 (m-80) cc_final: 0.8763 (m-80) REVERT: N 135 GLN cc_start: 0.8125 (mp10) cc_final: 0.7786 (mt0) REVERT: O 144 ASN cc_start: 0.9165 (t0) cc_final: 0.8865 (t0) REVERT: P 93 VAL cc_start: 0.9344 (t) cc_final: 0.9038 (p) REVERT: S 59 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8371 (mtm-85) REVERT: V 59 TYR cc_start: 0.7920 (m-10) cc_final: 0.7717 (m-80) REVERT: V 120 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8088 (mm) REVERT: W 86 MET cc_start: 0.8696 (mtp) cc_final: 0.8489 (mtt) REVERT: X 125 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8154 (tm-30) REVERT: b 9 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8603 (mtpt) REVERT: d 143 TYR cc_start: 0.8923 (m-80) cc_final: 0.8648 (m-80) REVERT: g 47 ASP cc_start: 0.8934 (t0) cc_final: 0.8626 (t0) REVERT: h 83 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7980 (ttt180) REVERT: i 179 MET cc_start: 0.8211 (mmp) cc_final: 0.7884 (mmt) REVERT: j 68 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: k 91 GLN cc_start: 0.8422 (pp30) cc_final: 0.7847 (pp30) REVERT: k 97 GLN cc_start: 0.7520 (pm20) cc_final: 0.7281 (pm20) REVERT: m 46 ASN cc_start: 0.9094 (m-40) cc_final: 0.8776 (m110) REVERT: m 57 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8295 (t80) REVERT: o 126 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8318 (m-40) REVERT: p 14 GLN cc_start: 0.8289 (mp10) cc_final: 0.7935 (mp10) REVERT: r 207 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8577 (mtp) REVERT: r 256 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7363 (p90) REVERT: r 282 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8225 (tt) REVERT: r 437 MET cc_start: 0.8723 (mpp) cc_final: 0.8144 (mpp) REVERT: s 85 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (mtp) REVERT: u 66 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7281 (t) REVERT: u 103 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8328 (mp10) REVERT: v 48 ASP cc_start: 0.8303 (m-30) cc_final: 0.7571 (m-30) REVERT: v 59 CYS cc_start: 0.8703 (m) cc_final: 0.8451 (m) REVERT: v 101 GLU cc_start: 0.8605 (tp30) cc_final: 0.8048 (tp30) REVERT: w 259 SER cc_start: 0.8302 (t) cc_final: 0.8083 (m) REVERT: w 264 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8060 (mp0) outliers start: 232 outliers final: 168 residues processed: 1300 average time/residue: 0.6331 time to fit residues: 1405.2536 Evaluate side-chains 1321 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1136 time to evaluate : 5.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 546 PHE Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 633 THR Chi-restraints excluded: chain M residue 672 SER Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 36 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain j residue 108 GLN Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 399 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 165 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 282 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain r residue 357 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 85 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 284 GLN Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 264 GLU Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 0.6980 chunk 690 optimal weight: 0.9980 chunk 151 optimal weight: 0.0970 chunk 450 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 767 optimal weight: 2.9990 chunk 636 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 498 GLN M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 669 ASN N 13 GLN O 69 ASN T 63 ASN b 126 GLN c 56 ASN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 ASN ** r 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 349 GLN u 16 GLN u 99 HIS ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 68418 Z= 0.154 Angle : 0.511 12.975 92514 Z= 0.252 Chirality : 0.039 0.264 10031 Planarity : 0.004 0.148 11549 Dihedral : 12.333 168.555 10352 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 2.60 % Allowed : 19.55 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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 (0.10), residues: 8027 helix: 1.81 (0.08), residues: 4245 sheet: 0.27 (0.26), residues: 434 loop : -0.52 (0.11), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS Q 223 PHE 0.029 0.001 PHE i 292 TYR 0.024 0.001 TYR l 422 ARG 0.010 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1188 time to evaluate : 5.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7878 (t0) cc_final: 0.7425 (t0) REVERT: B 76 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.7811 (t80) REVERT: E 18 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8281 (ttpt) REVERT: E 24 ASP cc_start: 0.8226 (t0) cc_final: 0.7857 (t0) REVERT: E 68 MET cc_start: 0.8328 (mmm) cc_final: 0.8086 (mmm) REVERT: F 73 GLN cc_start: 0.7227 (mp10) cc_final: 0.6837 (mp10) REVERT: G 81 ASP cc_start: 0.7698 (m-30) cc_final: 0.7286 (t0) REVERT: G 89 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7715 (mt) REVERT: G 134 ASP cc_start: 0.7242 (p0) cc_final: 0.7019 (p0) REVERT: I 13 ASN cc_start: 0.8425 (m-40) cc_final: 0.8198 (m110) REVERT: I 30 GLU cc_start: 0.8248 (pm20) cc_final: 0.7725 (pm20) REVERT: J 140 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7557 (p0) REVERT: M 277 MET cc_start: 0.9042 (tmm) cc_final: 0.8692 (tpp) REVERT: M 370 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: M 479 SER cc_start: 0.9262 (m) cc_final: 0.9051 (t) REVERT: N 9 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.4644 (ttp-170) REVERT: N 44 TYR cc_start: 0.8994 (m-80) cc_final: 0.8765 (m-80) REVERT: N 127 TYR cc_start: 0.9283 (p90) cc_final: 0.8838 (p90) REVERT: N 135 GLN cc_start: 0.8134 (mp10) cc_final: 0.7818 (mt0) REVERT: O 144 ASN cc_start: 0.9125 (t0) cc_final: 0.8833 (t0) REVERT: P 93 VAL cc_start: 0.9245 (t) cc_final: 0.8933 (p) REVERT: S 59 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8321 (mtm-85) REVERT: V 59 TYR cc_start: 0.7908 (m-10) cc_final: 0.7708 (m-80) REVERT: W 86 MET cc_start: 0.8733 (mtp) cc_final: 0.8520 (mtt) REVERT: X 125 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8144 (tm-30) REVERT: b 9 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8579 (mtpt) REVERT: d 143 TYR cc_start: 0.8833 (m-80) cc_final: 0.8488 (m-80) REVERT: e 148 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7505 (tm-30) REVERT: g 47 ASP cc_start: 0.8935 (t0) cc_final: 0.8582 (t0) REVERT: h 83 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7953 (ttt180) REVERT: i 100 MET cc_start: 0.8363 (mmm) cc_final: 0.8114 (mmt) REVERT: j 68 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: k 91 GLN cc_start: 0.8424 (pp30) cc_final: 0.7818 (pp30) REVERT: k 97 GLN cc_start: 0.7457 (pm20) cc_final: 0.6817 (mp10) REVERT: l 445 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: l 503 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: m 46 ASN cc_start: 0.9069 (m-40) cc_final: 0.8510 (m110) REVERT: m 173 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7602 (ttp-170) REVERT: o 126 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8272 (m-40) REVERT: p 14 GLN cc_start: 0.8285 (mp10) cc_final: 0.7888 (mp10) REVERT: r 186 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8787 (mp) REVERT: r 207 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8535 (mtp) REVERT: r 256 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7349 (p90) REVERT: r 437 MET cc_start: 0.8737 (mpp) cc_final: 0.8187 (mpp) REVERT: u 64 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8120 (m110) REVERT: u 66 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7663 (t) REVERT: u 90 ASP cc_start: 0.8889 (t70) cc_final: 0.8655 (t0) REVERT: u 103 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: v 16 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7673 (mm-30) REVERT: v 29 TYR cc_start: 0.7608 (t80) cc_final: 0.7335 (t80) REVERT: v 43 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8212 (mm-40) REVERT: v 48 ASP cc_start: 0.8336 (m-30) cc_final: 0.7597 (m-30) REVERT: v 52 MET cc_start: 0.7541 (mtp) cc_final: 0.7306 (mtp) REVERT: v 101 GLU cc_start: 0.8410 (tp30) cc_final: 0.7832 (tp30) REVERT: w 259 SER cc_start: 0.8216 (t) cc_final: 0.7960 (m) REVERT: w 264 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (mp0) outliers start: 183 outliers final: 117 residues processed: 1298 average time/residue: 0.6407 time to fit residues: 1418.7526 Evaluate side-chains 1279 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1145 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 126 GLN Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 399 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 357 THR Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 264 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 437 optimal weight: 3.9990 chunk 560 optimal weight: 3.9990 chunk 434 optimal weight: 0.0010 chunk 645 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 764 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 465 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 69 ASN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN ** b 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN i 322 GLN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 ASN r 139 GLN r 349 GLN s 287 HIS u 16 GLN u 99 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 68418 Z= 0.428 Angle : 0.631 12.612 92514 Z= 0.313 Chirality : 0.046 0.289 10031 Planarity : 0.005 0.151 11549 Dihedral : 12.446 171.534 10350 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 3.46 % Allowed : 19.13 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 0.81 (0.09), residues: 8027 helix: 1.55 (0.08), residues: 4244 sheet: -0.01 (0.25), residues: 442 loop : -0.70 (0.11), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS Q 223 PHE 0.033 0.002 PHE i 292 TYR 0.021 0.002 TYR r 406 ARG 0.010 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1143 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8101 (t0) cc_final: 0.7658 (t0) REVERT: A 175 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: B 76 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.8341 (t80) REVERT: E 18 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8285 (ttpt) REVERT: E 24 ASP cc_start: 0.8262 (t0) cc_final: 0.7844 (t0) REVERT: E 68 MET cc_start: 0.8358 (mmm) cc_final: 0.8155 (mmm) REVERT: E 99 GLN cc_start: 0.8893 (mp10) cc_final: 0.8687 (mp10) REVERT: F 73 GLN cc_start: 0.7229 (mp10) cc_final: 0.6864 (mp10) REVERT: G 81 ASP cc_start: 0.7686 (m-30) cc_final: 0.7296 (t0) REVERT: G 82 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6728 (mtp85) REVERT: G 89 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7605 (mt) REVERT: G 108 LEU cc_start: 0.6830 (mt) cc_final: 0.6475 (mp) REVERT: I 13 ASN cc_start: 0.8467 (m-40) cc_final: 0.8259 (m110) REVERT: I 30 GLU cc_start: 0.8214 (pm20) cc_final: 0.7702 (pm20) REVERT: J 140 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7717 (p0) REVERT: M 277 MET cc_start: 0.9056 (tmm) cc_final: 0.8754 (tpp) REVERT: M 370 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: M 546 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7769 (t80) REVERT: M 559 ASP cc_start: 0.8097 (p0) cc_final: 0.7892 (p0) REVERT: M 569 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: M 679 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8157 (mt) REVERT: N 9 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.4629 (ttp-170) REVERT: O 144 ASN cc_start: 0.9208 (t0) cc_final: 0.8868 (t0) REVERT: P 93 VAL cc_start: 0.9334 (t) cc_final: 0.9036 (p) REVERT: S 59 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8378 (mtm-85) REVERT: V 120 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8144 (mm) REVERT: X 125 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8188 (tm-30) REVERT: b 9 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8571 (mtpt) REVERT: e 87 MET cc_start: 0.8969 (tmm) cc_final: 0.8740 (tmm) REVERT: e 148 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7578 (tm-30) REVERT: g 47 ASP cc_start: 0.8943 (t0) cc_final: 0.8615 (t0) REVERT: h 83 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.8019 (ttt180) REVERT: i 100 MET cc_start: 0.8392 (mmm) cc_final: 0.8156 (mmt) REVERT: j 68 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: k 43 MET cc_start: 0.8528 (tpp) cc_final: 0.8300 (ttm) REVERT: k 91 GLN cc_start: 0.8431 (pp30) cc_final: 0.7819 (pp30) REVERT: k 97 GLN cc_start: 0.7449 (pm20) cc_final: 0.6814 (mp10) REVERT: l 445 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: l 503 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6861 (mt-10) REVERT: m 1 MET cc_start: 0.3769 (mmm) cc_final: 0.3212 (mmm) REVERT: m 46 ASN cc_start: 0.9120 (m-40) cc_final: 0.8796 (m110) REVERT: m 57 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8259 (t80) REVERT: o 126 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8386 (m-40) REVERT: p 14 GLN cc_start: 0.8387 (mp10) cc_final: 0.7908 (mp10) REVERT: r 186 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8796 (mp) REVERT: r 207 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: r 256 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7758 (p90) REVERT: r 282 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8343 (tt) REVERT: r 437 MET cc_start: 0.8807 (mpp) cc_final: 0.8219 (mpp) REVERT: u 36 CYS cc_start: 0.8044 (m) cc_final: 0.5896 (m) REVERT: u 64 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8156 (m110) REVERT: u 66 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7049 (t) REVERT: u 103 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: v 16 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7803 (mm-30) REVERT: v 29 TYR cc_start: 0.7669 (t80) cc_final: 0.7386 (t80) REVERT: v 48 ASP cc_start: 0.8358 (m-30) cc_final: 0.7671 (m-30) REVERT: v 101 GLU cc_start: 0.8552 (tp30) cc_final: 0.7982 (tp30) REVERT: v 105 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7575 (tm-30) REVERT: w 259 SER cc_start: 0.8350 (t) cc_final: 0.8140 (m) REVERT: w 296 MET cc_start: 0.8712 (mmm) cc_final: 0.8499 (mmm) outliers start: 244 outliers final: 183 residues processed: 1297 average time/residue: 0.6369 time to fit residues: 1402.6737 Evaluate side-chains 1324 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1118 time to evaluate : 5.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 485 ASP Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 546 PHE Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 569 GLN Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 312 ASP Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 36 MET Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 31 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 185 SER Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 306 THR Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 399 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 165 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 282 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 284 GLN Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 456 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 485 optimal weight: 3.9990 chunk 520 optimal weight: 2.9990 chunk 377 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 600 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 569 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN ** b 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN i 322 GLN k 7 ASN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 ASN r 139 GLN r 349 GLN u 16 GLN u 99 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 68418 Z= 0.169 Angle : 0.532 12.927 92514 Z= 0.263 Chirality : 0.040 0.253 10031 Planarity : 0.004 0.146 11549 Dihedral : 11.923 168.924 10350 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 2.40 % Allowed : 20.50 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 1.06 (0.10), residues: 8027 helix: 1.75 (0.08), residues: 4238 sheet: 0.16 (0.25), residues: 434 loop : -0.57 (0.11), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS b 127 PHE 0.028 0.001 PHE i 292 TYR 0.036 0.001 TYR d 143 ARG 0.012 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1176 time to evaluate : 6.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7946 (t0) cc_final: 0.7521 (t0) REVERT: A 175 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: B 72 MET cc_start: 0.8693 (tpp) cc_final: 0.8441 (tpp) REVERT: B 76 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.7884 (t80) REVERT: E 18 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8288 (ttpt) REVERT: E 24 ASP cc_start: 0.8195 (t0) cc_final: 0.7784 (t0) REVERT: E 68 MET cc_start: 0.8294 (mmm) cc_final: 0.8075 (mmm) REVERT: F 73 GLN cc_start: 0.7238 (mp10) cc_final: 0.6942 (mp10) REVERT: G 80 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7403 (ttmm) REVERT: G 81 ASP cc_start: 0.7677 (m-30) cc_final: 0.7249 (t0) REVERT: G 89 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7663 (mt) REVERT: I 13 ASN cc_start: 0.8447 (m-40) cc_final: 0.8232 (m110) REVERT: I 30 GLU cc_start: 0.8200 (pm20) cc_final: 0.7705 (pm20) REVERT: J 140 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7578 (p0) REVERT: M 277 MET cc_start: 0.9037 (tmm) cc_final: 0.8711 (tpp) REVERT: M 370 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: M 569 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: M 679 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.8003 (mt) REVERT: N 9 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.4598 (ttp-170) REVERT: N 41 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7959 (tm-30) REVERT: N 127 TYR cc_start: 0.9275 (p90) cc_final: 0.8820 (p90) REVERT: O 144 ASN cc_start: 0.9169 (t0) cc_final: 0.8867 (t0) REVERT: P 85 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: P 93 VAL cc_start: 0.9285 (t) cc_final: 0.8998 (p) REVERT: V 108 TYR cc_start: 0.7911 (m-80) cc_final: 0.7447 (m-80) REVERT: W 86 MET cc_start: 0.8732 (mtt) cc_final: 0.8516 (mtp) REVERT: X 125 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8137 (tm-30) REVERT: b 9 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8569 (mtpt) REVERT: e 148 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7575 (tm-30) REVERT: g 47 ASP cc_start: 0.8922 (t0) cc_final: 0.8587 (t0) REVERT: h 83 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.7982 (ttt180) REVERT: i 100 MET cc_start: 0.8366 (mmm) cc_final: 0.8120 (mmt) REVERT: j 68 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: k 43 MET cc_start: 0.8401 (tpp) cc_final: 0.8201 (ttm) REVERT: k 91 GLN cc_start: 0.8454 (pp30) cc_final: 0.7768 (pp30) REVERT: k 97 GLN cc_start: 0.7345 (pm20) cc_final: 0.6776 (mp10) REVERT: l 338 MET cc_start: 0.7889 (tpp) cc_final: 0.7021 (ttm) REVERT: l 445 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: m 1 MET cc_start: 0.4040 (mmm) cc_final: 0.3543 (mmm) REVERT: m 46 ASN cc_start: 0.9109 (m-40) cc_final: 0.8518 (m110) REVERT: m 128 TYR cc_start: 0.7991 (m-80) cc_final: 0.7538 (m-80) REVERT: o 126 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8302 (m-40) REVERT: p 14 GLN cc_start: 0.8276 (mp10) cc_final: 0.7836 (mp10) REVERT: r 186 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8789 (mp) REVERT: r 207 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8605 (mtp) REVERT: r 256 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7856 (p90) REVERT: r 437 MET cc_start: 0.8878 (mpp) cc_final: 0.8100 (mpp) REVERT: s 233 MET cc_start: 0.8291 (tmm) cc_final: 0.7854 (tmm) REVERT: u 36 CYS cc_start: 0.8205 (m) cc_final: 0.6448 (m) REVERT: u 66 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7091 (t) REVERT: u 90 ASP cc_start: 0.8870 (t70) cc_final: 0.8646 (t0) REVERT: u 103 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: v 43 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8274 (mm-40) REVERT: v 48 ASP cc_start: 0.8371 (m-30) cc_final: 0.7611 (m-30) REVERT: v 101 GLU cc_start: 0.8428 (tp30) cc_final: 0.7757 (tp30) REVERT: v 105 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7605 (tm-30) REVERT: w 259 SER cc_start: 0.8256 (t) cc_final: 0.8007 (m) REVERT: w 264 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: w 296 MET cc_start: 0.8627 (mmm) cc_final: 0.8363 (mmm) outliers start: 169 outliers final: 123 residues processed: 1279 average time/residue: 0.6449 time to fit residues: 1402.5847 Evaluate side-chains 1287 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1145 time to evaluate : 5.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 569 GLN Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 633 THR Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 399 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 264 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 4.9990 chunk 732 optimal weight: 0.8980 chunk 668 optimal weight: 5.9990 chunk 712 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 559 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 643 optimal weight: 5.9990 chunk 673 optimal weight: 0.9980 chunk 709 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN N 13 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN ** b 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN i 322 GLN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 349 GLN u 16 GLN u 99 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 68418 Z= 0.283 Angle : 0.572 12.797 92514 Z= 0.281 Chirality : 0.042 0.249 10031 Planarity : 0.004 0.146 11549 Dihedral : 11.814 169.907 10350 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 2.58 % Allowed : 20.51 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 0.99 (0.10), residues: 8027 helix: 1.71 (0.08), residues: 4236 sheet: 0.09 (0.25), residues: 438 loop : -0.61 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.011 0.001 HIS b 127 PHE 0.031 0.001 PHE i 292 TYR 0.033 0.001 TYR d 143 ARG 0.012 0.000 ARG Z 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1130 time to evaluate : 5.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8293 (mpt180) cc_final: 0.7636 (mmt-90) REVERT: A 134 ASP cc_start: 0.8026 (t0) cc_final: 0.7592 (t0) REVERT: A 175 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: B 72 MET cc_start: 0.8725 (tpp) cc_final: 0.8424 (tpp) REVERT: B 76 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8091 (t80) REVERT: E 18 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8333 (ttpt) REVERT: E 24 ASP cc_start: 0.8227 (t0) cc_final: 0.7818 (t0) REVERT: E 68 MET cc_start: 0.8282 (mmm) cc_final: 0.8059 (mmm) REVERT: F 73 GLN cc_start: 0.7293 (mp10) cc_final: 0.6969 (mp10) REVERT: G 80 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7428 (ttmm) REVERT: G 81 ASP cc_start: 0.7651 (m-30) cc_final: 0.7250 (t0) REVERT: G 82 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6743 (mtp85) REVERT: G 89 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7588 (mt) REVERT: H 58 MET cc_start: 0.7710 (mtm) cc_final: 0.7418 (mtm) REVERT: I 30 GLU cc_start: 0.8209 (pm20) cc_final: 0.7699 (pm20) REVERT: J 140 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7622 (p0) REVERT: M 277 MET cc_start: 0.9043 (tmm) cc_final: 0.8723 (tpp) REVERT: M 370 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: N 9 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.4624 (ttp-170) REVERT: N 41 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7945 (tm-30) REVERT: O 144 ASN cc_start: 0.9232 (t0) cc_final: 0.8922 (t0) REVERT: P 93 VAL cc_start: 0.9276 (t) cc_final: 0.8985 (p) REVERT: V 108 TYR cc_start: 0.7885 (m-80) cc_final: 0.7377 (m-80) REVERT: V 120 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8097 (mm) REVERT: X 125 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8159 (tm-30) REVERT: b 9 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8544 (mtpt) REVERT: e 148 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7576 (tm-30) REVERT: g 47 ASP cc_start: 0.8922 (t0) cc_final: 0.8590 (t0) REVERT: h 83 ARG cc_start: 0.8372 (ttp-170) cc_final: 0.8006 (ttt180) REVERT: i 100 MET cc_start: 0.8381 (mmm) cc_final: 0.8135 (mmt) REVERT: j 68 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: k 91 GLN cc_start: 0.8427 (pp30) cc_final: 0.7746 (pp30) REVERT: k 97 GLN cc_start: 0.7398 (pm20) cc_final: 0.6801 (mp10) REVERT: l 1 MET cc_start: 0.6277 (ppp) cc_final: 0.5878 (ppp) REVERT: l 338 MET cc_start: 0.7879 (tpp) cc_final: 0.7102 (ttm) REVERT: l 445 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: m 1 MET cc_start: 0.3928 (mmm) cc_final: 0.3509 (mmm) REVERT: m 46 ASN cc_start: 0.9115 (m-40) cc_final: 0.8788 (m110) REVERT: m 57 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8186 (t80) REVERT: o 126 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8296 (m-40) REVERT: p 14 GLN cc_start: 0.8348 (mp10) cc_final: 0.7881 (mp10) REVERT: r 186 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8791 (mp) REVERT: r 207 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8609 (mtp) REVERT: r 256 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7976 (p90) REVERT: r 282 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8222 (tt) REVERT: r 437 MET cc_start: 0.8932 (mpp) cc_final: 0.8051 (mpp) REVERT: u 36 CYS cc_start: 0.8057 (m) cc_final: 0.6055 (m) REVERT: u 64 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8149 (m110) REVERT: u 66 CYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7015 (t) REVERT: u 90 ASP cc_start: 0.8885 (t70) cc_final: 0.8645 (t0) REVERT: u 103 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: v 48 ASP cc_start: 0.8381 (m-30) cc_final: 0.7668 (m-30) REVERT: v 89 TYR cc_start: 0.9024 (t80) cc_final: 0.8816 (t80) REVERT: v 101 GLU cc_start: 0.8458 (tp30) cc_final: 0.7844 (tp30) REVERT: v 105 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7598 (tm-30) REVERT: w 259 SER cc_start: 0.8322 (t) cc_final: 0.8071 (m) REVERT: w 264 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8064 (mp0) outliers start: 182 outliers final: 137 residues processed: 1248 average time/residue: 0.6444 time to fit residues: 1365.8633 Evaluate side-chains 1282 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1124 time to evaluate : 7.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 403 VAL Chi-restraints excluded: chain M residue 465 ILE Chi-restraints excluded: chain M residue 479 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 633 THR Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 399 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 565 THR Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 57 PHE Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 132 SER Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 282 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 103 GLN Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 31 PHE Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 264 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 0.5980 chunk 753 optimal weight: 0.0670 chunk 459 optimal weight: 4.9990 chunk 357 optimal weight: 20.0000 chunk 523 optimal weight: 0.9980 chunk 790 optimal weight: 1.9990 chunk 727 optimal weight: 0.8980 chunk 629 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 485 optimal weight: 1.9990 chunk 385 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN O 69 ASN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN V 129 GLN a 90 ASN ** b 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN i 322 GLN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 ASN r 139 GLN u 16 GLN u 99 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 68418 Z= 0.161 Angle : 0.530 12.965 92514 Z= 0.260 Chirality : 0.040 0.305 10031 Planarity : 0.004 0.144 11549 Dihedral : 11.305 168.309 10350 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 2.09 % Allowed : 21.15 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 1.16 (0.10), residues: 8027 helix: 1.82 (0.08), residues: 4239 sheet: 0.20 (0.25), residues: 436 loop : -0.50 (0.11), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.011 0.001 HIS b 127 PHE 0.031 0.001 PHE i 292 TYR 0.030 0.001 TYR d 143 ARG 0.013 0.000 ARG Z 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16054 Ramachandran restraints generated. 8027 Oldfield, 0 Emsley, 8027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1174 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8223 (mpt180) cc_final: 0.7575 (mmt-90) REVERT: A 134 ASP cc_start: 0.7874 (t0) cc_final: 0.7475 (t0) REVERT: A 175 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: B 50 MET cc_start: 0.7927 (tpt) cc_final: 0.7660 (tpt) REVERT: B 72 MET cc_start: 0.8633 (tpp) cc_final: 0.8394 (tpp) REVERT: B 76 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.7723 (t80) REVERT: E 18 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8371 (ttpt) REVERT: E 24 ASP cc_start: 0.8144 (t0) cc_final: 0.7724 (t0) REVERT: E 68 MET cc_start: 0.8252 (mmm) cc_final: 0.8024 (mmm) REVERT: F 73 GLN cc_start: 0.7258 (mp10) cc_final: 0.6931 (mp10) REVERT: G 80 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7388 (ttmm) REVERT: G 81 ASP cc_start: 0.7680 (m-30) cc_final: 0.7285 (t0) REVERT: G 82 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: G 89 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7650 (mt) REVERT: I 30 GLU cc_start: 0.8258 (pm20) cc_final: 0.7730 (pm20) REVERT: J 140 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7586 (p0) REVERT: M 277 MET cc_start: 0.9041 (tmm) cc_final: 0.8705 (tpp) REVERT: M 370 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: N 9 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.4660 (ttp-170) REVERT: N 41 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7957 (tm-30) REVERT: O 144 ASN cc_start: 0.9144 (t0) cc_final: 0.8833 (t0) REVERT: P 93 VAL cc_start: 0.9264 (t) cc_final: 0.8961 (p) REVERT: V 108 TYR cc_start: 0.7882 (m-80) cc_final: 0.7363 (m-80) REVERT: X 125 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8122 (tm-30) REVERT: X 137 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8298 (ptpp) REVERT: b 9 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8566 (mtpt) REVERT: e 148 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7531 (tm-30) REVERT: g 47 ASP cc_start: 0.8924 (t0) cc_final: 0.8559 (t0) REVERT: h 83 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7987 (ttt180) REVERT: i 100 MET cc_start: 0.8360 (mmm) cc_final: 0.8146 (mmt) REVERT: j 68 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: k 91 GLN cc_start: 0.8427 (pp30) cc_final: 0.7739 (pp30) REVERT: k 97 GLN cc_start: 0.7320 (pm20) cc_final: 0.6754 (mp10) REVERT: l 1 MET cc_start: 0.6200 (ppp) cc_final: 0.5955 (ppp) REVERT: l 338 MET cc_start: 0.7794 (tpp) cc_final: 0.7073 (ttm) REVERT: l 445 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: m 1 MET cc_start: 0.3825 (mmm) cc_final: 0.3219 (mmm) REVERT: m 46 ASN cc_start: 0.9107 (m-40) cc_final: 0.8517 (m110) REVERT: m 128 TYR cc_start: 0.7930 (m-80) cc_final: 0.7539 (m-80) REVERT: o 126 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8276 (m-40) REVERT: p 14 GLN cc_start: 0.8310 (mp10) cc_final: 0.7875 (mp10) REVERT: r 158 LEU cc_start: 0.8825 (mt) cc_final: 0.8599 (mt) REVERT: r 186 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8806 (mp) REVERT: r 207 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: r 256 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7769 (p90) REVERT: r 282 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8039 (tt) REVERT: r 437 MET cc_start: 0.8938 (mpp) cc_final: 0.8043 (mpp) REVERT: u 22 SER cc_start: 0.8677 (t) cc_final: 0.8403 (p) REVERT: u 32 TYR cc_start: 0.9318 (t80) cc_final: 0.9109 (t80) REVERT: u 36 CYS cc_start: 0.8189 (m) cc_final: 0.6384 (m) REVERT: u 64 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8090 (m110) REVERT: u 66 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7068 (t) REVERT: u 90 ASP cc_start: 0.8840 (t70) cc_final: 0.8623 (t0) REVERT: v 43 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8189 (mm-40) REVERT: v 48 ASP cc_start: 0.8354 (m-30) cc_final: 0.7785 (m-30) REVERT: v 81 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8545 (mtpp) REVERT: v 94 ASP cc_start: 0.9066 (t0) cc_final: 0.8426 (t0) REVERT: v 101 GLU cc_start: 0.8368 (tp30) cc_final: 0.7755 (tp30) REVERT: v 105 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7609 (tm-30) REVERT: w 259 SER cc_start: 0.8213 (t) cc_final: 0.7943 (m) REVERT: w 264 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8048 (mp0) outliers start: 147 outliers final: 113 residues processed: 1265 average time/residue: 0.6355 time to fit residues: 1367.6503 Evaluate side-chains 1277 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1146 time to evaluate : 5.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 373 LYS Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 370 GLU Chi-restraints excluded: chain M residue 389 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 563 ASP Chi-restraints excluded: chain M residue 606 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 627 SER Chi-restraints excluded: chain M residue 685 VAL Chi-restraints excluded: chain M residue 690 THR Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 223 PHE Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 186 ILE Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 22 TYR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 445 GLU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 584 ILE Chi-restraints excluded: chain l residue 589 LEU Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain p residue 24 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 282 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain w residue 197 GLU Chi-restraints excluded: chain w residue 264 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 3.9990 chunk 670 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 580 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 174 optimal weight: 0.0020 chunk 630 optimal weight: 0.4980 chunk 263 optimal weight: 0.0970 chunk 647 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 666 GLN N 13 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN V 129 GLN ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN h 25 GLN i 322 GLN l 524 ASN ** l 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 GLN u 99 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.086876 restraints weight = 107045.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.089917 restraints weight = 51840.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.091871 restraints weight = 30491.314| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 68418 Z= 0.149 Angle : 0.526 12.470 92514 Z= 0.258 Chirality : 0.040 0.292 10031 Planarity : 0.004 0.146 11549 Dihedral : 10.867 167.638 10350 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 1.92 % Allowed : 21.55 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.85 % 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: 1.24 (0.10), residues: 8027 helix: 1.87 (0.08), residues: 4246 sheet: 0.29 (0.26), residues: 435 loop : -0.46 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS b 127 PHE 0.029 0.001 PHE i 292 TYR 0.028 0.001 TYR d 143 ARG 0.013 0.000 ARG Z 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18860.21 seconds wall clock time: 359 minutes 44.56 seconds (21584.56 seconds total)