Starting phenix.real_space_refine on Fri Feb 16 00:27:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w31_32269/02_2024/7w31_32269_updated.pdb" } resolution = 3.1 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 35 5.49 5 Mg 1 5.21 5 S 470 5.16 5 C 42944 2.51 5 N 11078 2.21 5 O 11919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "P TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 387": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 63": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n ARG 30": "NH1" <-> "NH2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66476 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3314 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} 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: "B" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1402 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 968 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2611 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 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: 5290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5290 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 657} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1636 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1735 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 192} 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: "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: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 571 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 26 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: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 847 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "c" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1287 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 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: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 889 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 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: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4704 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 38 Chain: "m" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 915 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 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: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1052 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 116} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1491 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "r" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3629 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 158} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "v" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 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: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 302 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2702 SG CYS A 382 49.067 49.087 174.491 1.00 20.96 S ATOM 3044 SG CYS A 425 48.235 45.495 179.962 1.00 13.42 S ATOM 2722 SG CYS A 385 45.759 44.655 174.258 1.00 29.31 S ATOM 2683 SG CYS A 379 43.714 49.719 178.281 1.00 4.97 S ATOM 3935 SG CYS B 113 39.573 66.721 139.978 1.00 19.29 S ATOM 3954 SG CYS B 116 44.368 63.775 143.902 1.00 16.91 S ATOM 3977 SG CYS B 119 45.713 66.620 138.548 1.00 0.00 S ATOM 4306 SG CYS B 162 42.881 60.986 138.896 1.00 0.00 S ATOM 4004 SG CYS B 123 52.089 69.222 134.265 1.00 0.00 S ATOM 4230 SG CYS B 152 50.207 67.744 128.155 1.00 9.27 S ATOM 4277 SG CYS B 158 48.043 64.054 132.865 1.00 19.67 S ATOM 4256 SG CYS B 155 54.101 63.950 131.442 1.00 0.00 S ATOM 5698 SG CYS C 166 56.618 67.634 124.268 1.00 6.80 S ATOM 4964 SG CYS C 71 61.714 67.270 120.339 1.00 0.00 S ATOM 4970 SG CYS C 72 57.976 69.175 118.251 1.00 1.70 S ATOM 4964 SG CYS C 71 61.714 67.270 120.339 1.00 0.00 S ATOM 5468 SG CYS C 136 59.448 71.990 123.160 1.00 0.00 S ATOM 14773 SG CYS M 131 43.412 63.576 155.907 1.00 3.38 S ATOM 14752 SG CYS M 128 46.923 58.948 152.569 1.00 0.00 S ATOM 14813 SG CYS M 137 48.878 62.139 157.975 1.00 0.00 S ATOM 15141 SG CYS M 179 47.067 61.919 169.137 1.00 1.66 S ATOM 15495 SG CYS M 226 44.176 64.854 164.942 1.00 23.17 S ATOM 15165 SG CYS M 182 41.764 64.714 170.908 1.00 7.22 S ATOM 15118 SG CYS M 176 41.367 59.265 167.236 1.00 13.19 S ATOM 14370 SG CYS M 78 58.398 56.399 172.815 1.00 26.80 S ATOM 14471 SG CYS M 92 56.535 58.411 175.126 1.00 21.41 S ATOM 14259 SG CYS M 64 52.306 58.849 172.925 1.00 17.74 S ATOM 14345 SG CYS M 75 53.253 56.953 169.797 1.00 0.00 S ATOM 21302 SG CYS O 135 31.773 32.322 181.370 1.00 45.92 S ATOM 21336 SG CYS O 140 31.597 28.880 182.564 1.00 53.57 S ATOM 21616 SG CYS O 176 36.309 33.421 184.241 1.00 55.89 S ATOM 21639 SG CYS O 180 36.568 30.274 185.304 1.00 43.39 S ATOM 28259 SG CYS T 86 31.289 53.624 147.414 1.00 18.31 S ATOM 28437 SG CYS T 111 32.724 56.916 148.376 1.00 17.17 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 26.49, per 1000 atoms: 0.40 Number of scatterers: 66476 At special positions: 0 Unit cell: (222.359, 219.137, 230.953, 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 470 16.00 P 35 15.00 Mg 1 11.99 O 11919 8.00 N 11078 7.00 C 42944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 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: 21.72 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 342 helices and 28 sheets defined 52.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.68 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 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.836A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (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 163 through 178 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.637A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 334 removed outlier: 5.253A 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 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.879A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.870A 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: 5.831A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.592A pdb=" N VAL C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.749A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 123 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 190 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.094A 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 107 removed outlier: 4.198A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 5.006A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 4.069A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.849A 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 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 54 through 57 Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain '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: 4.219A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.765A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 213 through 223 removed outlier: 4.574A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.994A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 323 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 356 removed outlier: 5.000A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.391A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.698A 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 removed outlier: 3.596A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.515A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 298 removed outlier: 4.969A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.587A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.718A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.703A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.431A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 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 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.641A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.539A 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: 3.792A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.140A 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 48 removed outlier: 3.705A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.694A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.033A 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: 4.129A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.613A 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: 4.357A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 286 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.584A 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: 4.470A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.231A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.790A 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 30 Proline residue: S 7 - end of helix removed outlier: 3.826A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.276A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 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 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.726A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.429A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.729A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.585A pdb=" N LEU Y 81 " --> pdb=" O SER Y 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 77 through 81' Processing helix chain 'Z' and resid 28 through 37 Processing helix chain 'Z' and resid 50 through 53 Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.726A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 removed outlier: 3.591A pdb=" N LEU b 10 " --> pdb=" O PRO b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 73 removed outlier: 3.602A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.672A 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 82 through 124 removed outlier: 3.700A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.901A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 132 removed outlier: 3.530A pdb=" N ALA e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 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: 3.799A 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 94 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.276A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.795A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.925A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 231 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: 4.409A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 332 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 54 through 78 Proline residue: j 74 - end of helix removed outlier: 5.845A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 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: 4.234A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.866A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.531A 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: 3.959A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 removed outlier: 3.512A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 4.061A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.117A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.703A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 252 through 262 removed outlier: 4.430A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 268 Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.395A 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: 3.708A 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: 4.154A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.637A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.327A 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: 3.512A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.679A 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: 4.362A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 removed outlier: 3.864A pdb=" N MET l 544 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.845A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.361A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.558A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 4.196A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 45 No H-bonds generated for 'chain 'n' and resid 43 through 45' Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 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: 3.718A pdb=" N GLU p 50 " --> pdb=" O ALA p 46 " (cutoff:3.500A) removed outlier: 4.969A 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 65 through 73 Processing helix chain 'p' and resid 94 through 96 No H-bonds generated for 'chain 'p' and resid 94 through 96' Processing helix chain 'p' and resid 102 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.617A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.931A 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: 4.114A 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: 4.202A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.851A 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: 3.651A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.535A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.446A 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 142 through 170 removed outlier: 4.337A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.200A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.162A 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 246 Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.965A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.676A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 350 No H-bonds generated for 'chain 'r' and resid 348 through 350' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.871A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.241A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 31 Proline residue: s 12 - end of helix removed outlier: 3.987A 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: 4.226A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.473A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.851A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.775A 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 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 4.903A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 9 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 81 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 50 through 52 No H-bonds generated for 'chain 'w' and resid 50 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.082A 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 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.922A 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: 7.198A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.317A 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: 6.073A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.344A 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: 6.399A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.660A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.684A 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: 7.474A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 366 through 368 removed outlier: 8.648A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.031A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.625A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.598A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.628A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.593A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.483A 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: 6.707A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (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 2924 hydrogen bonds defined for protein. 8211 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: 22.25 Time building geometry restraints manager: 23.80 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: 27242 1.40 - 1.62: 39975 1.62 - 1.85: 830 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 68127 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.268 0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.285 0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.296 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 68122 not shown) Histogram of bond angle deviations from ideal: 73.62 - 86.00: 76 86.00 - 98.38: 9 98.38 - 110.77: 23074 110.77 - 123.15: 65980 123.15 - 135.53: 3102 Bond angle restraints: 92241 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.72 -15.98 1.95e+00 2.62e-01 6.69e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 118.58 -14.74 1.91e+00 2.73e-01 5.93e+01 angle pdb=" N ARG P 125 " pdb=" CA ARG P 125 " pdb=" C ARG P 125 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.20e+01 angle pdb=" C GLY a 128 " pdb=" N PRO a 129 " pdb=" CA PRO a 129 " ideal model delta sigma weight residual 119.32 127.50 -8.18 1.14e+00 7.69e-01 5.15e+01 angle pdb=" C11 CDL u 201 " pdb=" CA5 CDL u 201 " pdb=" OA6 CDL u 201 " ideal model delta sigma weight residual 111.33 120.62 -9.29 1.32e+00 5.72e-01 4.94e+01 ... (remaining 92236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 39718 35.09 - 70.17: 1455 70.17 - 105.26: 116 105.26 - 140.34: 21 140.34 - 175.43: 20 Dihedral angle restraints: 41330 sinusoidal: 17535 harmonic: 23795 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 82.16 175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 98.71 -158.71 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CB CYS v 69 " pdb=" SG CYS v 69 " pdb=" SG CYS v 80 " pdb=" CB CYS v 80 " ideal model delta sinusoidal sigma weight residual -86.00 -29.46 -56.54 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 41327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9116 0.074 - 0.149: 878 0.149 - 0.223: 41 0.223 - 0.297: 12 0.297 - 0.371: 6 Chirality restraints: 10053 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 -2.38 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA SER m 25 " pdb=" N SER m 25 " pdb=" C SER m 25 " pdb=" CB SER m 25 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA TYR M 695 " pdb=" N TYR M 695 " pdb=" C TYR M 695 " pdb=" CB TYR M 695 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 10050 not shown) Planarity restraints: 11555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " 0.372 2.00e-02 2.50e+03 4.94e-01 3.05e+03 pdb=" C11 UQ s 401 " 0.204 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " 0.581 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " -0.713 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " -0.444 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.483 2.00e-02 2.50e+03 4.19e-01 2.19e+03 pdb=" C13 UQ s 401 " -0.536 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.415 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.041 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.428 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.208 2.00e-02 2.50e+03 2.32e-01 6.71e+02 pdb=" C18 UQ s 401 " 0.152 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.358 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.033 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.269 2.00e-02 2.50e+03 ... (remaining 11552 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 562 2.57 - 3.15: 53505 3.15 - 3.73: 106932 3.73 - 4.32: 150428 4.32 - 4.90: 248991 Nonbonded interactions: 560418 Sorted by model distance: nonbonded pdb=" O ASP c 80 " pdb=" O ARG c 81 " model vdw 1.986 3.040 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.197 2.440 nonbonded pdb=" OG SER B 47 " pdb=" OD1 ASP B 49 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR c 55 " pdb=" O ASP c 74 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG Q 368 " model vdw 2.205 2.520 ... (remaining 560413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 96 or (resid 97 through 99 and (na \ me N or name CA or name C or name O or name CB )) or resid 100 through 101 or (r \ esid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 t \ hrough 113 or (resid 114 and (name N or name CA or name C or name O or name CB ) \ ) or resid 115 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.050 Extract box with map and model: 8.930 Check model and map are aligned: 0.770 Set scattering table: 0.470 Process input model: 161.270 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.313 68127 Z= 0.427 Angle : 0.802 17.455 92241 Z= 0.412 Chirality : 0.044 0.371 10053 Planarity : 0.009 0.494 11555 Dihedral : 17.998 175.429 25964 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.02 % Rotamer: Outliers : 0.36 % Allowed : 14.16 % Favored : 85.48 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 8065 helix: 1.43 (0.08), residues: 4256 sheet: 0.06 (0.25), residues: 410 loop : -0.54 (0.11), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.038 0.001 HIS v 4 PHE 0.027 0.001 PHE r 151 TYR 0.040 0.002 TYR v 58 ARG 0.027 0.000 ARG b 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1138 time to evaluate : 5.778 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: P 146 TYR cc_start: 0.8578 (p90) cc_final: 0.8315 (p90) REVERT: c 150 TYR cc_start: 0.7479 (m-80) cc_final: 0.7211 (m-80) REVERT: i 190 MET cc_start: 0.8566 (mtp) cc_final: 0.8278 (mtp) REVERT: v 104 ARG cc_start: 0.6927 (tmm-80) cc_final: 0.6313 (ttt90) outliers start: 25 outliers final: 13 residues processed: 1151 average time/residue: 0.6448 time to fit residues: 1262.2148 Evaluate side-chains 1122 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1109 time to evaluate : 5.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain Z residue 73 TRP Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain l residue 346 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain v residue 33 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 673 optimal weight: 5.9990 chunk 604 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 chunk 624 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 464 optimal weight: 10.0000 chunk 723 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 418 GLN C 123 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN P 196 HIS T 117 GLN Y 54 GLN Y 57 GLN ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN e 148 GLN g 14 GLN i 47 ASN i 235 ASN l 205 ASN l 323 HIS l 479 ASN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 534 HIS r 103 GLN r 331 ASN r 440 HIS ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 306 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 68127 Z= 0.396 Angle : 0.684 12.138 92241 Z= 0.342 Chirality : 0.046 0.208 10053 Planarity : 0.006 0.074 11555 Dihedral : 14.311 177.959 10168 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 2.86 % Allowed : 14.35 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8065 helix: 1.15 (0.08), residues: 4258 sheet: -0.14 (0.25), residues: 418 loop : -0.68 (0.11), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP u 86 HIS 0.009 0.002 HIS Q 183 PHE 0.032 0.002 PHE r 151 TYR 0.028 0.002 TYR v 58 ARG 0.011 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1176 time to evaluate : 6.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8400 (mmm) cc_final: 0.8114 (mmm) REVERT: B 76 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8140 (t80) REVERT: F 62 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: I 92 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6970 (tptt) REVERT: K 93 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8466 (tt) REVERT: M 84 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8043 (mmtm) REVERT: O 180 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8584 (m) REVERT: P 146 TYR cc_start: 0.8751 (p90) cc_final: 0.8466 (p90) REVERT: Y 72 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.4995 (mmm160) REVERT: Z 63 PHE cc_start: 0.7888 (t80) cc_final: 0.7366 (t80) REVERT: a 131 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7669 (tptm) REVERT: f 71 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6856 (ttp-110) REVERT: g 116 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7516 (pt0) REVERT: i 190 MET cc_start: 0.8940 (mtp) cc_final: 0.8689 (mtp) REVERT: i 215 MET cc_start: 0.9196 (tpt) cc_final: 0.8587 (tpt) REVERT: l 238 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7925 (mm-30) REVERT: l 338 MET cc_start: 0.7607 (ptm) cc_final: 0.7378 (ptm) REVERT: l 351 ASN cc_start: 0.7688 (m-40) cc_final: 0.7310 (m-40) REVERT: l 445 GLU cc_start: 0.7615 (tt0) cc_final: 0.7158 (tt0) REVERT: l 500 LEU cc_start: 0.8322 (mp) cc_final: 0.8087 (mp) REVERT: m 135 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: o 114 LYS cc_start: 0.8080 (tptp) cc_final: 0.7761 (tptt) REVERT: p 24 LEU cc_start: 0.7232 (mt) cc_final: 0.7029 (mt) REVERT: p 106 ASP cc_start: 0.7601 (m-30) cc_final: 0.7341 (m-30) REVERT: r 138 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7399 (p0) REVERT: v 52 MET cc_start: 0.7280 (mmm) cc_final: 0.7004 (mmm) REVERT: v 68 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7140 (tptt) REVERT: v 104 ARG cc_start: 0.7120 (tmm-80) cc_final: 0.6790 (ttt180) REVERT: v 106 ARG cc_start: 0.7524 (ttt90) cc_final: 0.7316 (ptm160) REVERT: w 296 MET cc_start: 0.8708 (mmm) cc_final: 0.8461 (mmt) outliers start: 200 outliers final: 101 residues processed: 1308 average time/residue: 0.6485 time to fit residues: 1432.1433 Evaluate side-chains 1219 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1109 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 270 ASN Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 53 SER Chi-restraints excluded: chain Y residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 109 SER Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 27 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 402 optimal weight: 9.9990 chunk 224 optimal weight: 0.6980 chunk 602 optimal weight: 6.9990 chunk 492 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 725 optimal weight: 0.9990 chunk 783 optimal weight: 7.9990 chunk 645 optimal weight: 10.0000 chunk 719 optimal weight: 0.9980 chunk 247 optimal weight: 0.0000 chunk 581 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN F 93 ASN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN e 132 ASN g 14 GLN i 235 ASN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 GLN p 124 GLN r 251 ASN r 304 GLN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 299 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 68127 Z= 0.218 Angle : 0.567 12.312 92241 Z= 0.284 Chirality : 0.041 0.180 10053 Planarity : 0.005 0.069 11555 Dihedral : 13.480 179.669 10146 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 2.39 % Allowed : 16.15 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 8065 helix: 1.39 (0.08), residues: 4263 sheet: -0.09 (0.25), residues: 421 loop : -0.59 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS w 186 PHE 0.027 0.001 PHE l 335 TYR 0.021 0.001 TYR l 422 ARG 0.006 0.000 ARG g 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1196 time to evaluate : 5.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7705 (t80) REVERT: C 67 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: I 92 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6810 (tptt) REVERT: J 336 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7240 (pm20) REVERT: L 112 MET cc_start: 0.8786 (mmm) cc_final: 0.8531 (mmm) REVERT: M 84 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8085 (mmtm) REVERT: O 180 CYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8537 (m) REVERT: P 146 TYR cc_start: 0.8713 (p90) cc_final: 0.8470 (p90) REVERT: S 1 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7647 (ttm) REVERT: U 10 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7391 (mmmm) REVERT: X 124 ASP cc_start: 0.7682 (t0) cc_final: 0.6876 (m-30) REVERT: b 23 LEU cc_start: 0.8386 (mt) cc_final: 0.8104 (mt) REVERT: b 113 THR cc_start: 0.6283 (m) cc_final: 0.6058 (m) REVERT: e 116 GLU cc_start: 0.7943 (mp0) cc_final: 0.7464 (mp0) REVERT: f 71 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.6830 (ttp-110) REVERT: g 64 LEU cc_start: 0.8549 (tp) cc_final: 0.8339 (tp) REVERT: g 116 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7525 (pt0) REVERT: i 14 MET cc_start: 0.9065 (mtp) cc_final: 0.8855 (mtt) REVERT: i 190 MET cc_start: 0.8778 (mtp) cc_final: 0.8558 (mtp) REVERT: i 215 MET cc_start: 0.9205 (tpt) cc_final: 0.8654 (tpt) REVERT: i 244 MET cc_start: 0.8460 (ttm) cc_final: 0.8088 (ttm) REVERT: l 60 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: l 179 ASP cc_start: 0.8721 (m-30) cc_final: 0.8506 (m-30) REVERT: l 238 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7860 (mm-30) REVERT: l 351 ASN cc_start: 0.7632 (m-40) cc_final: 0.7248 (m-40) REVERT: l 571 MET cc_start: 0.3631 (mtt) cc_final: 0.3250 (mtp) REVERT: m 135 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: p 24 LEU cc_start: 0.7305 (mt) cc_final: 0.7013 (mt) REVERT: r 138 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7189 (p0) REVERT: v 39 MET cc_start: 0.3940 (ppp) cc_final: 0.2969 (ptt) REVERT: v 52 MET cc_start: 0.7322 (mmm) cc_final: 0.6872 (mmm) REVERT: v 68 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7126 (tptt) REVERT: v 104 ARG cc_start: 0.6951 (tmm-80) cc_final: 0.6735 (ttt180) REVERT: w 173 MET cc_start: 0.7131 (mtp) cc_final: 0.6554 (mtp) REVERT: w 265 ASP cc_start: 0.5621 (p0) cc_final: 0.5245 (p0) outliers start: 167 outliers final: 102 residues processed: 1298 average time/residue: 0.6519 time to fit residues: 1437.5761 Evaluate side-chains 1240 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1129 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain a residue 68 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain l residue 454 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 191 SER Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 275 ILE Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 716 optimal weight: 0.8980 chunk 545 optimal weight: 3.9990 chunk 376 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 486 optimal weight: 8.9990 chunk 727 optimal weight: 4.9990 chunk 770 optimal weight: 10.0000 chunk 380 optimal weight: 0.9990 chunk 689 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN F 93 ASN H 50 GLN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN N 52 ASN ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN g 14 GLN i 91 ASN i 235 ASN l 109 HIS l 295 GLN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 169 HIS r 139 GLN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 68127 Z= 0.275 Angle : 0.591 12.044 92241 Z= 0.295 Chirality : 0.043 0.194 10053 Planarity : 0.005 0.065 11555 Dihedral : 12.775 177.549 10146 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 3.33 % Allowed : 16.32 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8065 helix: 1.40 (0.08), residues: 4239 sheet: -0.13 (0.25), residues: 421 loop : -0.62 (0.11), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.007 0.001 HIS d 65 PHE 0.031 0.002 PHE l 335 TYR 0.024 0.002 TYR Q 308 ARG 0.007 0.000 ARG l 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1178 time to evaluate : 6.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8320 (mmm) cc_final: 0.8069 (mmm) REVERT: B 76 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7765 (t80) REVERT: C 67 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: C 142 TYR cc_start: 0.9471 (OUTLIER) cc_final: 0.7919 (t80) REVERT: F 62 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: I 92 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6943 (tptt) REVERT: J 79 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8468 (tp40) REVERT: M 84 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8097 (mmtm) REVERT: M 431 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9136 (tp) REVERT: U 10 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7441 (mmmm) REVERT: X 103 HIS cc_start: 0.7509 (t-90) cc_final: 0.7019 (t-90) REVERT: X 123 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6151 (mt-10) REVERT: X 124 ASP cc_start: 0.7710 (t0) cc_final: 0.7182 (m-30) REVERT: a 131 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7915 (tttt) REVERT: b 23 LEU cc_start: 0.8514 (mt) cc_final: 0.8307 (mt) REVERT: f 71 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.6834 (ttp-110) REVERT: g 64 LEU cc_start: 0.8642 (tp) cc_final: 0.8398 (tp) REVERT: g 116 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7584 (pt0) REVERT: i 69 MET cc_start: 0.8782 (mtm) cc_final: 0.8575 (mtm) REVERT: i 190 MET cc_start: 0.8876 (mtp) cc_final: 0.8670 (mtp) REVERT: i 215 MET cc_start: 0.9225 (tpt) cc_final: 0.8719 (tpt) REVERT: i 244 MET cc_start: 0.8460 (ttm) cc_final: 0.8145 (ttm) REVERT: j 4 MET cc_start: 0.7270 (mmm) cc_final: 0.6984 (mmm) REVERT: l 123 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8895 (mt) REVERT: l 238 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7964 (mm-30) REVERT: l 351 ASN cc_start: 0.7574 (m-40) cc_final: 0.7268 (m-40) REVERT: l 500 LEU cc_start: 0.8273 (mp) cc_final: 0.8022 (mp) REVERT: m 135 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: s 76 ILE cc_start: 0.8781 (mm) cc_final: 0.8561 (mm) REVERT: u 128 VAL cc_start: 0.8811 (p) cc_final: 0.8580 (t) REVERT: v 39 MET cc_start: 0.4257 (ppp) cc_final: 0.3351 (ptt) REVERT: v 52 MET cc_start: 0.7271 (mmm) cc_final: 0.6817 (mmm) REVERT: v 68 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7206 (mmtm) REVERT: v 104 ARG cc_start: 0.7063 (tmm-80) cc_final: 0.6701 (ttt180) REVERT: w 173 MET cc_start: 0.7109 (mtp) cc_final: 0.6734 (mtp) REVERT: w 265 ASP cc_start: 0.5623 (p0) cc_final: 0.5226 (p0) outliers start: 233 outliers final: 157 residues processed: 1329 average time/residue: 0.6385 time to fit residues: 1442.5276 Evaluate side-chains 1288 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1120 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 68 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 235 ASN Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 247 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 211 MET Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain l residue 454 ILE Chi-restraints excluded: chain l residue 494 THR Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 150 LEU Chi-restraints excluded: chain r residue 191 SER Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 66 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 641 optimal weight: 1.9990 chunk 437 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 573 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 657 optimal weight: 0.9980 chunk 532 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 691 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN F 93 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 HIS e 132 ASN i 235 ASN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 251 ASN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 68127 Z= 0.223 Angle : 0.560 14.388 92241 Z= 0.279 Chirality : 0.041 0.183 10053 Planarity : 0.005 0.064 11555 Dihedral : 12.327 177.118 10146 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 3.03 % Allowed : 17.47 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8065 helix: 1.49 (0.08), residues: 4248 sheet: -0.13 (0.25), residues: 422 loop : -0.54 (0.11), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS w 186 PHE 0.028 0.001 PHE l 335 TYR 0.022 0.001 TYR l 422 ARG 0.006 0.000 ARG g 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1175 time to evaluate : 6.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8340 (mmm) cc_final: 0.8074 (mmm) REVERT: B 76 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 67 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: C 142 TYR cc_start: 0.9457 (OUTLIER) cc_final: 0.7896 (t80) REVERT: F 62 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: G 124 ASP cc_start: 0.7178 (p0) cc_final: 0.6926 (m-30) REVERT: G 136 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: I 92 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6677 (tptt) REVERT: J 85 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7773 (ptt180) REVERT: M 84 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8129 (mmtm) REVERT: M 431 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9121 (tp) REVERT: N 122 GLN cc_start: 0.8157 (mt0) cc_final: 0.7828 (mt0) REVERT: O 180 CYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8601 (m) REVERT: P 183 ASP cc_start: 0.8676 (p0) cc_final: 0.8349 (p0) REVERT: Q 376 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: S 12 MET cc_start: 0.9200 (ttp) cc_final: 0.8966 (mtp) REVERT: U 10 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7393 (mmmm) REVERT: X 123 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6174 (mt-10) REVERT: X 124 ASP cc_start: 0.7704 (t0) cc_final: 0.7342 (m-30) REVERT: a 131 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7904 (tttt) REVERT: e 116 GLU cc_start: 0.7818 (mp0) cc_final: 0.7437 (mp0) REVERT: f 71 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6800 (ttp-110) REVERT: g 64 LEU cc_start: 0.8614 (tp) cc_final: 0.8389 (tp) REVERT: g 116 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7581 (pt0) REVERT: i 190 MET cc_start: 0.8831 (mtp) cc_final: 0.8612 (mtp) REVERT: i 215 MET cc_start: 0.9214 (tpt) cc_final: 0.8660 (tpt) REVERT: i 244 MET cc_start: 0.8410 (ttm) cc_final: 0.8140 (ttm) REVERT: j 4 MET cc_start: 0.7198 (mmm) cc_final: 0.6996 (mmm) REVERT: l 123 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8879 (mt) REVERT: l 238 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7921 (mm-30) REVERT: l 351 ASN cc_start: 0.7587 (m-40) cc_final: 0.7255 (m-40) REVERT: m 135 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: r 138 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7293 (p0) REVERT: s 76 ILE cc_start: 0.8801 (mm) cc_final: 0.8577 (mm) REVERT: v 39 MET cc_start: 0.4122 (ppp) cc_final: 0.3325 (ptt) REVERT: v 52 MET cc_start: 0.7251 (mmm) cc_final: 0.6744 (mmm) REVERT: v 68 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7188 (tptt) REVERT: v 83 GLU cc_start: 0.8125 (mp0) cc_final: 0.7769 (mp0) REVERT: v 104 ARG cc_start: 0.7062 (tmm-80) cc_final: 0.6726 (ttt180) REVERT: w 173 MET cc_start: 0.7074 (mtp) cc_final: 0.6774 (mtp) REVERT: w 265 ASP cc_start: 0.5511 (p0) cc_final: 0.5212 (p0) outliers start: 212 outliers final: 154 residues processed: 1311 average time/residue: 0.6478 time to fit residues: 1437.4117 Evaluate side-chains 1289 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1120 time to evaluate : 5.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 180 CYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 376 GLU Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain a residue 68 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 143 TYR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 8 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 247 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 115 TYR Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 150 LEU Chi-restraints excluded: chain r residue 191 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 127 TYR Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain u residue 158 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 259 optimal weight: 0.7980 chunk 693 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 771 optimal weight: 10.0000 chunk 640 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 255 optimal weight: 0.1980 chunk 404 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN F 93 ASN H 53 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 HIS ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 HIS e 132 ASN ** i 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 124 GLN ** r 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 68127 Z= 0.242 Angle : 0.569 14.415 92241 Z= 0.283 Chirality : 0.042 0.183 10053 Planarity : 0.005 0.062 11555 Dihedral : 12.010 177.104 10146 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 3.35 % Allowed : 17.48 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 8065 helix: 1.49 (0.08), residues: 4255 sheet: -0.12 (0.25), residues: 414 loop : -0.53 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.006 0.001 HIS w 186 PHE 0.028 0.001 PHE l 335 TYR 0.022 0.001 TYR l 422 ARG 0.007 0.000 ARG g 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1397 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1163 time to evaluate : 5.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8335 (mmm) cc_final: 0.8052 (mmm) REVERT: B 76 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 79 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8440 (ptp-170) REVERT: C 67 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: C 142 TYR cc_start: 0.9459 (OUTLIER) cc_final: 0.7895 (t80) REVERT: F 62 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: G 124 ASP cc_start: 0.7089 (p0) cc_final: 0.6841 (m-30) REVERT: G 136 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: I 92 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6770 (tptt) REVERT: J 79 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8466 (tp40) REVERT: J 85 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7703 (ptt180) REVERT: K 77 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: M 84 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8127 (mmtm) REVERT: M 431 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9120 (tp) REVERT: N 122 GLN cc_start: 0.8156 (mt0) cc_final: 0.7815 (mt0) REVERT: P 183 ASP cc_start: 0.8664 (p0) cc_final: 0.8344 (p0) REVERT: Q 376 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: U 10 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7352 (mmmm) REVERT: V 8 LYS cc_start: 0.5473 (ptmt) cc_final: 0.5264 (ptmm) REVERT: V 140 LYS cc_start: 0.8635 (pttt) cc_final: 0.8401 (pttt) REVERT: X 103 HIS cc_start: 0.7419 (t-90) cc_final: 0.6961 (t-90) REVERT: X 124 ASP cc_start: 0.7752 (t0) cc_final: 0.7316 (m-30) REVERT: a 120 TRP cc_start: 0.7916 (OUTLIER) cc_final: 0.7661 (t-100) REVERT: a 131 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7927 (tttt) REVERT: e 116 GLU cc_start: 0.7809 (mp0) cc_final: 0.7474 (mp0) REVERT: f 41 TRP cc_start: 0.7619 (m100) cc_final: 0.6201 (m-10) REVERT: g 116 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7631 (pt0) REVERT: i 89 MET cc_start: 0.8655 (tpt) cc_final: 0.8127 (tpt) REVERT: i 215 MET cc_start: 0.9231 (tpt) cc_final: 0.8708 (tpt) REVERT: i 346 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5902 (mp) REVERT: l 123 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8893 (mt) REVERT: l 238 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7922 (mm-30) REVERT: l 351 ASN cc_start: 0.7558 (m-40) cc_final: 0.7262 (m-40) REVERT: l 571 MET cc_start: 0.3624 (mtt) cc_final: 0.3163 (mtp) REVERT: m 135 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: r 138 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7296 (p0) REVERT: s 55 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9018 (mp) REVERT: s 76 ILE cc_start: 0.8817 (mm) cc_final: 0.8587 (mm) REVERT: v 39 MET cc_start: 0.4281 (ppp) cc_final: 0.3430 (ptt) REVERT: v 52 MET cc_start: 0.7253 (mmm) cc_final: 0.6712 (mmm) REVERT: v 68 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7273 (mmtm) REVERT: v 83 GLU cc_start: 0.8121 (mp0) cc_final: 0.7785 (mp0) REVERT: v 104 ARG cc_start: 0.7071 (tmm-80) cc_final: 0.6799 (ttt180) REVERT: w 173 MET cc_start: 0.6943 (mtp) cc_final: 0.6606 (mtp) REVERT: w 265 ASP cc_start: 0.5468 (p0) cc_final: 0.5090 (p0) outliers start: 234 outliers final: 177 residues processed: 1318 average time/residue: 0.6409 time to fit residues: 1434.7536 Evaluate side-chains 1317 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1120 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 590 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 376 GLU Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 68 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 120 TRP Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 143 TYR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 8 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 245 MET Chi-restraints excluded: chain i residue 247 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain i residue 346 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 163 ASP Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain l residue 454 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 191 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 55 LEU Chi-restraints excluded: chain s residue 108 MET Chi-restraints excluded: chain s residue 127 TYR Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain u residue 158 LEU Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 743 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 439 optimal weight: 0.9990 chunk 563 optimal weight: 7.9990 chunk 436 optimal weight: 2.9990 chunk 649 optimal weight: 10.0000 chunk 430 optimal weight: 8.9990 chunk 768 optimal weight: 20.0000 chunk 480 optimal weight: 9.9990 chunk 468 optimal weight: 6.9990 chunk 354 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN d 23 GLN e 115 GLN e 132 ASN l 400 ASN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 78 GLN r 51 ASN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 68127 Z= 0.327 Angle : 0.624 14.502 92241 Z= 0.311 Chirality : 0.044 0.278 10053 Planarity : 0.005 0.072 11555 Dihedral : 12.004 177.953 10146 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 3.71 % Allowed : 17.60 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8065 helix: 1.31 (0.08), residues: 4263 sheet: -0.27 (0.25), residues: 415 loop : -0.65 (0.11), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Z 51 HIS 0.006 0.001 HIS Q 183 PHE 0.024 0.002 PHE l 335 TYR 0.022 0.002 TYR r 406 ARG 0.014 0.001 ARG c 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1175 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8508 (mtmt) REVERT: B 76 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8026 (t80) REVERT: B 79 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8639 (ptp-170) REVERT: C 67 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: C 142 TYR cc_start: 0.9480 (OUTLIER) cc_final: 0.7933 (t80) REVERT: F 62 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: G 124 ASP cc_start: 0.7101 (p0) cc_final: 0.6848 (m-30) REVERT: G 136 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: I 92 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6934 (tptt) REVERT: J 79 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8515 (tp40) REVERT: J 85 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7728 (ptt180) REVERT: K 77 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7104 (mp10) REVERT: L 148 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: M 84 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8091 (mmtm) REVERT: M 336 ASN cc_start: 0.8094 (t0) cc_final: 0.7858 (t0) REVERT: M 431 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9141 (tp) REVERT: N 122 GLN cc_start: 0.8162 (mt0) cc_final: 0.7816 (mt0) REVERT: P 183 ASP cc_start: 0.8694 (p0) cc_final: 0.8483 (p0) REVERT: Q 246 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8272 (mm-30) REVERT: Q 376 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: V 8 LYS cc_start: 0.5454 (ptmt) cc_final: 0.5212 (ptmm) REVERT: V 140 LYS cc_start: 0.8584 (pttt) cc_final: 0.8328 (pttt) REVERT: X 103 HIS cc_start: 0.7491 (t-90) cc_final: 0.7097 (t-90) REVERT: X 124 ASP cc_start: 0.7866 (t0) cc_final: 0.7425 (m-30) REVERT: a 120 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.7672 (t-100) REVERT: a 131 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8098 (tttt) REVERT: e 119 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7236 (ttt90) REVERT: f 41 TRP cc_start: 0.7707 (m100) cc_final: 0.6346 (m-10) REVERT: i 157 MET cc_start: 0.9212 (mtm) cc_final: 0.8964 (mtp) REVERT: i 215 MET cc_start: 0.9176 (tpt) cc_final: 0.8650 (tpt) REVERT: i 244 MET cc_start: 0.8350 (ttm) cc_final: 0.8059 (ttm) REVERT: i 346 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6052 (mp) REVERT: j 4 MET cc_start: 0.7282 (mmm) cc_final: 0.7005 (mmm) REVERT: l 123 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8911 (mt) REVERT: l 197 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7007 (t0) REVERT: l 331 MET cc_start: 0.7999 (mmt) cc_final: 0.7792 (mmt) REVERT: l 351 ASN cc_start: 0.7581 (m-40) cc_final: 0.7304 (m-40) REVERT: l 456 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7360 (ttp-110) REVERT: l 500 LEU cc_start: 0.8290 (mp) cc_final: 0.8073 (mp) REVERT: l 571 MET cc_start: 0.4173 (mtt) cc_final: 0.3626 (mtp) REVERT: m 135 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: n 30 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.6800 (mmm-85) REVERT: p 75 GLN cc_start: 0.7629 (pt0) cc_final: 0.7256 (pt0) REVERT: r 138 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7166 (p0) REVERT: s 55 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8965 (mp) REVERT: v 39 MET cc_start: 0.4474 (OUTLIER) cc_final: 0.3579 (ptt) REVERT: v 51 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6337 (mt) REVERT: v 52 MET cc_start: 0.7336 (mmm) cc_final: 0.6900 (mmm) REVERT: v 68 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7266 (mmtm) REVERT: v 83 GLU cc_start: 0.8138 (mp0) cc_final: 0.7793 (mp0) REVERT: v 104 ARG cc_start: 0.7039 (tmm-80) cc_final: 0.6743 (ttt180) REVERT: w 115 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6078 (mt-10) REVERT: w 147 LEU cc_start: 0.8106 (mm) cc_final: 0.7871 (tp) REVERT: w 173 MET cc_start: 0.7038 (mtp) cc_final: 0.6753 (mtp) REVERT: w 265 ASP cc_start: 0.5346 (p0) cc_final: 0.5039 (p0) outliers start: 259 outliers final: 197 residues processed: 1346 average time/residue: 0.6543 time to fit residues: 1487.1468 Evaluate side-chains 1352 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1131 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 347 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 551 ASP Chi-restraints excluded: chain M residue 590 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 270 ASN Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 376 GLU Chi-restraints excluded: chain Q residue 462 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 68 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 120 TRP Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 143 TYR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 8 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 171 ASN Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 245 MET Chi-restraints excluded: chain i residue 247 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain i residue 346 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 163 ASP Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 419 THR Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 27 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 131 ILE Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 191 SER Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 408 LEU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 55 LEU Chi-restraints excluded: chain s residue 108 MET Chi-restraints excluded: chain s residue 127 TYR Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain s residue 267 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain u residue 158 LEU Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 39 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 60 ILE Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 475 optimal weight: 0.3980 chunk 306 optimal weight: 0.6980 chunk 458 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 488 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 379 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 603 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 454 GLN U 46 ASN ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN i 235 ASN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 ASN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68127 Z= 0.172 Angle : 0.553 14.107 92241 Z= 0.274 Chirality : 0.040 0.402 10053 Planarity : 0.004 0.068 11555 Dihedral : 11.459 176.769 10146 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.65 % Allowed : 19.14 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 8065 helix: 1.57 (0.08), residues: 4262 sheet: -0.19 (0.25), residues: 423 loop : -0.51 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Z 51 HIS 0.005 0.001 HIS w 186 PHE 0.028 0.001 PHE l 335 TYR 0.030 0.001 TYR H 44 ARG 0.012 0.000 ARG T 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1180 time to evaluate : 6.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7448 (t80) REVERT: B 79 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8144 (ptp-170) REVERT: C 67 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: C 142 TYR cc_start: 0.9445 (OUTLIER) cc_final: 0.7925 (t80) REVERT: F 62 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7469 (mt0) REVERT: G 124 ASP cc_start: 0.7048 (p0) cc_final: 0.6833 (m-30) REVERT: G 136 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: I 92 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6737 (tptt) REVERT: J 79 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8350 (tp40) REVERT: J 85 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7713 (ptt180) REVERT: K 77 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: M 84 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8133 (mmtm) REVERT: N 122 GLN cc_start: 0.8097 (mt0) cc_final: 0.7738 (mt0) REVERT: P 183 ASP cc_start: 0.8705 (p0) cc_final: 0.8428 (p0) REVERT: Q 376 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: S 1 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7465 (ttm) REVERT: U 10 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7320 (mmmm) REVERT: V 8 LYS cc_start: 0.5268 (ptmt) cc_final: 0.5027 (ptmm) REVERT: W 52 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7891 (mtpp) REVERT: X 103 HIS cc_start: 0.7491 (t-90) cc_final: 0.7109 (t-90) REVERT: X 110 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7278 (mp) REVERT: X 124 ASP cc_start: 0.7838 (t0) cc_final: 0.7483 (m-30) REVERT: a 120 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7612 (t-100) REVERT: a 131 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7928 (tttt) REVERT: b 113 THR cc_start: 0.6461 (m) cc_final: 0.6260 (m) REVERT: e 115 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7740 (tp40) REVERT: f 41 TRP cc_start: 0.7601 (m100) cc_final: 0.6268 (m-10) REVERT: i 89 MET cc_start: 0.8674 (tpt) cc_final: 0.8138 (tpt) REVERT: i 190 MET cc_start: 0.8640 (mtp) cc_final: 0.8413 (mtp) REVERT: i 215 MET cc_start: 0.9186 (tpt) cc_final: 0.8699 (tpt) REVERT: j 4 MET cc_start: 0.7196 (mmm) cc_final: 0.6914 (mmm) REVERT: l 123 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8890 (mt) REVERT: l 238 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7867 (mm-30) REVERT: l 351 ASN cc_start: 0.7489 (m-40) cc_final: 0.7263 (m-40) REVERT: l 571 MET cc_start: 0.4301 (mtt) cc_final: 0.3761 (mtp) REVERT: m 1 MET cc_start: 0.3317 (tpp) cc_final: 0.3021 (tpt) REVERT: m 135 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: n 30 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7304 (mmt-90) REVERT: n 54 GLU cc_start: 0.6578 (mp0) cc_final: 0.6372 (mp0) REVERT: r 138 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6927 (p0) REVERT: s 55 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8938 (mp) REVERT: s 76 ILE cc_start: 0.8812 (mm) cc_final: 0.8538 (mm) REVERT: s 289 LEU cc_start: 0.8593 (tp) cc_final: 0.8288 (tp) REVERT: v 39 MET cc_start: 0.4330 (ppp) cc_final: 0.3504 (ptt) REVERT: v 51 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6213 (mt) REVERT: v 52 MET cc_start: 0.7143 (mmm) cc_final: 0.6633 (mmm) REVERT: v 68 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7196 (mmtm) REVERT: v 83 GLU cc_start: 0.8162 (mp0) cc_final: 0.7911 (mp0) REVERT: w 147 LEU cc_start: 0.8121 (mm) cc_final: 0.7898 (tp) REVERT: w 173 MET cc_start: 0.7046 (mtp) cc_final: 0.6785 (mtp) REVERT: w 265 ASP cc_start: 0.5473 (p0) cc_final: 0.5150 (p0) REVERT: w 326 ARG cc_start: 0.6271 (ttp80) cc_final: 0.6052 (ttp-170) REVERT: w 353 TRP cc_start: 0.8213 (p-90) cc_final: 0.7955 (p-90) outliers start: 185 outliers final: 132 residues processed: 1298 average time/residue: 0.6683 time to fit residues: 1468.3173 Evaluate side-chains 1292 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1139 time to evaluate : 5.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 590 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 213 ILE Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 376 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 120 TRP Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 143 TYR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 408 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 55 LEU Chi-restraints excluded: chain s residue 127 TYR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 698 optimal weight: 4.9990 chunk 735 optimal weight: 0.9980 chunk 671 optimal weight: 6.9990 chunk 715 optimal weight: 0.6980 chunk 430 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 562 optimal weight: 10.0000 chunk 219 optimal weight: 0.0970 chunk 646 optimal weight: 9.9990 chunk 677 optimal weight: 6.9990 chunk 713 optimal weight: 0.0170 overall best weight: 1.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN Z 33 GLN ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 ASN o 79 ASN o 126 ASN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68127 Z= 0.185 Angle : 0.558 14.003 92241 Z= 0.275 Chirality : 0.040 0.178 10053 Planarity : 0.005 0.061 11555 Dihedral : 11.165 176.269 10146 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 2.53 % Allowed : 19.10 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8065 helix: 1.61 (0.08), residues: 4259 sheet: -0.16 (0.25), residues: 421 loop : -0.45 (0.11), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Z 51 HIS 0.006 0.001 HIS w 186 PHE 0.028 0.001 PHE l 335 TYR 0.023 0.001 TYR J 291 ARG 0.012 0.000 ARG T 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1177 time to evaluate : 5.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 79 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8223 (ptp-170) REVERT: C 67 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8653 (m-80) REVERT: C 142 TYR cc_start: 0.9442 (OUTLIER) cc_final: 0.7884 (t80) REVERT: F 62 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7491 (mt0) REVERT: G 124 ASP cc_start: 0.7051 (p0) cc_final: 0.6827 (m-30) REVERT: G 136 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: I 92 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6845 (tptt) REVERT: J 79 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8357 (tp40) REVERT: J 85 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7709 (ptt180) REVERT: K 77 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: L 148 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: M 84 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8113 (mmtm) REVERT: P 183 ASP cc_start: 0.8686 (p0) cc_final: 0.8419 (p0) REVERT: Q 52 MET cc_start: 0.4337 (tpt) cc_final: 0.4095 (tpt) REVERT: Q 246 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8191 (mm-30) REVERT: Q 376 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: S 1 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7543 (ttm) REVERT: V 8 LYS cc_start: 0.5092 (ptmt) cc_final: 0.4878 (ptmm) REVERT: W 52 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7902 (mtpp) REVERT: X 103 HIS cc_start: 0.7475 (t-90) cc_final: 0.7111 (t-90) REVERT: X 110 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7288 (mp) REVERT: X 124 ASP cc_start: 0.7880 (t0) cc_final: 0.7530 (m-30) REVERT: a 120 TRP cc_start: 0.7871 (OUTLIER) cc_final: 0.7615 (t-100) REVERT: a 131 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7971 (tttt) REVERT: f 41 TRP cc_start: 0.7584 (m100) cc_final: 0.6278 (m-10) REVERT: i 89 MET cc_start: 0.8761 (tpt) cc_final: 0.8197 (tpt) REVERT: i 190 MET cc_start: 0.8714 (mtp) cc_final: 0.8447 (mtp) REVERT: i 215 MET cc_start: 0.9228 (tpt) cc_final: 0.8743 (tpt) REVERT: j 4 MET cc_start: 0.7190 (mmm) cc_final: 0.6944 (mmm) REVERT: l 123 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8890 (mt) REVERT: l 238 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7831 (mm-30) REVERT: l 351 ASN cc_start: 0.7484 (m-40) cc_final: 0.7280 (m-40) REVERT: l 500 LEU cc_start: 0.8201 (mp) cc_final: 0.7992 (mp) REVERT: l 571 MET cc_start: 0.4337 (mtt) cc_final: 0.3780 (mtp) REVERT: m 135 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: m 170 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8126 (mm-30) REVERT: n 30 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6836 (mmm-85) REVERT: r 138 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.7049 (p0) REVERT: s 55 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8939 (mp) REVERT: s 222 MET cc_start: 0.8126 (mmp) cc_final: 0.7861 (mtp) REVERT: s 277 TYR cc_start: 0.8816 (m-80) cc_final: 0.8420 (m-80) REVERT: v 4 HIS cc_start: 0.6950 (p90) cc_final: 0.6750 (p90) REVERT: v 16 GLU cc_start: 0.5246 (mp0) cc_final: 0.4695 (tt0) REVERT: v 39 MET cc_start: 0.4338 (OUTLIER) cc_final: 0.3587 (ptt) REVERT: v 51 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6197 (mt) REVERT: v 52 MET cc_start: 0.7158 (mmm) cc_final: 0.6568 (mmm) REVERT: v 68 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7191 (mmtm) REVERT: v 83 GLU cc_start: 0.8167 (mp0) cc_final: 0.7897 (mp0) REVERT: w 147 LEU cc_start: 0.8114 (mm) cc_final: 0.7890 (tp) REVERT: w 173 MET cc_start: 0.7037 (mtp) cc_final: 0.6777 (mtp) REVERT: w 241 TYR cc_start: 0.5598 (OUTLIER) cc_final: 0.4347 (m-80) REVERT: w 265 ASP cc_start: 0.5383 (p0) cc_final: 0.5080 (p0) REVERT: w 326 ARG cc_start: 0.6294 (ttp80) cc_final: 0.6053 (ttp-170) REVERT: w 353 TRP cc_start: 0.8239 (p-90) cc_final: 0.7931 (p-90) outliers start: 177 outliers final: 141 residues processed: 1289 average time/residue: 0.6436 time to fit residues: 1402.2259 Evaluate side-chains 1309 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1146 time to evaluate : 7.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 590 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 376 GLU Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 120 TRP Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 143 TYR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 131 ILE Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 55 LEU Chi-restraints excluded: chain s residue 127 TYR Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain s residue 172 ILE Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 158 LEU Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 39 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 470 optimal weight: 4.9990 chunk 756 optimal weight: 7.9990 chunk 462 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 526 optimal weight: 0.9990 chunk 794 optimal weight: 2.9990 chunk 730 optimal weight: 4.9990 chunk 632 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 488 optimal weight: 5.9990 chunk 387 optimal weight: 0.0770 overall best weight: 1.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN Q 67 ASN ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 GLN e 148 GLN l 109 HIS ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 ASN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 68127 Z= 0.217 Angle : 0.576 15.578 92241 Z= 0.283 Chirality : 0.041 0.199 10053 Planarity : 0.005 0.061 11555 Dihedral : 11.088 176.366 10146 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 2.69 % Allowed : 18.93 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8065 helix: 1.59 (0.08), residues: 4253 sheet: -0.11 (0.25), residues: 419 loop : -0.49 (0.11), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Z 51 HIS 0.007 0.001 HIS w 186 PHE 0.028 0.001 PHE l 335 TYR 0.021 0.001 TYR l 422 ARG 0.011 0.000 ARG T 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1149 time to evaluate : 5.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7639 (t80) REVERT: B 79 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8428 (ptp-170) REVERT: C 67 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: C 142 TYR cc_start: 0.9450 (OUTLIER) cc_final: 0.7896 (t80) REVERT: F 62 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: G 124 ASP cc_start: 0.6993 (p0) cc_final: 0.6753 (m-30) REVERT: G 136 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: I 92 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6756 (tptt) REVERT: J 79 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: J 85 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7765 (ptt180) REVERT: K 77 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: L 148 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: M 84 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8110 (mmtm) REVERT: P 183 ASP cc_start: 0.8691 (p0) cc_final: 0.8411 (p0) REVERT: Q 52 MET cc_start: 0.4535 (tpt) cc_final: 0.4245 (tpt) REVERT: Q 246 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8221 (mm-30) REVERT: Q 376 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: S 1 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7559 (ttm) REVERT: V 8 LYS cc_start: 0.5232 (ptmt) cc_final: 0.4969 (ptmm) REVERT: W 52 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7913 (mtpp) REVERT: X 103 HIS cc_start: 0.7498 (t-90) cc_final: 0.7121 (t-90) REVERT: X 124 ASP cc_start: 0.7912 (t0) cc_final: 0.7562 (m-30) REVERT: X 155 TYR cc_start: 0.3946 (m-80) cc_final: 0.2545 (m-80) REVERT: a 120 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.7630 (t-100) REVERT: a 131 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7980 (tttt) REVERT: f 41 TRP cc_start: 0.7564 (m100) cc_final: 0.6271 (m-10) REVERT: i 89 MET cc_start: 0.8758 (tpt) cc_final: 0.8301 (tpt) REVERT: i 215 MET cc_start: 0.9235 (tpt) cc_final: 0.8757 (tpt) REVERT: j 4 MET cc_start: 0.7218 (mmm) cc_final: 0.6983 (mmm) REVERT: l 123 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8896 (mt) REVERT: l 197 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7004 (t70) REVERT: l 238 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7849 (mm-30) REVERT: l 384 PRO cc_start: 0.8136 (Cg_exo) cc_final: 0.7927 (Cg_endo) REVERT: l 571 MET cc_start: 0.4373 (mtt) cc_final: 0.3777 (mtp) REVERT: m 135 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: m 173 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6434 (ttm170) REVERT: n 30 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.6915 (mmm-85) REVERT: p 75 GLN cc_start: 0.7350 (pt0) cc_final: 0.7081 (pt0) REVERT: r 138 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.7084 (p0) REVERT: s 55 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8942 (mp) REVERT: s 277 TYR cc_start: 0.8855 (m-80) cc_final: 0.8440 (m-80) REVERT: v 16 GLU cc_start: 0.5433 (mp0) cc_final: 0.4884 (mt-10) REVERT: v 39 MET cc_start: 0.4558 (ppp) cc_final: 0.3835 (ptt) REVERT: v 51 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6194 (mt) REVERT: v 52 MET cc_start: 0.7176 (mmm) cc_final: 0.6784 (mmm) REVERT: v 68 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7104 (mmtm) REVERT: v 83 GLU cc_start: 0.8183 (mp0) cc_final: 0.7920 (mp0) REVERT: w 147 LEU cc_start: 0.8107 (mm) cc_final: 0.7903 (tp) REVERT: w 173 MET cc_start: 0.7002 (mtp) cc_final: 0.6731 (mtp) REVERT: w 241 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.4525 (m-80) REVERT: w 265 ASP cc_start: 0.5462 (p0) cc_final: 0.5125 (p0) REVERT: w 326 ARG cc_start: 0.6316 (ttp80) cc_final: 0.6064 (ttp-170) REVERT: w 353 TRP cc_start: 0.8237 (p-90) cc_final: 0.7871 (p-90) outliers start: 188 outliers final: 145 residues processed: 1267 average time/residue: 0.6425 time to fit residues: 1379.9424 Evaluate side-chains 1298 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1131 time to evaluate : 5.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 238 GLN Chi-restraints excluded: chain J residue 327 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 355 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 590 THR Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 260 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 376 GLU Chi-restraints excluded: chain Q residue 435 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 120 TRP Chi-restraints excluded: chain a residue 131 LYS Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 143 TYR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 65 ASP Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain g residue 115 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 86 ILE Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 339 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain l residue 301 ILE Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 338 MET Chi-restraints excluded: chain l residue 342 CYS Chi-restraints excluded: chain l residue 359 MET Chi-restraints excluded: chain l residue 369 THR Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 440 LEU Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 131 ILE Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 266 MET Chi-restraints excluded: chain r residue 313 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 400 MET Chi-restraints excluded: chain r residue 408 LEU Chi-restraints excluded: chain r residue 410 MET Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 55 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 127 TYR Chi-restraints excluded: chain s residue 145 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 158 LEU Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 77 ILE Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 332 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 502 optimal weight: 0.9990 chunk 673 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 582 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 633 optimal weight: 0.0030 chunk 265 optimal weight: 9.9990 chunk 650 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 109 HIS ** l 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120795 restraints weight = 93871.654| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.69 r_work: 0.3090 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 68127 Z= 0.249 Angle : 0.630 59.200 92241 Z= 0.325 Chirality : 0.042 0.612 10053 Planarity : 0.005 0.061 11555 Dihedral : 11.088 176.364 10146 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 2.59 % Allowed : 19.18 % Favored : 78.23 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8065 helix: 1.59 (0.08), residues: 4253 sheet: -0.11 (0.25), residues: 419 loop : -0.48 (0.11), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Z 51 HIS 0.006 0.001 HIS w 186 PHE 0.047 0.001 PHE w 245 TYR 0.021 0.001 TYR l 422 ARG 0.013 0.000 ARG v 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20664.03 seconds wall clock time: 360 minutes 57.69 seconds (21657.69 seconds total)