Starting phenix.real_space_refine on Sat Mar 23 18:41:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enj_3899/03_2024/6enj_3899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enj_3899/03_2024/6enj_3899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enj_3899/03_2024/6enj_3899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enj_3899/03_2024/6enj_3899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enj_3899/03_2024/6enj_3899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enj_3899/03_2024/6enj_3899_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 4693 5.49 5 S 154 5.16 5 C 73978 2.51 5 N 27394 2.21 5 O 40892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "b TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147111 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 61641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2871, 61641 Classifications: {'RNA': 2871} Modifications used: {'p5*END': 1, 'rna2p_pur': 233, 'rna2p_pyr': 99, 'rna3p_pur': 1426, 'rna3p_pyr': 1113} Link IDs: {'rna2p': 332, 'rna3p': 2538} Chain breaks: 2 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 52} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 637 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p_pur': 103, 'rna2p_pyr': 50, 'rna3p_pur': 771, 'rna3p_pyr': 615} Link IDs: {'rna2p': 153, 'rna3p': 1385} Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "w" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1461 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'CIS': 8, 'PTRANS': 8, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KEO:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "x" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 61} Chain: "7" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1663 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 6 Chain: "9" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1653 Classifications: {'RNA': 77, 'peptide': 1} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 14, 'rna3p': 62, None: 1} Not linked: pdbres=" A 9 76 " pdbres="PRO 9 101 " Time building chain proxies: 57.57, per 1000 atoms: 0.39 Number of scatterers: 147111 At special positions: 0 Unit cell: (267.748, 278.588, 220.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 4693 15.00 O 40892 8.00 N 27394 7.00 C 73978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " 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=0, symmetry=0 Time building additional restraints: 55.47 Conformation dependent library (CDL) restraints added in 6.9 seconds 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10918 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 170 helices and 71 sheets defined 36.2% alpha, 16.9% beta 1085 base pairs and 2697 stacking pairs defined. Time for finding SS restraints: 72.76 Creating SS restraints... Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.811A pdb=" N ARG C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 16' Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.045A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 4.321A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.937A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.149A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.733A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.717A pdb=" N HIS C 199 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.526A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.555A pdb=" N TRP D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 4.326A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 101 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.624A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.670A pdb=" N LEU E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.538A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.575A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 162' Processing helix chain 'E' and resid 176 through 182 removed outlier: 3.567A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 182' Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.802A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.505A pdb=" N ARG E 21 " --> pdb=" O GLU E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 16 through 21' Processing helix chain 'F' and resid 1 through 20 removed outlier: 3.973A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.457A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 59 " --> pdb=" O ASP F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.649A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.768A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.581A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Proline residue: F 138 - end of helix No H-bonds generated for 'chain 'F' and resid 133 through 138' Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.455A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.975A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 65 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.699A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.576A pdb=" N ALA J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.506A pdb=" N ILE J 93 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.669A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.900A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.617A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.647A pdb=" N SER K 109 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.643A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.180A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.754A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.177A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 6.354A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.509A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.526A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 31 removed outlier: 3.682A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.502A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 5.120A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.280A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 81 removed outlier: 3.525A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 88 removed outlier: 3.740A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 3.525A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.571A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 63' Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.663A pdb=" N ALA O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.512A pdb=" N ARG O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 3.844A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.781A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.846A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.519A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 30' Processing helix chain 'Q' and resid 38 through 60 removed outlier: 3.505A pdb=" N ASP Q 48 " --> pdb=" O TYR Q 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.652A pdb=" N ARG Q 69 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 4.019A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY Q 81 " --> pdb=" O LYS Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.648A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 3.589A pdb=" N THR Q 106 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.996A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.565A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.637A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 11 removed outlier: 4.315A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 4.165A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.561A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.817A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 4.287A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.060A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.473A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.605A pdb=" N MET X 55 " --> pdb=" O SER X 51 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 removed outlier: 3.667A pdb=" N LEU X 67 " --> pdb=" O ILE X 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA X 68 " --> pdb=" O ASP X 64 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA X 72 " --> pdb=" O ALA X 68 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.387A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 5.903A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.904A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.507A pdb=" N LEU Z 23 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.821A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 18 removed outlier: 3.621A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 removed outlier: 3.655A pdb=" N ARG 2 12 " --> pdb=" O SER 2 8 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 24 removed outlier: 4.921A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.522A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.646A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 45 removed outlier: 3.530A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.864A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '6' and resid 43 through 54 removed outlier: 4.160A pdb=" N LYS 6 47 " --> pdb=" O PHE 6 43 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG 6 49 " --> pdb=" O THR 6 45 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL 6 51 " --> pdb=" O LYS 6 47 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 43 through 54' Processing helix chain '6' and resid 56 through 65 removed outlier: 3.564A pdb=" N PHE 6 60 " --> pdb=" O ARG 6 56 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN 6 65 " --> pdb=" O ASN 6 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix removed outlier: 3.565A pdb=" N GLU b 51 " --> pdb=" O PRO b 47 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA b 60 " --> pdb=" O LEU b 56 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER b 61 " --> pdb=" O ASN b 57 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS b 63 " --> pdb=" O ILE b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 87 removed outlier: 6.795A pdb=" N SER b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA b 83 " --> pdb=" O VAL b 79 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.885A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN b 119 " --> pdb=" O ASP b 115 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.903A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 removed outlier: 3.802A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.928A pdb=" N ALA b 175 " --> pdb=" O ALA b 171 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 4.307A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU b 211 " --> pdb=" O ARG b 207 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU b 213 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR b 219 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 12 removed outlier: 3.644A pdb=" N ILE c 9 " --> pdb=" O HIS c 5 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU c 11 " --> pdb=" O ASN c 7 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLY c 12 " --> pdb=" O GLY c 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 5 through 12' Processing helix chain 'c' and resid 24 through 47 removed outlier: 5.009A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN c 31 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU c 32 " --> pdb=" O PHE c 28 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS c 44 " --> pdb=" O GLN c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.812A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 5.390A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.761A pdb=" N ALA c 116 " --> pdb=" O ALA c 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN c 122 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU c 124 " --> pdb=" O THR c 120 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.938A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.704A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG d 13 " --> pdb=" O LYS d 9 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.961A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR d 64 " --> pdb=" O VAL d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.530A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR d 74 " --> pdb=" O GLN d 70 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU d 77 " --> pdb=" O ASN d 73 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 5.327A pdb=" N ASN d 88 " --> pdb=" O ASN d 84 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU d 89 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA d 91 " --> pdb=" O GLU d 87 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU d 92 " --> pdb=" O ASN d 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 removed outlier: 3.746A pdb=" N VAL d 101 " --> pdb=" O LEU d 97 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR d 102 " --> pdb=" O ASP d 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET d 104 " --> pdb=" O VAL d 100 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY d 105 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 120 removed outlier: 3.506A pdb=" N LEU d 116 " --> pdb=" O GLU d 112 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER d 118 " --> pdb=" O ARG d 114 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N HIS d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 164 removed outlier: 4.943A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 3.866A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 4.136A pdb=" N LEU d 190 " --> pdb=" O ARG d 187 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER d 191 " --> pdb=" O SER d 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.534A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN e 69 " --> pdb=" O LYS e 65 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.742A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 156 removed outlier: 3.678A pdb=" N VAL e 136 " --> pdb=" O PRO e 132 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP e 141 " --> pdb=" O ARG e 137 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN e 147 " --> pdb=" O LEU e 143 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Proline residue: e 149 - end of helix removed outlier: 3.689A pdb=" N VAL e 152 " --> pdb=" O SER e 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS e 155 " --> pdb=" O MET e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.653A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 159 through 165' Processing helix chain 'f' and resid 15 through 33 Proline residue: f 19 - end of helix removed outlier: 3.871A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.551A pdb=" N ASP f 72 " --> pdb=" O GLN f 68 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR f 76 " --> pdb=" O ASP f 72 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.513A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET g 30 " --> pdb=" O VAL g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.575A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER g 40 " --> pdb=" O SER g 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL g 42 " --> pdb=" O ALA g 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU g 47 " --> pdb=" O TYR g 43 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA g 50 " --> pdb=" O LEU g 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.567A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU g 65 " --> pdb=" O PHE g 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.060A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG g 101 " --> pdb=" O ALA g 97 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.942A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU g 123 " --> pdb=" O LEU g 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA g 127 " --> pdb=" O LEU g 123 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN g 129 " --> pdb=" O ASP g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 147 removed outlier: 4.212A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL g 140 " --> pdb=" O LYS g 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET g 143 " --> pdb=" O ASP g 139 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 removed outlier: 3.718A pdb=" N VAL h 33 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU h 41 " --> pdb=" O ASN h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.817A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 38 removed outlier: 3.683A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 45 through 53 Proline residue: i 50 - end of helix removed outlier: 4.940A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.791A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 101 removed outlier: 5.040A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 32 removed outlier: 3.816A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU j 27 " --> pdb=" O ALA j 23 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.977A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.516A pdb=" N SER k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.348A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 73 removed outlier: 3.795A pdb=" N GLN k 63 " --> pdb=" O PRO k 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 5.812A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA k 101 " --> pdb=" O ARG k 97 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 removed outlier: 3.726A pdb=" N LEU l 6 " --> pdb=" O THR l 2 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL l 7 " --> pdb=" O VAL l 3 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG l 8 " --> pdb=" O ASN l 4 " (cutoff:3.500A) Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.100A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 3.570A pdb=" N LEU m 18 " --> pdb=" O ALA m 14 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 4.350A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA m 35 " --> pdb=" O ALA m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 63 removed outlier: 3.570A pdb=" N ILE m 52 " --> pdb=" O SER m 48 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL m 59 " --> pdb=" O LEU m 55 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA m 60 " --> pdb=" O ARG m 56 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 48 through 63' Processing helix chain 'm' and resid 65 through 83 removed outlier: 4.300A pdb=" N ARG m 69 " --> pdb=" O GLU m 65 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG m 70 " --> pdb=" O GLY m 66 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER m 75 " --> pdb=" O GLU m 71 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU m 79 " --> pdb=" O SER m 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP m 81 " --> pdb=" O LYS m 77 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 removed outlier: 3.515A pdb=" N ARG m 89 " --> pdb=" O TYR m 85 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS m 90 " --> pdb=" O ARG m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 removed outlier: 3.677A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS n 18 " --> pdb=" O ALA n 14 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR n 19 " --> pdb=" O LEU n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 29 removed outlier: 3.741A pdb=" N ALA n 28 " --> pdb=" O ALA n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 52 removed outlier: 3.604A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA n 44 " --> pdb=" O ASP n 40 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS n 47 " --> pdb=" O ASN n 43 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.156A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.719A pdb=" N VAL n 84 " --> pdb=" O SER n 80 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA n 87 " --> pdb=" O LYS n 83 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 14 removed outlier: 3.604A pdb=" N LYS o 9 " --> pdb=" O GLU o 5 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 46 removed outlier: 3.761A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE o 42 " --> pdb=" O LEU o 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA o 43 " --> pdb=" O GLN o 39 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS o 45 " --> pdb=" O HIS o 41 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS o 46 " --> pdb=" O PHE o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 73 removed outlier: 4.455A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER o 60 " --> pdb=" O LEU o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.667A pdb=" N LEU o 80 " --> pdb=" O ARG o 76 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU o 82 " --> pdb=" O THR o 78 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY o 85 " --> pdb=" O ILE o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 64 removed outlier: 5.192A pdb=" N ALA p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY p 62 " --> pdb=" O ALA p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.585A pdb=" N ALA p 72 " --> pdb=" O SER p 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU p 77 " --> pdb=" O ALA p 73 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 4.035A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLY r 16 " --> pdb=" O PHE r 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 11 through 16' Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.722A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 4.153A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY r 45 " --> pdb=" O SER r 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 40 through 45' Processing helix chain 'r' and resid 48 through 65 removed outlier: 4.041A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG r 56 " --> pdb=" O ARG r 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU r 64 " --> pdb=" O ARG r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 25 removed outlier: 3.668A pdb=" N LEU s 15 " --> pdb=" O ASP s 11 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER s 24 " --> pdb=" O LYS s 20 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.748A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 41 removed outlier: 4.877A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG t 23 " --> pdb=" O HIS t 19 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET t 26 " --> pdb=" O SER t 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE t 31 " --> pdb=" O MET t 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS t 33 " --> pdb=" O THR t 29 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR t 35 " --> pdb=" O ILE t 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE t 38 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 removed outlier: 3.505A pdb=" N ALA t 46 " --> pdb=" O ASP t 42 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN t 47 " --> pdb=" O LYS t 43 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS t 48 " --> pdb=" O ALA t 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN t 51 " --> pdb=" O GLN t 47 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU t 52 " --> pdb=" O LYS t 48 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.548A pdb=" N ASP t 58 " --> pdb=" O GLN t 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG t 59 " --> pdb=" O PRO t 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN t 60 " --> pdb=" O ILE t 56 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA t 61 " --> pdb=" O VAL t 57 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS t 63 " --> pdb=" O ARG t 59 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 6.170A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR t 79 " --> pdb=" O LYS t 75 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.587A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 33 removed outlier: 4.519A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 26 through 33' Processing helix chain 'u' and resid 38 through 61 removed outlier: 3.614A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG u 44 " --> pdb=" O PRO u 40 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG u 54 " --> pdb=" O SER u 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS u 57 " --> pdb=" O LYS u 53 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS u 58 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG u 61 " --> pdb=" O LYS u 57 " (cutoff:3.500A) Processing helix chain 'w' and resid 5 through 10 removed outlier: 3.541A pdb=" N PHE w 9 " --> pdb=" O TYR w 5 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG w 10 " --> pdb=" O SER w 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 5 through 10' Processing helix chain 'w' and resid 96 through 101 removed outlier: 3.664A pdb=" N ILE w 100 " --> pdb=" O ASP w 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY w 101 " --> pdb=" O ALA w 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 96 through 101' Processing helix chain '7' and resid 7 through 16 removed outlier: 5.260A pdb=" N ILE 7 11 " --> pdb=" O ARG 7 7 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG 7 12 " --> pdb=" O MET 7 8 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU 7 13 " --> pdb=" O ARG 7 9 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS 7 14 " --> pdb=" O VAL 7 10 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL 7 15 " --> pdb=" O ILE 7 11 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP 7 16 " --> pdb=" O ARG 7 12 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 7 through 16' Processing helix chain '7' and resid 25 through 30 removed outlier: 4.267A pdb=" N LEU 7 29 " --> pdb=" O GLU 7 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 7 30 " --> pdb=" O ALA 7 26 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 25 through 30' Processing helix chain '7' and resid 81 through 91 removed outlier: 4.190A pdb=" N GLU 7 85 " --> pdb=" O GLY 7 81 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS 7 88 " --> pdb=" O ALA 7 84 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA 7 89 " --> pdb=" O GLU 7 85 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA 7 90 " --> pdb=" O ALA 7 86 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY 7 91 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 107 removed outlier: 4.006A pdb=" N ALA 7 101 " --> pdb=" O MET 7 97 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP 7 102 " --> pdb=" O GLU 7 98 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN 7 103 " --> pdb=" O ASP 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 120 through 126 removed outlier: 4.164A pdb=" N VAL 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN 7 126 " --> pdb=" O ARG 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 129 through 136 Proline residue: 7 133 - end of helix Processing helix chain '7' and resid 149 through 160 removed outlier: 5.123A pdb=" N LYS 7 154 " --> pdb=" O ALA 7 150 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA 7 158 " --> pdb=" O LYS 7 154 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY 7 159 " --> pdb=" O ASN 7 155 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 201 removed outlier: 3.514A pdb=" N GLU 7 187 " --> pdb=" O ASP 7 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN 7 188 " --> pdb=" O LYS 7 184 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL 7 194 " --> pdb=" O GLU 7 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA 7 195 " --> pdb=" O ALA 7 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 7 196 " --> pdb=" O LEU 7 192 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS 7 200 " --> pdb=" O LEU 7 196 " (cutoff:3.500A) Proline residue: 7 201 - end of helix Processing sheet with id= 1, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.529A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.387A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 163 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 90 through 96 removed outlier: 4.907A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.338A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.501A pdb=" N ILE D 14 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE D 22 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 32 through 35 removed outlier: 4.362A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 47 through 51 Processing sheet with id= 8, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.795A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 64 through 67 removed outlier: 3.745A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 21 through 26 removed outlier: 6.038A pdb=" N GLN G 21 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 93 through 98 removed outlier: 7.476A pdb=" N ASN G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.462A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS G 85 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 14, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 15, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.925A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 17, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.675A pdb=" N ARG K 71 " --> pdb=" O SER K 75 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU M 104 " --> pdb=" O TRP M 64 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.648A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY M 32 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.493A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.665A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA O 37 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'P' and resid 37 through 44 removed outlier: 3.614A pdb=" N VAL P 29 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.895A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.850A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.566A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 57 through 60 removed outlier: 5.060A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.076A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 4 through 8 Processing sheet with id= 29, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.647A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU T 32 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG T 77 " --> pdb=" O LYS T 66 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'U' and resid 39 through 44 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'V' and resid 27 through 32 removed outlier: 3.951A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'V' and resid 39 through 42 removed outlier: 6.325A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'W' and resid 45 through 48 Processing sheet with id= 34, first strand: chain 'W' and resid 50 through 54 removed outlier: 6.935A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.579A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'X' and resid 34 through 38 Processing sheet with id= 37, first strand: chain 'Z' and resid 33 through 38 removed outlier: 4.457A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '0' and resid 27 through 30 removed outlier: 5.921A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '1' and resid 19 through 23 removed outlier: 3.780A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '3' and resid 21 through 24 No H-bonds generated for sheet with id= 40 Processing sheet with id= 41, first strand: chain '4' and resid 14 through 19 removed outlier: 6.490A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN 4 37 " --> pdb=" O ILE 4 23 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '6' and resid 12 through 15 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'b' and resid 30 through 33 removed outlier: 4.430A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 88 through 91 removed outlier: 3.802A pdb=" N LEU b 67 " --> pdb=" O ALA b 159 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 52 through 58 removed outlier: 3.549A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL c 65 " --> pdb=" O GLN c 99 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 163 through 169 removed outlier: 3.626A pdb=" N ARG c 163 " --> pdb=" O GLY c 154 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'd' and resid 140 through 143 removed outlier: 5.745A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'e' and resid 11 through 15 removed outlier: 3.944A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS e 13 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 92 through 97 removed outlier: 3.809A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.808A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 39 through 42 removed outlier: 4.121A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL f 7 " --> pdb=" O MET f 88 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 53, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.707A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 73 through 76 removed outlier: 4.911A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 4 through 10 removed outlier: 3.657A pdb=" N GLY i 7 " --> pdb=" O VAL i 18 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL i 18 " --> pdb=" O GLY i 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG i 17 " --> pdb=" O THR i 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR i 65 " --> pdb=" O ARG i 17 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 35 through 38 removed outlier: 8.259A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG j 37 " --> pdb=" O ASP j 75 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP j 75 " --> pdb=" O ARG j 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.873A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE j 67 " --> pdb=" O GLU j 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 59, first strand: chain 'l' and resid 35 through 38 removed outlier: 4.779A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 80 through 84 removed outlier: 4.807A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG l 93 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 6 through 10 removed outlier: 3.576A pdb=" N ILE q 60 " --> pdb=" O LEU q 7 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'q' and resid 19 through 29 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 's' and resid 29 through 33 removed outlier: 3.939A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'w' and resid 26 through 31 removed outlier: 3.880A pdb=" N ALA w 26 " --> pdb=" O LYS w 42 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU w 28 " --> pdb=" O ARG w 40 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG w 40 " --> pdb=" O GLU w 28 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'w' and resid 68 through 72 removed outlier: 4.351A pdb=" N VAL w 68 " --> pdb=" O LEU w 117 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET w 70 " --> pdb=" O VAL w 115 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL w 115 " --> pdb=" O MET w 70 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS w 113 " --> pdb=" O LEU w 72 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER w 124 " --> pdb=" O THR w 116 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'w' and resid 81 through 86 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'w' and resid 130 through 134 removed outlier: 3.525A pdb=" N VAL w 131 " --> pdb=" O VAL w 176 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'w' and resid 152 through 156 removed outlier: 4.318A pdb=" N ALA w 160 " --> pdb=" O LEU w 156 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '7' and resid 60 through 64 removed outlier: 4.166A pdb=" N GLY 7 61 " --> pdb=" O ARG 7 164 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR 7 63 " --> pdb=" O ARG 7 162 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG 7 162 " --> pdb=" O THR 7 63 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '7' and resid 75 through 79 removed outlier: 3.572A pdb=" N ALA 7 76 " --> pdb=" O VAL 7 113 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '7' and resid 170 through 177 removed outlier: 5.734A pdb=" N VAL 7 212 " --> pdb=" O ASN 7 47 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER 7 213 " --> pdb=" O ASP 7 225 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA 7 223 " --> pdb=" O SER 7 215 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR 7 217 " --> pdb=" O GLY 7 221 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLY 7 221 " --> pdb=" O THR 7 217 " (cutoff:3.500A) 1231 hydrogen bonds defined for protein. 3642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2615 hydrogen bonds 4184 hydrogen bond angles 0 basepair planarities 1085 basepair parallelities 2697 stacking parallelities Total time for adding SS restraints: 241.81 Time building geometry restraints manager: 60.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.34: 33159 1.34 - 1.58: 117000 1.58 - 1.81: 9649 1.81 - 2.05: 3 2.05 - 2.28: 1 Bond restraints: 159812 Sorted by residual: bond pdb=" O3' G x 40 " pdb=" P A x 41 " ideal model delta sigma weight residual 1.607 2.283 -0.676 1.50e-02 4.44e+03 2.03e+03 bond pdb=" C THR W 10 " pdb=" N ARG W 11 " ideal model delta sigma weight residual 1.334 1.105 0.229 1.49e-02 4.50e+03 2.36e+02 bond pdb=" C3' A 9 76 " pdb=" O3' A 9 76 " ideal model delta sigma weight residual 1.417 1.269 0.148 1.50e-02 4.44e+03 9.74e+01 bond pdb=" O3' G A2252 " pdb=" P G A2253 " ideal model delta sigma weight residual 1.607 1.468 0.139 1.50e-02 4.44e+03 8.53e+01 bond pdb=" C3' G A2252 " pdb=" O3' G A2252 " ideal model delta sigma weight residual 1.417 1.337 0.080 1.50e-02 4.44e+03 2.85e+01 ... (remaining 159807 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.91: 9104 102.91 - 111.23: 87263 111.23 - 119.55: 68260 119.55 - 127.87: 66279 127.87 - 136.19: 8110 Bond angle restraints: 239016 Sorted by residual: angle pdb=" O3' G A2252 " pdb=" C3' G A2252 " pdb=" C2' G A2252 " ideal model delta sigma weight residual 113.70 94.59 19.11 1.50e+00 4.44e-01 1.62e+02 angle pdb=" O3' A 9 76 " pdb=" C3' A 9 76 " pdb=" C2' A 9 76 " ideal model delta sigma weight residual 113.70 97.58 16.12 1.50e+00 4.44e-01 1.15e+02 angle pdb=" C3' G A2252 " pdb=" C2' G A2252 " pdb=" O2' G A2252 " ideal model delta sigma weight residual 110.70 124.29 -13.59 1.50e+00 4.44e-01 8.20e+01 angle pdb=" O2' G A2251 " pdb=" C2' G A2251 " pdb=" C1' G A2251 " ideal model delta sigma weight residual 108.40 96.61 11.79 1.50e+00 4.44e-01 6.18e+01 angle pdb=" O3' G A2251 " pdb=" C3' G A2251 " pdb=" C2' G A2251 " ideal model delta sigma weight residual 113.70 124.19 -10.49 1.50e+00 4.44e-01 4.89e+01 ... (remaining 239011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 90483 35.77 - 71.54: 10549 71.54 - 107.32: 1290 107.32 - 143.09: 14 143.09 - 178.86: 44 Dihedral angle restraints: 102380 sinusoidal: 85452 harmonic: 16928 Sorted by residual: dihedral pdb=" CA THR q 69 " pdb=" C THR q 69 " pdb=" N LYS q 70 " pdb=" CA LYS q 70 " ideal model delta harmonic sigma weight residual -180.00 -111.74 -68.26 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA ALA m 4 " pdb=" C ALA m 4 " pdb=" N GLY m 5 " pdb=" CA GLY m 5 " ideal model delta harmonic sigma weight residual -180.00 -121.77 -58.23 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" C4' A x 73 " pdb=" C3' A x 73 " pdb=" C2' A x 73 " pdb=" C1' A x 73 " ideal model delta sinusoidal sigma weight residual -35.00 35.87 -70.87 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 102377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 29386 0.080 - 0.159: 1038 0.159 - 0.239: 89 0.239 - 0.319: 26 0.319 - 0.398: 8 Chirality restraints: 30547 Sorted by residual: chirality pdb=" C1' G A2251 " pdb=" O4' G A2251 " pdb=" C2' G A2251 " pdb=" N9 G A2251 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C3' G x 2 " pdb=" C4' G x 2 " pdb=" O3' G x 2 " pdb=" C2' G x 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C3' G a1432 " pdb=" C4' G a1432 " pdb=" O3' G a1432 " pdb=" C2' G a1432 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 30544 not shown) Planarity restraints: 12841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A2252 " 0.144 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" N9 G A2252 " -0.098 2.00e-02 2.50e+03 pdb=" C8 G A2252 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G A2252 " -0.052 2.00e-02 2.50e+03 pdb=" C5 G A2252 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A2252 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A2252 " 0.063 2.00e-02 2.50e+03 pdb=" N1 G A2252 " 0.025 2.00e-02 2.50e+03 pdb=" C2 G A2252 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A2252 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A2252 " -0.071 2.00e-02 2.50e+03 pdb=" C4 G A2252 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2251 " 0.119 2.00e-02 2.50e+03 4.88e-02 7.15e+01 pdb=" N9 G A2251 " -0.089 2.00e-02 2.50e+03 pdb=" C8 G A2251 " -0.014 2.00e-02 2.50e+03 pdb=" N7 G A2251 " -0.034 2.00e-02 2.50e+03 pdb=" C5 G A2251 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A2251 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G A2251 " 0.050 2.00e-02 2.50e+03 pdb=" N1 G A2251 " 0.017 2.00e-02 2.50e+03 pdb=" C2 G A2251 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A2251 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G A2251 " -0.049 2.00e-02 2.50e+03 pdb=" C4 G A2251 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C x 71 " 0.026 2.00e-02 2.50e+03 2.21e-02 1.10e+01 pdb=" N1 C x 71 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C x 71 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C x 71 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C x 71 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C x 71 " -0.044 2.00e-02 2.50e+03 pdb=" N4 C x 71 " 0.035 2.00e-02 2.50e+03 pdb=" C5 C x 71 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C x 71 " 0.004 2.00e-02 2.50e+03 ... (remaining 12838 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 10 1.97 - 2.70: 8056 2.70 - 3.43: 180988 3.43 - 4.17: 462993 4.17 - 4.90: 641803 Nonbonded interactions: 1293850 Sorted by model distance: nonbonded pdb=" O3' A 9 76 " pdb=" C PRO 9 101 " model vdw 1.234 3.270 nonbonded pdb=" O6 G A2251 " pdb=" N4 C x 75 " model vdw 1.410 2.520 nonbonded pdb=" N3 C x 1 " pdb=" N2 G x 72 " model vdw 1.611 2.560 nonbonded pdb=" N3 U A2555 " pdb=" C5 C 9 74 " model vdw 1.726 2.736 nonbonded pdb=" N1 G A2251 " pdb=" N3 C x 75 " model vdw 1.728 2.560 ... (remaining 1293845 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 '9' and resid 1 through 76) selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 15.470 Check model and map are aligned: 1.620 Set scattering table: 1.020 Process input model: 534.680 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 561.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.003 0.676 159812 Z= 0.210 Angle : 0.613 19.111 239016 Z= 0.331 Chirality : 0.033 0.398 30547 Planarity : 0.005 0.073 12841 Dihedral : 22.593 178.862 91459 Min Nonbonded Distance : 1.234 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.42 % Favored : 91.28 % Rotamer: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.11 % Twisted Proline : 0.51 % Twisted General : 0.32 % 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: -4.96 (0.08), residues: 5834 helix: -4.75 (0.04), residues: 1486 sheet: -2.21 (0.15), residues: 924 loop : -3.00 (0.08), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 212 HIS 0.012 0.001 HIS 6 6 PHE 0.035 0.002 PHE u 36 TYR 0.020 0.002 TYR N 112 ARG 0.019 0.001 ARG W 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2082 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2079 time to evaluate : 6.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 VAL cc_start: 0.8777 (t) cc_final: 0.8524 (p) REVERT: C 81 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7766 (mt-10) REVERT: C 160 TYR cc_start: 0.8902 (p90) cc_final: 0.8494 (p90) REVERT: C 190 THR cc_start: 0.9108 (m) cc_final: 0.8407 (p) REVERT: D 20 VAL cc_start: 0.7876 (t) cc_final: 0.7595 (m) REVERT: D 35 THR cc_start: 0.7722 (p) cc_final: 0.7402 (t) REVERT: D 46 ARG cc_start: 0.7561 (ptm160) cc_final: 0.7269 (ttm-80) REVERT: D 62 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7798 (mmmt) REVERT: D 88 GLU cc_start: 0.6050 (pm20) cc_final: 0.5825 (pm20) REVERT: D 148 GLN cc_start: 0.8568 (mp10) cc_final: 0.8198 (mp10) REVERT: D 205 PRO cc_start: 0.8670 (Cg_exo) cc_final: 0.8427 (Cg_endo) REVERT: E 27 LEU cc_start: 0.8517 (tp) cc_final: 0.8260 (tp) REVERT: E 35 TYR cc_start: 0.6957 (t80) cc_final: 0.6567 (t80) REVERT: E 63 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8651 (mtpp) REVERT: E 99 LYS cc_start: 0.8444 (mttt) cc_final: 0.7566 (mttm) REVERT: F 161 SER cc_start: 0.7852 (p) cc_final: 0.7330 (t) REVERT: G 79 THR cc_start: 0.7473 (m) cc_final: 0.7271 (p) REVERT: J 68 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7814 (mtmm) REVERT: K 23 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8090 (mtpp) REVERT: L 6 LEU cc_start: 0.7901 (mt) cc_final: 0.7695 (mt) REVERT: L 39 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7613 (mtmt) REVERT: L 51 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7061 (mt-10) REVERT: L 55 MET cc_start: 0.7339 (tpp) cc_final: 0.6872 (mmp) REVERT: M 3 GLN cc_start: 0.7919 (tt0) cc_final: 0.7360 (pt0) REVERT: M 6 ARG cc_start: 0.7019 (ppp-140) cc_final: 0.6745 (ttp80) REVERT: M 34 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8111 (ttpp) REVERT: M 104 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8157 (mt-10) REVERT: O 92 PHE cc_start: 0.8285 (t80) cc_final: 0.8065 (t80) REVERT: O 95 SER cc_start: 0.8320 (m) cc_final: 0.7738 (t) REVERT: Q 3 VAL cc_start: 0.9238 (t) cc_final: 0.8919 (p) REVERT: Q 77 LYS cc_start: 0.7587 (mtpt) cc_final: 0.6942 (mmtt) REVERT: Q 109 VAL cc_start: 0.8684 (t) cc_final: 0.8396 (t) REVERT: S 29 VAL cc_start: 0.8127 (t) cc_final: 0.7726 (p) REVERT: T 30 ILE cc_start: 0.8527 (tt) cc_final: 0.8240 (pt) REVERT: W 16 SER cc_start: 0.7261 (m) cc_final: 0.6929 (p) REVERT: X 55 MET cc_start: 0.7992 (mtp) cc_final: 0.7788 (mtt) REVERT: X 67 LEU cc_start: 0.8276 (mp) cc_final: 0.7893 (tp) REVERT: Z 38 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6835 (mp0) REVERT: 0 15 ARG cc_start: 0.8962 (ttp-110) cc_final: 0.8753 (ttm110) REVERT: 2 26 ASN cc_start: 0.7240 (m-40) cc_final: 0.6960 (m-40) REVERT: 3 2 LYS cc_start: 0.7908 (ptpt) cc_final: 0.7674 (pttt) REVERT: 3 6 VAL cc_start: 0.9401 (t) cc_final: 0.9155 (m) REVERT: b 47 PRO cc_start: 0.7628 (Cg_exo) cc_final: 0.7300 (Cg_endo) REVERT: b 178 LEU cc_start: 0.5980 (pt) cc_final: 0.5569 (tp) REVERT: c 27 GLU cc_start: 0.6656 (pm20) cc_final: 0.6236 (tm-30) REVERT: c 138 GLN cc_start: 0.7283 (mt0) cc_final: 0.6716 (tm-30) REVERT: c 176 THR cc_start: 0.8864 (m) cc_final: 0.8542 (p) REVERT: d 68 GLU cc_start: 0.7373 (tp30) cc_final: 0.6616 (tp30) REVERT: d 97 LEU cc_start: 0.7625 (tp) cc_final: 0.7349 (tt) REVERT: e 134 ASN cc_start: 0.8048 (m-40) cc_final: 0.7787 (m110) REVERT: g 16 LYS cc_start: 0.6974 (ttmt) cc_final: 0.6611 (mtpp) REVERT: g 147 ASN cc_start: 0.7156 (t0) cc_final: 0.6718 (t0) REVERT: h 4 ASP cc_start: 0.8050 (t0) cc_final: 0.7587 (t0) REVERT: i 6 TYR cc_start: 0.7518 (t80) cc_final: 0.7052 (t80) REVERT: i 41 GLU cc_start: 0.3819 (mp0) cc_final: 0.3088 (mp0) REVERT: k 69 CYS cc_start: 0.7042 (t) cc_final: 0.6657 (t) REVERT: m 71 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7375 (tt0) REVERT: o 80 LEU cc_start: 0.8265 (tp) cc_final: 0.7839 (mm) REVERT: q 17 GLU cc_start: 0.6636 (tt0) cc_final: 0.6019 (tp30) REVERT: q 61 ARG cc_start: 0.6966 (ppt90) cc_final: 0.6762 (tmm160) REVERT: r 50 TYR cc_start: 0.8360 (m-80) cc_final: 0.8037 (m-80) REVERT: t 68 LYS cc_start: 0.7291 (pttp) cc_final: 0.7069 (tptp) REVERT: w 14 LYS cc_start: 0.7550 (mmtm) cc_final: 0.6295 (mtpt) REVERT: w 126 THR cc_start: 0.7812 (m) cc_final: 0.7569 (p) REVERT: 7 6 LYS cc_start: 0.5033 (mttt) cc_final: 0.4392 (pttt) REVERT: 7 97 MET cc_start: 0.6732 (mmm) cc_final: 0.6411 (ttp) outliers start: 3 outliers final: 2 residues processed: 2079 average time/residue: 1.4326 time to fit residues: 4901.8150 Evaluate side-chains 1367 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1365 time to evaluate : 6.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain w residue 107 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 876 optimal weight: 8.9990 chunk 786 optimal weight: 5.9990 chunk 436 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 530 optimal weight: 4.9990 chunk 420 optimal weight: 0.9990 chunk 813 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 494 optimal weight: 7.9990 chunk 605 optimal weight: 10.0000 chunk 942 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 114 GLN C 142 ASN C 196 ASN C 225 ASN C 238 ASN D 32 ASN E 92 HIS E 94 GLN E 136 GLN E 156 ASN E 163 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 63 GLN G 114 HIS K 3 GLN K 5 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN P 11 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN R 43 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS W 46 HIS W 57 HIS Y 58 ASN 0 5 ASN 3 30 HIS 6 41 HIS b 38 HIS b 119 GLN ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 ASN d 73 ASN d 115 GLN e 42 ASN e 69 ASN e 72 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS g 27 ASN g 121 ASN h 3 GLN h 17 GLN i 36 GLN i 49 GLN i 74 GLN j 58 ASN m 104 ASN ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 GLN n 71 HIS p 63 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS s 13 HIS w 71 ASN w 119 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 159812 Z= 0.250 Angle : 0.658 17.709 239016 Z= 0.339 Chirality : 0.038 0.291 30547 Planarity : 0.006 0.071 12841 Dihedral : 23.525 179.726 79852 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.17 % Favored : 90.59 % Rotamer: Outliers : 4.65 % Allowed : 13.63 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.85 (0.09), residues: 5834 helix: -3.01 (0.10), residues: 1555 sheet: -1.75 (0.15), residues: 995 loop : -2.64 (0.09), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 212 HIS 0.010 0.002 HIS q 30 PHE 0.024 0.002 PHE R 93 TYR 0.041 0.002 TYR b 212 ARG 0.013 0.001 ARG 2 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1698 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1473 time to evaluate : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 VAL cc_start: 0.8891 (t) cc_final: 0.8677 (p) REVERT: C 65 ASP cc_start: 0.7856 (t70) cc_final: 0.7608 (t70) REVERT: C 81 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7950 (mt-10) REVERT: C 268 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7137 (ttt-90) REVERT: D 46 ARG cc_start: 0.7676 (ptm160) cc_final: 0.7068 (ttm-80) REVERT: D 62 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7744 (mmmt) REVERT: D 88 GLU cc_start: 0.5947 (pm20) cc_final: 0.5560 (pm20) REVERT: D 148 GLN cc_start: 0.8700 (mp10) cc_final: 0.8361 (mp10) REVERT: E 80 SER cc_start: 0.8106 (t) cc_final: 0.7882 (p) REVERT: F 23 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7256 (p) REVERT: F 80 GLN cc_start: 0.7281 (tp40) cc_final: 0.6402 (tp40) REVERT: F 161 SER cc_start: 0.7931 (p) cc_final: 0.7694 (t) REVERT: G 105 SER cc_start: 0.8339 (m) cc_final: 0.7605 (p) REVERT: J 68 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7892 (mtmm) REVERT: J 80 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7424 (t-90) REVERT: K 41 ILE cc_start: 0.9178 (pp) cc_final: 0.8955 (pt) REVERT: K 93 GLN cc_start: 0.8130 (mp10) cc_final: 0.7753 (mp10) REVERT: L 55 MET cc_start: 0.7597 (tpp) cc_final: 0.7012 (mmp) REVERT: M 3 GLN cc_start: 0.8041 (tt0) cc_final: 0.7748 (pt0) REVERT: M 6 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7013 (ttp80) REVERT: M 31 PHE cc_start: 0.7507 (m-80) cc_final: 0.6950 (m-10) REVERT: M 64 TRP cc_start: 0.8586 (m-90) cc_final: 0.8181 (m-90) REVERT: M 93 VAL cc_start: 0.9145 (m) cc_final: 0.8874 (p) REVERT: N 107 ASN cc_start: 0.8706 (t0) cc_final: 0.8120 (t0) REVERT: O 95 SER cc_start: 0.8683 (m) cc_final: 0.8006 (t) REVERT: P 56 SER cc_start: 0.8686 (m) cc_final: 0.8251 (m) REVERT: P 108 ARG cc_start: 0.7813 (ptt90) cc_final: 0.7449 (ptt180) REVERT: R 81 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8832 (mmtt) REVERT: R 82 HIS cc_start: 0.7830 (t-170) cc_final: 0.7617 (t-170) REVERT: S 18 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7516 (ttp80) REVERT: S 33 LEU cc_start: 0.6642 (tp) cc_final: 0.6318 (tp) REVERT: T 30 ILE cc_start: 0.8471 (tt) cc_final: 0.8253 (pt) REVERT: U 21 ARG cc_start: 0.6580 (mmm160) cc_final: 0.6082 (tpp80) REVERT: V 47 VAL cc_start: 0.8722 (t) cc_final: 0.8341 (t) REVERT: W 20 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8212 (mmt-90) REVERT: Y 58 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7321 (m110) REVERT: Z 38 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6981 (mp0) REVERT: 0 11 LYS cc_start: 0.8681 (tptm) cc_final: 0.8241 (tppt) REVERT: 3 5 THR cc_start: 0.9131 (m) cc_final: 0.8637 (p) REVERT: c 90 VAL cc_start: 0.8372 (p) cc_final: 0.8164 (p) REVERT: c 138 GLN cc_start: 0.7526 (mt0) cc_final: 0.6935 (tm-30) REVERT: c 139 ASN cc_start: 0.7458 (m-40) cc_final: 0.7256 (m-40) REVERT: c 176 THR cc_start: 0.8961 (m) cc_final: 0.8693 (p) REVERT: f 46 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7482 (tm-30) REVERT: g 4 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6797 (mtt180) REVERT: h 100 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8956 (pp) REVERT: h 104 SER cc_start: 0.8793 (t) cc_final: 0.8519 (p) REVERT: j 19 ASP cc_start: 0.8046 (t0) cc_final: 0.7794 (t0) REVERT: k 92 ARG cc_start: 0.6833 (ttm-80) cc_final: 0.6633 (ttm-80) REVERT: l 81 ILE cc_start: 0.9079 (mm) cc_final: 0.8801 (mt) REVERT: m 89 ARG cc_start: 0.8302 (mtp85) cc_final: 0.8095 (mtp85) REVERT: n 6 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8162 (tptt) REVERT: n 43 ASN cc_start: 0.8256 (m-40) cc_final: 0.7891 (t0) REVERT: p 1 MET cc_start: 0.6575 (ptp) cc_final: 0.5972 (ttt) REVERT: r 22 TYR cc_start: 0.8048 (p90) cc_final: 0.7479 (p90) REVERT: r 50 TYR cc_start: 0.8440 (m-80) cc_final: 0.8186 (m-80) REVERT: r 64 LEU cc_start: 0.9096 (mt) cc_final: 0.8783 (mt) REVERT: s 47 THR cc_start: 0.7820 (p) cc_final: 0.7600 (t) REVERT: t 68 LYS cc_start: 0.7639 (pttp) cc_final: 0.6979 (tptp) REVERT: t 82 ILE cc_start: 0.4106 (OUTLIER) cc_final: 0.3849 (pp) REVERT: u 35 GLU cc_start: 0.5409 (tp30) cc_final: 0.5111 (tp30) REVERT: 7 6 LYS cc_start: 0.5271 (mttt) cc_final: 0.4594 (pttt) REVERT: 7 97 MET cc_start: 0.6884 (mmm) cc_final: 0.6446 (ttp) REVERT: 7 137 MET cc_start: 0.6818 (mmm) cc_final: 0.6020 (ptt) outliers start: 225 outliers final: 145 residues processed: 1579 average time/residue: 1.3888 time to fit residues: 3714.4423 Evaluate side-chains 1453 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1302 time to evaluate : 6.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 53 CYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 96 ASP Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 146 THR Chi-restraints excluded: chain w residue 152 LYS Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain 7 residue 149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 523 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 784 optimal weight: 3.9990 chunk 641 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 944 optimal weight: 2.9990 chunk 1020 optimal weight: 6.9990 chunk 841 optimal weight: 0.8980 chunk 936 optimal weight: 2.9990 chunk 321 optimal weight: 0.4980 chunk 757 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 ASN C 238 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 29 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN N 3 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN R 82 HIS ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 ASN b 176 ASN c 40 GLN c 184 ASN e 69 ASN e 72 ASN e 145 ASN f 55 HIS ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 ASN i 36 GLN i 125 GLN j 58 ASN k 37 GLN p 29 ASN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN q 46 HIS t 47 GLN 7 139 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 159812 Z= 0.183 Angle : 0.580 16.931 239016 Z= 0.300 Chirality : 0.034 0.275 30547 Planarity : 0.005 0.067 12841 Dihedral : 23.497 179.531 79852 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.26 % Favored : 90.56 % Rotamer: Outliers : 5.59 % Allowed : 16.71 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.18 (0.10), residues: 5834 helix: -2.10 (0.11), residues: 1600 sheet: -1.41 (0.16), residues: 1027 loop : -2.38 (0.10), residues: 3207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 212 HIS 0.029 0.001 HIS 3 30 PHE 0.043 0.002 PHE u 36 TYR 0.029 0.002 TYR b 212 ARG 0.009 0.001 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1389 time to evaluate : 6.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8140 (mt-10) REVERT: C 268 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7089 (ttt-90) REVERT: D 46 ARG cc_start: 0.7632 (ptm160) cc_final: 0.7023 (ttm-80) REVERT: D 70 LYS cc_start: 0.7798 (tmtt) cc_final: 0.7549 (tttt) REVERT: D 88 GLU cc_start: 0.6170 (pm20) cc_final: 0.5728 (pm20) REVERT: E 30 GLN cc_start: 0.8835 (tp40) cc_final: 0.8611 (tm-30) REVERT: E 35 TYR cc_start: 0.7363 (t80) cc_final: 0.7046 (t80) REVERT: E 80 SER cc_start: 0.8211 (t) cc_final: 0.7949 (p) REVERT: F 95 MET cc_start: 0.7273 (ptm) cc_final: 0.7016 (ptm) REVERT: F 103 ILE cc_start: 0.8480 (pt) cc_final: 0.8095 (mt) REVERT: F 161 SER cc_start: 0.7928 (p) cc_final: 0.7646 (t) REVERT: J 43 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7448 (mp0) REVERT: J 69 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6876 (ttm-80) REVERT: J 80 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: K 93 GLN cc_start: 0.7979 (mp10) cc_final: 0.7679 (mp10) REVERT: L 55 MET cc_start: 0.7652 (tpp) cc_final: 0.6960 (mmp) REVERT: L 78 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7132 (mtp-110) REVERT: M 3 GLN cc_start: 0.8189 (tt0) cc_final: 0.7930 (pt0) REVERT: M 6 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7185 (ttp80) REVERT: M 53 MET cc_start: 0.6999 (ttm) cc_final: 0.6568 (mtp) REVERT: M 93 VAL cc_start: 0.9184 (m) cc_final: 0.8896 (p) REVERT: N 107 ASN cc_start: 0.8712 (t0) cc_final: 0.8185 (t0) REVERT: O 95 SER cc_start: 0.8665 (m) cc_final: 0.8037 (t) REVERT: P 28 LYS cc_start: 0.8312 (mptt) cc_final: 0.7806 (mppt) REVERT: P 56 SER cc_start: 0.8586 (m) cc_final: 0.8141 (m) REVERT: P 108 ARG cc_start: 0.7787 (ptt90) cc_final: 0.7533 (ptt180) REVERT: Q 80 ASN cc_start: 0.7858 (t0) cc_final: 0.7652 (m-40) REVERT: S 18 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7321 (ttp80) REVERT: T 59 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8029 (p0) REVERT: T 69 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6885 (ttp-110) REVERT: U 11 ILE cc_start: 0.7613 (tt) cc_final: 0.7256 (tt) REVERT: U 21 ARG cc_start: 0.6703 (mmm160) cc_final: 0.6330 (tpt-90) REVERT: V 10 LYS cc_start: 0.8119 (tppt) cc_final: 0.7474 (pttm) REVERT: V 50 MET cc_start: 0.7843 (mpp) cc_final: 0.7467 (mpp) REVERT: W 16 SER cc_start: 0.7126 (m) cc_final: 0.6372 (p) REVERT: Y 4 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7658 (mptt) REVERT: Z 38 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7040 (mp0) REVERT: 0 11 LYS cc_start: 0.8736 (tptm) cc_final: 0.8247 (tppt) REVERT: 2 1 MET cc_start: 0.5502 (ptm) cc_final: 0.4736 (ptm) REVERT: 2 12 ARG cc_start: 0.9002 (ttt-90) cc_final: 0.8791 (tpt-90) REVERT: 3 14 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7474 (mmtm) REVERT: 4 1 MET cc_start: 0.6784 (ptm) cc_final: 0.6571 (ptt) REVERT: 4 3 VAL cc_start: 0.8763 (m) cc_final: 0.8477 (p) REVERT: b 62 ARG cc_start: 0.8529 (mmp80) cc_final: 0.8238 (mmm160) REVERT: b 99 MET cc_start: 0.8268 (ptm) cc_final: 0.7742 (ptm) REVERT: b 156 LEU cc_start: 0.7158 (tp) cc_final: 0.6741 (pp) REVERT: c 138 GLN cc_start: 0.7231 (mt0) cc_final: 0.6754 (tm-30) REVERT: c 139 ASN cc_start: 0.7521 (m-40) cc_final: 0.7304 (m-40) REVERT: c 176 THR cc_start: 0.8954 (m) cc_final: 0.8689 (p) REVERT: d 168 THR cc_start: 0.6787 (OUTLIER) cc_final: 0.6511 (t) REVERT: h 57 GLU cc_start: 0.8167 (pm20) cc_final: 0.7966 (pm20) REVERT: h 100 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8988 (pp) REVERT: i 99 LYS cc_start: 0.8228 (mmmm) cc_final: 0.7884 (mttt) REVERT: j 7 ARG cc_start: 0.6804 (mmt180) cc_final: 0.6398 (mmt180) REVERT: j 9 ARG cc_start: 0.7789 (ptm-80) cc_final: 0.7415 (ptm160) REVERT: j 19 ASP cc_start: 0.8223 (t0) cc_final: 0.8016 (t0) REVERT: j 28 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7803 (t) REVERT: k 33 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8805 (tp) REVERT: k 92 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6701 (ttm-80) REVERT: l 81 ILE cc_start: 0.9097 (mm) cc_final: 0.8824 (mt) REVERT: n 6 LYS cc_start: 0.8383 (tmtt) cc_final: 0.8032 (ttmt) REVERT: n 43 ASN cc_start: 0.8308 (m-40) cc_final: 0.7984 (t0) REVERT: o 16 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7705 (ttp-110) REVERT: o 25 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: o 82 GLU cc_start: 0.7298 (mp0) cc_final: 0.6970 (mp0) REVERT: o 84 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7240 (mp) REVERT: p 1 MET cc_start: 0.6510 (ptp) cc_final: 0.5701 (ttt) REVERT: p 12 LYS cc_start: 0.5894 (pttm) cc_final: 0.5282 (pttm) REVERT: q 4 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.5962 (tp) REVERT: q 17 GLU cc_start: 0.6596 (tt0) cc_final: 0.6276 (tp30) REVERT: r 50 TYR cc_start: 0.8519 (m-80) cc_final: 0.8140 (m-80) REVERT: s 47 THR cc_start: 0.7539 (p) cc_final: 0.7332 (t) REVERT: t 68 LYS cc_start: 0.7925 (pttp) cc_final: 0.7002 (tptp) REVERT: u 44 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7059 (ptp90) REVERT: w 76 TYR cc_start: 0.5326 (t80) cc_final: 0.4885 (t80) REVERT: 7 137 MET cc_start: 0.6674 (mmm) cc_final: 0.6104 (ptt) REVERT: 7 179 ASP cc_start: 0.6141 (p0) cc_final: 0.5853 (p0) outliers start: 270 outliers final: 183 residues processed: 1514 average time/residue: 1.3193 time to fit residues: 3397.0448 Evaluate side-chains 1478 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1283 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 47 HIS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 9 HIS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 53 CYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 96 ASP Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 126 THR Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 180 SER Chi-restraints excluded: chain 7 residue 10 VAL Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 932 optimal weight: 5.9990 chunk 709 optimal weight: 10.0000 chunk 490 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 450 optimal weight: 0.1980 chunk 634 optimal weight: 10.0000 chunk 947 optimal weight: 0.5980 chunk 1003 optimal weight: 10.0000 chunk 495 optimal weight: 1.9990 chunk 898 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN C 238 ASN E 163 ASN F 36 ASN J 135 GLN J 136 GLN L 54 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN N 107 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 18 HIS 2 26 ASN b 50 ASN ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN e 72 ASN i 31 GLN i 36 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 ASN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 HIS ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 159812 Z= 0.180 Angle : 0.572 15.481 239016 Z= 0.295 Chirality : 0.034 0.279 30547 Planarity : 0.005 0.068 12841 Dihedral : 23.473 179.021 79852 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % Rotamer: Outliers : 6.02 % Allowed : 18.00 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.83 (0.10), residues: 5834 helix: -1.58 (0.12), residues: 1578 sheet: -1.28 (0.16), residues: 1001 loop : -2.27 (0.10), residues: 3255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 212 HIS 0.025 0.001 HIS f 55 PHE 0.040 0.002 PHE u 36 TYR 0.030 0.002 TYR b 212 ARG 0.013 0.001 ARG j 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1623 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1332 time to evaluate : 6.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8232 (mt-10) REVERT: C 131 MET cc_start: 0.7916 (mmm) cc_final: 0.7691 (mtp) REVERT: C 268 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7171 (ttt-90) REVERT: D 46 ARG cc_start: 0.7548 (ptm160) cc_final: 0.6866 (ttm-80) REVERT: D 79 LEU cc_start: 0.7912 (mp) cc_final: 0.7652 (mm) REVERT: D 88 GLU cc_start: 0.6182 (pm20) cc_final: 0.5749 (pm20) REVERT: D 157 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8726 (ttpt) REVERT: E 35 TYR cc_start: 0.7298 (t80) cc_final: 0.7030 (t80) REVERT: E 80 SER cc_start: 0.8320 (t) cc_final: 0.8037 (p) REVERT: F 95 MET cc_start: 0.7255 (ptm) cc_final: 0.6991 (ptm) REVERT: G 162 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7854 (ptp-110) REVERT: J 43 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7480 (mp0) REVERT: J 80 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7548 (t-90) REVERT: J 136 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7412 (mm-40) REVERT: K 93 GLN cc_start: 0.8019 (mp10) cc_final: 0.7783 (mp10) REVERT: M 3 GLN cc_start: 0.8233 (tt0) cc_final: 0.8029 (pt0) REVERT: M 6 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7262 (ttp80) REVERT: M 31 PHE cc_start: 0.7721 (m-80) cc_final: 0.7434 (m-10) REVERT: M 53 MET cc_start: 0.6944 (ttm) cc_final: 0.6668 (mtp) REVERT: M 64 TRP cc_start: 0.8490 (m-90) cc_final: 0.8284 (m100) REVERT: M 93 VAL cc_start: 0.9091 (m) cc_final: 0.8871 (p) REVERT: M 103 TYR cc_start: 0.7299 (m-80) cc_final: 0.6954 (m-80) REVERT: N 20 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8490 (tpp) REVERT: N 24 MET cc_start: 0.7864 (ttp) cc_final: 0.7546 (mtm) REVERT: N 107 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8285 (t0) REVERT: O 95 SER cc_start: 0.8712 (m) cc_final: 0.8080 (t) REVERT: P 28 LYS cc_start: 0.8436 (mptt) cc_final: 0.7772 (mppt) REVERT: P 56 SER cc_start: 0.8540 (m) cc_final: 0.8114 (m) REVERT: Q 69 ARG cc_start: 0.6921 (mtm180) cc_final: 0.6714 (mtm180) REVERT: Q 80 ASN cc_start: 0.7754 (t0) cc_final: 0.7528 (m-40) REVERT: S 18 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7366 (ttp80) REVERT: T 59 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8131 (p0) REVERT: T 69 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.6929 (ttp-110) REVERT: U 8 ASP cc_start: 0.7801 (t0) cc_final: 0.7553 (t0) REVERT: U 21 ARG cc_start: 0.6739 (mmm160) cc_final: 0.5975 (mmt90) REVERT: V 10 LYS cc_start: 0.8226 (tppt) cc_final: 0.7467 (pttm) REVERT: V 42 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7602 (pp) REVERT: V 50 MET cc_start: 0.8195 (mpp) cc_final: 0.7614 (mpp) REVERT: W 36 ILE cc_start: 0.9346 (mt) cc_final: 0.9002 (tt) REVERT: X 43 LYS cc_start: 0.7558 (mttm) cc_final: 0.7311 (mttm) REVERT: Y 4 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7765 (mppt) REVERT: Z 38 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7072 (mp0) REVERT: 0 11 LYS cc_start: 0.8534 (tptm) cc_final: 0.8105 (tppt) REVERT: 2 1 MET cc_start: 0.5557 (ptm) cc_final: 0.5155 (ptm) REVERT: 3 11 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7637 (mttt) REVERT: 4 3 VAL cc_start: 0.8768 (m) cc_final: 0.8504 (p) REVERT: b 62 ARG cc_start: 0.8538 (mmp80) cc_final: 0.8268 (mmm160) REVERT: b 99 MET cc_start: 0.8166 (ptm) cc_final: 0.7744 (ptm) REVERT: c 138 GLN cc_start: 0.7106 (mt0) cc_final: 0.6726 (tm-30) REVERT: c 176 THR cc_start: 0.8966 (m) cc_final: 0.8714 (p) REVERT: d 168 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6501 (t) REVERT: e 25 LYS cc_start: 0.8635 (tptp) cc_final: 0.8419 (tptt) REVERT: g 143 MET cc_start: 0.6845 (mmm) cc_final: 0.6515 (mmt) REVERT: h 100 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8971 (pp) REVERT: i 99 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7947 (mttt) REVERT: j 7 ARG cc_start: 0.7171 (mmt180) cc_final: 0.6652 (mmt-90) REVERT: j 19 ASP cc_start: 0.8266 (t0) cc_final: 0.8047 (t0) REVERT: k 105 ARG cc_start: 0.7577 (mtp85) cc_final: 0.7374 (mtp85) REVERT: l 30 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7704 (ttt180) REVERT: n 6 LYS cc_start: 0.8317 (tmtt) cc_final: 0.7941 (mttm) REVERT: n 43 ASN cc_start: 0.8311 (m-40) cc_final: 0.7989 (t0) REVERT: o 82 GLU cc_start: 0.7253 (mp0) cc_final: 0.7044 (mp0) REVERT: p 1 MET cc_start: 0.6695 (ptp) cc_final: 0.5794 (ttt) REVERT: q 4 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6186 (tp) REVERT: q 17 GLU cc_start: 0.6511 (tt0) cc_final: 0.6229 (tp30) REVERT: r 22 TYR cc_start: 0.8245 (p90) cc_final: 0.7929 (p90) REVERT: s 47 THR cc_start: 0.7657 (p) cc_final: 0.7395 (t) REVERT: t 32 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8129 (mtmm) REVERT: t 82 ILE cc_start: 0.4414 (OUTLIER) cc_final: 0.4166 (pp) REVERT: w 76 TYR cc_start: 0.5201 (t80) cc_final: 0.4844 (t80) REVERT: 7 114 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.6726 (m) REVERT: 7 137 MET cc_start: 0.6669 (mmm) cc_final: 0.6000 (ptt) REVERT: 7 198 LYS cc_start: 0.4698 (mmmm) cc_final: 0.3673 (pttp) outliers start: 291 outliers final: 194 residues processed: 1475 average time/residue: 1.2883 time to fit residues: 3264.2366 Evaluate side-chains 1453 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1246 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 9 HIS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 53 CYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 68 VAL Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 96 ASP Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 146 THR Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 180 SER Chi-restraints excluded: chain 7 residue 10 VAL Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 124 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 835 optimal weight: 3.9990 chunk 569 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 747 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 856 optimal weight: 10.0000 chunk 693 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 512 optimal weight: 0.9990 chunk 900 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 18 HIS 2 26 ASN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN e 72 ASN f 37 HIS f 55 HIS ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 ASN h 20 ASN i 31 GLN i 36 GLN j 35 GLN k 63 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 HIS ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 ASN ** w 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 165 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 159812 Z= 0.298 Angle : 0.689 16.664 239016 Z= 0.351 Chirality : 0.039 0.310 30547 Planarity : 0.005 0.076 12841 Dihedral : 23.634 179.612 79852 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.16 % Favored : 88.58 % Rotamer: Outliers : 6.99 % Allowed : 18.74 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.90 (0.10), residues: 5834 helix: -1.56 (0.12), residues: 1585 sheet: -1.44 (0.16), residues: 979 loop : -2.32 (0.10), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 212 HIS 0.008 0.002 HIS 7 172 PHE 0.036 0.002 PHE u 36 TYR 0.042 0.002 TYR O 99 ARG 0.019 0.001 ARG j 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1324 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8303 (mt-10) REVERT: C 131 MET cc_start: 0.7923 (mmm) cc_final: 0.7712 (mtp) REVERT: C 268 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7244 (ttt-90) REVERT: E 1 MET cc_start: 0.5033 (tpp) cc_final: 0.4192 (ttp) REVERT: E 30 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8857 (tm-30) REVERT: E 80 SER cc_start: 0.8413 (t) cc_final: 0.8136 (p) REVERT: F 95 MET cc_start: 0.7266 (ptm) cc_final: 0.6992 (ptm) REVERT: F 174 PHE cc_start: 0.5383 (t80) cc_final: 0.5171 (t80) REVERT: G 38 ASP cc_start: 0.8038 (t70) cc_final: 0.7746 (t70) REVERT: J 58 ASN cc_start: 0.8537 (m110) cc_final: 0.7882 (m110) REVERT: J 80 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7608 (t-90) REVERT: M 3 GLN cc_start: 0.8340 (tt0) cc_final: 0.8135 (pt0) REVERT: M 6 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7282 (ttp80) REVERT: M 31 PHE cc_start: 0.7774 (m-80) cc_final: 0.7464 (m-10) REVERT: M 53 MET cc_start: 0.6915 (ttm) cc_final: 0.6602 (mtp) REVERT: N 13 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7984 (p0) REVERT: O 19 GLN cc_start: 0.7826 (pp30) cc_final: 0.7533 (pp30) REVERT: P 16 VAL cc_start: 0.8816 (t) cc_final: 0.8581 (p) REVERT: Q 77 LYS cc_start: 0.7789 (mtpt) cc_final: 0.6979 (mmtt) REVERT: R 98 ILE cc_start: 0.8285 (mm) cc_final: 0.8021 (mm) REVERT: S 18 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7327 (ttp80) REVERT: S 86 MET cc_start: 0.8438 (mtp) cc_final: 0.8122 (mtp) REVERT: T 59 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8159 (p0) REVERT: T 69 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6918 (ttp-110) REVERT: V 10 LYS cc_start: 0.8231 (tppt) cc_final: 0.7531 (pttm) REVERT: V 42 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7801 (pp) REVERT: V 50 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7554 (mpp) REVERT: W 30 SER cc_start: 0.9290 (t) cc_final: 0.8815 (p) REVERT: W 36 ILE cc_start: 0.9321 (mt) cc_final: 0.9049 (tt) REVERT: W 68 LYS cc_start: 0.8862 (tppp) cc_final: 0.8426 (ttmm) REVERT: X 7 THR cc_start: 0.8913 (p) cc_final: 0.8570 (m) REVERT: Y 4 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7811 (mppt) REVERT: Y 48 ARG cc_start: 0.8474 (mpt-90) cc_final: 0.8163 (mmt180) REVERT: Z 38 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6934 (mp0) REVERT: 3 5 THR cc_start: 0.9177 (m) cc_final: 0.8823 (p) REVERT: 4 3 VAL cc_start: 0.8918 (m) cc_final: 0.8677 (p) REVERT: b 62 ARG cc_start: 0.8471 (mmp80) cc_final: 0.8269 (mmm160) REVERT: b 63 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8157 (mppt) REVERT: b 94 ARG cc_start: 0.7277 (ptt90) cc_final: 0.7014 (ttp80) REVERT: c 134 LYS cc_start: 0.8637 (tttt) cc_final: 0.8376 (ttpp) REVERT: d 80 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.5117 (ppp-140) REVERT: d 112 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7605 (mm-30) REVERT: g 6 ILE cc_start: 0.2544 (OUTLIER) cc_final: 0.2204 (pp) REVERT: h 100 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8948 (pp) REVERT: i 114 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8443 (mmtp) REVERT: j 7 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6585 (mmt-90) REVERT: j 19 ASP cc_start: 0.8278 (t0) cc_final: 0.7973 (t0) REVERT: k 33 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8860 (tp) REVERT: l 30 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7590 (ttt180) REVERT: n 6 LYS cc_start: 0.8312 (tmtt) cc_final: 0.7996 (mttm) REVERT: n 20 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6699 (m-10) REVERT: o 25 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: o 80 LEU cc_start: 0.8258 (tp) cc_final: 0.7787 (mm) REVERT: o 82 GLU cc_start: 0.7139 (mp0) cc_final: 0.6787 (mp0) REVERT: p 1 MET cc_start: 0.6748 (ptp) cc_final: 0.5907 (ttt) REVERT: q 4 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6226 (tp) REVERT: r 22 TYR cc_start: 0.8250 (p90) cc_final: 0.7885 (p90) REVERT: r 28 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8088 (mp) REVERT: s 31 ARG cc_start: 0.6995 (mmt180) cc_final: 0.6721 (ttm110) REVERT: s 56 HIS cc_start: 0.7698 (m90) cc_final: 0.7387 (m90) REVERT: t 32 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8210 (mtmm) REVERT: t 54 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8159 (tm-30) REVERT: t 82 ILE cc_start: 0.4584 (OUTLIER) cc_final: 0.4330 (pp) REVERT: u 44 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6948 (ptp90) REVERT: w 40 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8622 (mtm-85) REVERT: w 76 TYR cc_start: 0.5273 (t80) cc_final: 0.4943 (t80) REVERT: w 155 THR cc_start: 0.7737 (m) cc_final: 0.7505 (p) REVERT: 7 137 MET cc_start: 0.6854 (mmm) cc_final: 0.6040 (ptt) outliers start: 338 outliers final: 257 residues processed: 1506 average time/residue: 1.3072 time to fit residues: 3391.6854 Evaluate side-chains 1524 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1248 time to evaluate : 6.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 53 CYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 62 LYS Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 63 LYS Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 65 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 80 ARG Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 20 ASN Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 38 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 69 ASP Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 126 THR Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 133 LEU Chi-restraints excluded: chain w residue 146 THR Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 180 SER Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 7 residue 10 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 115 ILE Chi-restraints excluded: chain 7 residue 124 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 172 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 337 optimal weight: 0.4980 chunk 903 optimal weight: 0.5980 chunk 198 optimal weight: 10.0000 chunk 589 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 1004 optimal weight: 10.0000 chunk 833 optimal weight: 5.9990 chunk 464 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 527 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN E 163 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN M 13 HIS N 9 GLN N 107 ASN P 76 HIS ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN V 44 HIS 0 5 ASN 2 26 ASN b 50 ASN c 122 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN e 72 ASN f 55 HIS h 15 ASN i 4 GLN i 36 GLN k 63 GLN m 7 ASN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN t 60 GLN w 103 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 159812 Z= 0.133 Angle : 0.548 12.854 239016 Z= 0.283 Chirality : 0.032 0.295 30547 Planarity : 0.004 0.072 12841 Dihedral : 23.505 178.946 79852 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.79 % Favored : 91.07 % Rotamer: Outliers : 5.17 % Allowed : 21.53 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.52 (0.10), residues: 5834 helix: -1.15 (0.13), residues: 1588 sheet: -1.21 (0.16), residues: 999 loop : -2.14 (0.10), residues: 3247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 38 HIS 0.007 0.001 HIS M 13 PHE 0.030 0.001 PHE u 36 TYR 0.037 0.001 TYR b 212 ARG 0.009 0.001 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1311 time to evaluate : 6.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8193 (mt-10) REVERT: C 268 ARG cc_start: 0.7353 (ttp80) cc_final: 0.7058 (ttt-90) REVERT: D 79 LEU cc_start: 0.7639 (mp) cc_final: 0.7370 (mm) REVERT: E 1 MET cc_start: 0.4576 (tpp) cc_final: 0.4167 (ttp) REVERT: E 30 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8897 (tm-30) REVERT: E 80 SER cc_start: 0.8326 (t) cc_final: 0.8026 (p) REVERT: F 62 GLN cc_start: 0.8717 (pm20) cc_final: 0.8073 (pt0) REVERT: F 95 MET cc_start: 0.7221 (ptm) cc_final: 0.6983 (ptm) REVERT: F 103 ILE cc_start: 0.8542 (pt) cc_final: 0.8213 (mt) REVERT: F 132 ARG cc_start: 0.6259 (mtp85) cc_final: 0.5971 (mtt180) REVERT: F 161 SER cc_start: 0.8198 (t) cc_final: 0.7661 (p) REVERT: F 176 PHE cc_start: 0.6940 (t80) cc_final: 0.6729 (t80) REVERT: G 38 ASP cc_start: 0.7975 (t70) cc_final: 0.7681 (t70) REVERT: J 80 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7660 (t-90) REVERT: K 1 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6237 (mtp) REVERT: M 6 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7270 (ttp80) REVERT: M 64 TRP cc_start: 0.8365 (m-90) cc_final: 0.8025 (m-90) REVERT: M 103 TYR cc_start: 0.6550 (m-80) cc_final: 0.6331 (m-80) REVERT: N 13 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8057 (p0) REVERT: N 24 MET cc_start: 0.7819 (ttp) cc_final: 0.7550 (mtm) REVERT: N 107 ASN cc_start: 0.8608 (t0) cc_final: 0.8229 (t0) REVERT: P 28 LYS cc_start: 0.8710 (mptt) cc_final: 0.7514 (mppt) REVERT: Q 58 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6808 (mt0) REVERT: R 98 ILE cc_start: 0.8171 (mm) cc_final: 0.7928 (mm) REVERT: S 18 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7277 (ttp80) REVERT: S 86 MET cc_start: 0.8375 (mtp) cc_final: 0.8092 (mtp) REVERT: T 59 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8039 (p0) REVERT: T 69 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6952 (ttp-110) REVERT: U 8 ASP cc_start: 0.7762 (t0) cc_final: 0.7382 (t0) REVERT: V 10 LYS cc_start: 0.7963 (tppt) cc_final: 0.7327 (pttm) REVERT: V 50 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7633 (mpp) REVERT: W 30 SER cc_start: 0.9279 (t) cc_final: 0.8703 (p) REVERT: W 68 LYS cc_start: 0.8787 (tppp) cc_final: 0.8502 (ttmm) REVERT: X 53 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8101 (ttmt) REVERT: Y 4 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7791 (mppt) REVERT: Y 48 ARG cc_start: 0.8400 (mpt-90) cc_final: 0.8169 (mmt180) REVERT: Z 38 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6970 (mp0) REVERT: 3 5 THR cc_start: 0.9071 (m) cc_final: 0.8719 (p) REVERT: 3 11 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7824 (mttt) REVERT: 3 14 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7478 (mmtm) REVERT: 4 3 VAL cc_start: 0.8756 (m) cc_final: 0.8479 (p) REVERT: 4 37 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: b 94 ARG cc_start: 0.7290 (ptt90) cc_final: 0.7079 (ttp80) REVERT: b 99 MET cc_start: 0.8047 (ptm) cc_final: 0.7668 (ptm) REVERT: b 139 GLU cc_start: 0.7525 (tt0) cc_final: 0.7242 (tt0) REVERT: c 2 GLN cc_start: 0.7610 (pm20) cc_final: 0.7328 (pt0) REVERT: c 90 VAL cc_start: 0.8074 (p) cc_final: 0.7804 (p) REVERT: c 107 LYS cc_start: 0.8134 (mptt) cc_final: 0.7737 (mppt) REVERT: e 65 LYS cc_start: 0.8262 (mttm) cc_final: 0.7958 (mtpt) REVERT: e 94 PHE cc_start: 0.8156 (t80) cc_final: 0.7916 (t80) REVERT: e 146 MET cc_start: 0.8553 (ttm) cc_final: 0.8349 (ttm) REVERT: f 8 PHE cc_start: 0.8873 (p90) cc_final: 0.8563 (p90) REVERT: f 17 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: f 79 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6879 (ttt-90) REVERT: f 90 MET cc_start: 0.7804 (mtp) cc_final: 0.7231 (mtt) REVERT: h 33 VAL cc_start: 0.7869 (m) cc_final: 0.7580 (p) REVERT: h 48 PHE cc_start: 0.6652 (p90) cc_final: 0.6344 (p90) REVERT: h 100 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8994 (pp) REVERT: i 30 ASN cc_start: 0.8170 (m110) cc_final: 0.7755 (t0) REVERT: j 7 ARG cc_start: 0.7020 (mmt180) cc_final: 0.6439 (mmt-90) REVERT: j 19 ASP cc_start: 0.8303 (t0) cc_final: 0.8055 (t0) REVERT: j 62 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7362 (mtp85) REVERT: l 30 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7281 (ttt180) REVERT: m 90 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6747 (t-90) REVERT: o 80 LEU cc_start: 0.8131 (tp) cc_final: 0.7712 (mm) REVERT: p 1 MET cc_start: 0.6517 (ptp) cc_final: 0.5750 (ttt) REVERT: p 74 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8312 (tp) REVERT: q 4 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6363 (tp) REVERT: r 22 TYR cc_start: 0.8173 (p90) cc_final: 0.7795 (p90) REVERT: s 31 ARG cc_start: 0.6882 (mmt180) cc_final: 0.6639 (ttm110) REVERT: s 47 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7677 (t) REVERT: t 82 ILE cc_start: 0.4445 (OUTLIER) cc_final: 0.4242 (pp) REVERT: w 68 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7077 (t) REVERT: w 76 TYR cc_start: 0.5143 (t80) cc_final: 0.4862 (t80) REVERT: 7 97 MET cc_start: 0.5799 (mmt) cc_final: 0.5248 (mmm) REVERT: 7 137 MET cc_start: 0.6538 (mmm) cc_final: 0.5848 (ptt) outliers start: 250 outliers final: 165 residues processed: 1428 average time/residue: 1.3635 time to fit residues: 3338.8514 Evaluate side-chains 1392 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1209 time to evaluate : 6.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 68 VAL Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain 7 residue 115 ILE Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 172 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 968 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 572 optimal weight: 1.9990 chunk 733 optimal weight: 10.0000 chunk 568 optimal weight: 2.9990 chunk 845 optimal weight: 5.9990 chunk 560 optimal weight: 0.0870 chunk 1000 optimal weight: 5.9990 chunk 626 optimal weight: 10.0000 chunk 609 optimal weight: 20.0000 chunk 461 optimal weight: 0.7980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN D 49 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN E 163 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN 3 30 HIS ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN e 72 ASN f 55 HIS i 30 ASN i 36 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 159812 Z= 0.133 Angle : 0.533 11.917 239016 Z= 0.273 Chirality : 0.031 0.291 30547 Planarity : 0.004 0.069 12841 Dihedral : 23.435 178.435 79852 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.27 % Favored : 90.56 % Rotamer: Outliers : 4.65 % Allowed : 22.22 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.32 (0.10), residues: 5834 helix: -0.89 (0.13), residues: 1592 sheet: -1.15 (0.16), residues: 1018 loop : -2.06 (0.10), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 38 HIS 0.032 0.001 HIS f 55 PHE 0.033 0.002 PHE u 36 TYR 0.039 0.002 TYR b 212 ARG 0.013 0.000 ARG b 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1298 time to evaluate : 6.431 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: C 81 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8322 (mt-10) REVERT: C 268 ARG cc_start: 0.7378 (ttp80) cc_final: 0.7052 (ttt-90) REVERT: D 79 LEU cc_start: 0.7779 (mp) cc_final: 0.7515 (mm) REVERT: D 131 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: E 1 MET cc_start: 0.4713 (tpp) cc_final: 0.4437 (ttp) REVERT: E 25 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7260 (mt-10) REVERT: E 30 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8805 (tm-30) REVERT: E 35 TYR cc_start: 0.7137 (t80) cc_final: 0.6851 (t80) REVERT: E 80 SER cc_start: 0.8324 (t) cc_final: 0.8021 (p) REVERT: F 62 GLN cc_start: 0.8740 (pm20) cc_final: 0.8199 (pt0) REVERT: F 103 ILE cc_start: 0.8468 (pt) cc_final: 0.8091 (mt) REVERT: F 176 PHE cc_start: 0.7128 (t80) cc_final: 0.6904 (t80) REVERT: G 2 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6596 (mtp-110) REVERT: J 80 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7660 (t-90) REVERT: J 99 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7439 (mmm-85) REVERT: K 1 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6140 (mtp) REVERT: L 51 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7335 (mt-10) REVERT: M 6 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7291 (ttp80) REVERT: N 13 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8063 (p0) REVERT: N 24 MET cc_start: 0.7895 (ttp) cc_final: 0.7617 (mtm) REVERT: N 107 ASN cc_start: 0.8735 (t0) cc_final: 0.8407 (t0) REVERT: O 53 THR cc_start: 0.8437 (p) cc_final: 0.8164 (p) REVERT: Q 46 TYR cc_start: 0.8534 (t80) cc_final: 0.8299 (t80) REVERT: Q 58 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.6762 (mt0) REVERT: R 84 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7710 (ptt90) REVERT: R 98 ILE cc_start: 0.8124 (mm) cc_final: 0.7694 (mm) REVERT: S 18 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7262 (ttp80) REVERT: S 86 MET cc_start: 0.8410 (mtp) cc_final: 0.8105 (mtp) REVERT: T 30 ILE cc_start: 0.8568 (tt) cc_final: 0.8356 (pt) REVERT: T 59 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8044 (p0) REVERT: V 10 LYS cc_start: 0.7942 (tppt) cc_final: 0.7291 (pttm) REVERT: V 50 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7577 (mpp) REVERT: W 30 SER cc_start: 0.9255 (t) cc_final: 0.8626 (p) REVERT: W 68 LYS cc_start: 0.8778 (tppp) cc_final: 0.8433 (ttmm) REVERT: X 43 LYS cc_start: 0.7538 (mttm) cc_final: 0.7291 (mttp) REVERT: Y 4 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7755 (mppt) REVERT: Y 48 ARG cc_start: 0.8344 (mpt-90) cc_final: 0.8140 (mmt180) REVERT: Z 38 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6973 (mp0) REVERT: 2 37 LYS cc_start: 0.7864 (tttt) cc_final: 0.7250 (tttt) REVERT: 3 5 THR cc_start: 0.9066 (m) cc_final: 0.8713 (p) REVERT: 3 7 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8284 (mmm-85) REVERT: 3 14 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7504 (mmtm) REVERT: 4 3 VAL cc_start: 0.8756 (m) cc_final: 0.8510 (p) REVERT: b 99 MET cc_start: 0.7998 (ptm) cc_final: 0.7639 (ptm) REVERT: b 119 GLN cc_start: 0.8365 (pm20) cc_final: 0.7258 (pp30) REVERT: c 2 GLN cc_start: 0.7714 (pm20) cc_final: 0.7455 (pt0) REVERT: c 69 THR cc_start: 0.6973 (m) cc_final: 0.6750 (m) REVERT: c 107 LYS cc_start: 0.8133 (mptt) cc_final: 0.7754 (mmtt) REVERT: e 65 LYS cc_start: 0.8244 (mttm) cc_final: 0.7906 (mtpt) REVERT: e 146 MET cc_start: 0.8407 (ttm) cc_final: 0.8148 (ttm) REVERT: f 22 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6896 (tp) REVERT: f 79 ARG cc_start: 0.7328 (ttm-80) cc_final: 0.6855 (ttt-90) REVERT: f 90 MET cc_start: 0.7886 (mtp) cc_final: 0.7214 (mtp) REVERT: h 12 ARG cc_start: 0.7951 (mtp85) cc_final: 0.7705 (mtt-85) REVERT: h 33 VAL cc_start: 0.7881 (m) cc_final: 0.7612 (p) REVERT: h 48 PHE cc_start: 0.6782 (p90) cc_final: 0.6423 (p90) REVERT: h 100 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8967 (pp) REVERT: i 6 TYR cc_start: 0.6911 (t80) cc_final: 0.6620 (t80) REVERT: i 30 ASN cc_start: 0.8155 (m-40) cc_final: 0.7764 (t0) REVERT: i 31 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7354 (mm-40) REVERT: j 7 ARG cc_start: 0.7017 (mmt180) cc_final: 0.6466 (mmt-90) REVERT: j 19 ASP cc_start: 0.8244 (t0) cc_final: 0.8001 (t0) REVERT: j 37 ARG cc_start: 0.5359 (mmp80) cc_final: 0.4880 (mmt90) REVERT: j 62 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7368 (mtp85) REVERT: l 30 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7278 (ttt180) REVERT: m 77 LYS cc_start: 0.8414 (ptpt) cc_final: 0.7944 (ptpp) REVERT: m 90 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6763 (t-90) REVERT: n 6 LYS cc_start: 0.7953 (tptt) cc_final: 0.7569 (ttmt) REVERT: o 80 LEU cc_start: 0.8148 (tp) cc_final: 0.7660 (mm) REVERT: o 83 ARG cc_start: 0.7145 (ttt180) cc_final: 0.6939 (tmm-80) REVERT: p 1 MET cc_start: 0.6468 (ptp) cc_final: 0.5753 (ttt) REVERT: p 74 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8316 (tp) REVERT: q 4 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6450 (tp) REVERT: r 22 TYR cc_start: 0.8205 (p90) cc_final: 0.7868 (p90) REVERT: r 50 TYR cc_start: 0.8462 (m-80) cc_final: 0.8203 (m-80) REVERT: s 31 ARG cc_start: 0.6795 (mmt180) cc_final: 0.6594 (ttm110) REVERT: s 47 THR cc_start: 0.7954 (p) cc_final: 0.7706 (t) REVERT: s 54 ARG cc_start: 0.8072 (ptt180) cc_final: 0.7754 (ptp-170) REVERT: t 32 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8177 (mtmm) REVERT: u 38 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7479 (tm-30) REVERT: u 44 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6881 (ptp90) REVERT: w 70 MET cc_start: 0.7038 (pmm) cc_final: 0.6292 (ptt) REVERT: w 76 TYR cc_start: 0.5111 (t80) cc_final: 0.4843 (t80) REVERT: w 149 THR cc_start: 0.6162 (m) cc_final: 0.5371 (p) REVERT: 7 97 MET cc_start: 0.5193 (mmt) cc_final: 0.4735 (mmm) REVERT: 7 121 MET cc_start: 0.3988 (tpp) cc_final: 0.3607 (tpt) REVERT: 7 137 MET cc_start: 0.6509 (mmm) cc_final: 0.5823 (ptt) outliers start: 225 outliers final: 169 residues processed: 1401 average time/residue: 1.3092 time to fit residues: 3152.9248 Evaluate side-chains 1414 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1228 time to evaluate : 6.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 126 THR Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 146 THR Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 180 SER Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 618 optimal weight: 10.0000 chunk 399 optimal weight: 0.8980 chunk 597 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 636 optimal weight: 10.0000 chunk 681 optimal weight: 10.0000 chunk 494 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 786 optimal weight: 8.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN O 104 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN b 14 HIS ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN i 4 GLN i 36 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 159812 Z= 0.286 Angle : 0.693 18.396 239016 Z= 0.351 Chirality : 0.038 0.316 30547 Planarity : 0.005 0.125 12841 Dihedral : 23.648 179.892 79852 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.18 % Favored : 88.60 % Rotamer: Outliers : 5.92 % Allowed : 21.78 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.59 (0.10), residues: 5834 helix: -1.12 (0.13), residues: 1609 sheet: -1.31 (0.16), residues: 983 loop : -2.22 (0.10), residues: 3242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 38 HIS 0.007 0.002 HIS k 117 PHE 0.036 0.002 PHE u 36 TYR 0.038 0.003 TYR O 99 ARG 0.014 0.001 ARG b 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1268 time to evaluate : 6.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8412 (mt-10) REVERT: C 268 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7230 (ttt-90) REVERT: E 25 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7304 (mt-10) REVERT: E 30 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8824 (tm-30) REVERT: E 80 SER cc_start: 0.8460 (t) cc_final: 0.8170 (p) REVERT: E 131 THR cc_start: 0.7948 (p) cc_final: 0.7699 (p) REVERT: F 99 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: G 71 LEU cc_start: 0.6757 (mm) cc_final: 0.6546 (mm) REVERT: G 163 TYR cc_start: 0.8051 (m-80) cc_final: 0.7657 (m-80) REVERT: J 58 ASN cc_start: 0.8443 (m110) cc_final: 0.7814 (m110) REVERT: J 80 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7502 (t-90) REVERT: J 106 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8260 (tttt) REVERT: L 51 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7350 (mt-10) REVERT: M 6 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7324 (ttp80) REVERT: N 13 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7971 (p0) REVERT: N 107 ASN cc_start: 0.8880 (t0) cc_final: 0.8654 (t0) REVERT: O 19 GLN cc_start: 0.7871 (pp30) cc_final: 0.7647 (pp30) REVERT: O 53 THR cc_start: 0.8498 (p) cc_final: 0.8208 (p) REVERT: Q 80 ASN cc_start: 0.7135 (m-40) cc_final: 0.6745 (m-40) REVERT: R 84 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (ptt90) REVERT: R 98 ILE cc_start: 0.8219 (mm) cc_final: 0.7959 (mm) REVERT: S 18 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7440 (ttp80) REVERT: S 86 MET cc_start: 0.8408 (mtp) cc_final: 0.8112 (mtp) REVERT: T 59 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8130 (p0) REVERT: T 69 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.7047 (ttp-110) REVERT: U 21 ARG cc_start: 0.6938 (mmm160) cc_final: 0.6171 (mmt90) REVERT: V 10 LYS cc_start: 0.8112 (tppt) cc_final: 0.7442 (pttm) REVERT: V 50 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7611 (mpp) REVERT: W 30 SER cc_start: 0.9306 (t) cc_final: 0.8851 (p) REVERT: W 68 LYS cc_start: 0.8798 (tppp) cc_final: 0.8429 (ttmm) REVERT: Y 4 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7784 (mppt) REVERT: Y 48 ARG cc_start: 0.8431 (mpt-90) cc_final: 0.8159 (mmt180) REVERT: Z 38 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6899 (mp0) REVERT: 0 33 SER cc_start: 0.8276 (m) cc_final: 0.7801 (t) REVERT: 4 3 VAL cc_start: 0.8893 (m) cc_final: 0.8639 (p) REVERT: 4 37 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: b 119 GLN cc_start: 0.8360 (pm20) cc_final: 0.7222 (pp30) REVERT: c 2 GLN cc_start: 0.7641 (pm20) cc_final: 0.7400 (pt0) REVERT: e 13 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7208 (pptt) REVERT: g 30 MET cc_start: 0.7558 (mmp) cc_final: 0.7188 (mmp) REVERT: g 55 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7071 (mtmm) REVERT: h 12 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7799 (mtt-85) REVERT: h 33 VAL cc_start: 0.8118 (m) cc_final: 0.7820 (p) REVERT: h 48 PHE cc_start: 0.7158 (p90) cc_final: 0.6795 (p90) REVERT: h 100 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8871 (pp) REVERT: i 30 ASN cc_start: 0.8145 (m-40) cc_final: 0.7674 (t0) REVERT: j 7 ARG cc_start: 0.7200 (mmt180) cc_final: 0.6554 (mmt180) REVERT: j 19 ASP cc_start: 0.8308 (t0) cc_final: 0.8037 (t0) REVERT: j 62 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7184 (mtp85) REVERT: j 65 TYR cc_start: 0.8107 (m-80) cc_final: 0.7904 (m-80) REVERT: j 90 LEU cc_start: 0.7053 (mt) cc_final: 0.6544 (tp) REVERT: l 30 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7348 (ttt180) REVERT: m 90 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6909 (t-90) REVERT: o 80 LEU cc_start: 0.8181 (tp) cc_final: 0.7738 (mm) REVERT: p 1 MET cc_start: 0.6690 (ptp) cc_final: 0.5858 (ttt) REVERT: p 69 ASP cc_start: 0.7207 (p0) cc_final: 0.6769 (p0) REVERT: q 4 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6225 (tp) REVERT: s 31 ARG cc_start: 0.6895 (mmt180) cc_final: 0.6691 (ttm110) REVERT: s 47 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7719 (t) REVERT: t 84 LYS cc_start: 0.7559 (ttpt) cc_final: 0.6000 (mmtp) REVERT: u 44 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6899 (ptp90) REVERT: w 40 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8580 (mtm-85) REVERT: w 70 MET cc_start: 0.7456 (pmm) cc_final: 0.6634 (ptt) REVERT: w 149 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6222 (p) REVERT: 7 97 MET cc_start: 0.5790 (mmt) cc_final: 0.5280 (mmm) REVERT: 7 137 MET cc_start: 0.6689 (mmm) cc_final: 0.5894 (ptt) outliers start: 286 outliers final: 217 residues processed: 1422 average time/residue: 1.3307 time to fit residues: 3258.3224 Evaluate side-chains 1448 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1212 time to evaluate : 6.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 6 residue 62 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 92 ASP Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 80 ARG Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 38 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 62 THR Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 75 LEU Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 126 THR Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 146 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 180 SER Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 7 residue 109 MET Chi-restraints excluded: chain 7 residue 115 ILE Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 910 optimal weight: 0.7980 chunk 958 optimal weight: 0.6980 chunk 874 optimal weight: 0.9980 chunk 932 optimal weight: 0.7980 chunk 561 optimal weight: 0.5980 chunk 406 optimal weight: 6.9990 chunk 732 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 842 optimal weight: 0.0570 chunk 881 optimal weight: 0.8980 chunk 929 optimal weight: 9.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN D 49 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 2 26 ASN ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 GLN c 122 GLN c 138 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN i 4 GLN i 36 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 45 ASN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN 7 20 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 159812 Z= 0.125 Angle : 0.551 10.892 239016 Z= 0.282 Chirality : 0.032 0.303 30547 Planarity : 0.004 0.068 12841 Dihedral : 23.474 179.089 79850 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.24 % Favored : 91.64 % Rotamer: Outliers : 3.54 % Allowed : 24.56 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.29 (0.10), residues: 5834 helix: -0.81 (0.13), residues: 1614 sheet: -1.20 (0.16), residues: 1011 loop : -2.04 (0.10), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 38 HIS 0.006 0.001 HIS q 46 PHE 0.030 0.001 PHE u 36 TYR 0.057 0.002 TYR O 99 ARG 0.013 0.001 ARG b 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1480 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1309 time to evaluate : 6.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8072 (mt-10) REVERT: C 268 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7079 (ttt-90) REVERT: E 25 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7215 (mt-10) REVERT: E 30 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8797 (tm-30) REVERT: E 80 SER cc_start: 0.8326 (t) cc_final: 0.8008 (p) REVERT: E 131 THR cc_start: 0.8016 (p) cc_final: 0.7747 (p) REVERT: F 62 GLN cc_start: 0.8851 (pm20) cc_final: 0.8243 (pt0) REVERT: F 99 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: F 161 SER cc_start: 0.8200 (t) cc_final: 0.7745 (p) REVERT: F 176 PHE cc_start: 0.6793 (t80) cc_final: 0.6511 (t80) REVERT: J 80 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7466 (t-90) REVERT: J 99 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: K 1 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5967 (mtp) REVERT: M 6 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7375 (ttp80) REVERT: N 13 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (p0) REVERT: N 24 MET cc_start: 0.7797 (ttp) cc_final: 0.7555 (mtm) REVERT: N 107 ASN cc_start: 0.8748 (t0) cc_final: 0.8474 (t0) REVERT: O 53 THR cc_start: 0.8420 (p) cc_final: 0.8161 (p) REVERT: Q 58 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.6796 (mt0) REVERT: Q 73 ILE cc_start: 0.8728 (tt) cc_final: 0.8488 (tt) REVERT: S 18 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7231 (ttp80) REVERT: S 86 MET cc_start: 0.8461 (mtp) cc_final: 0.8216 (mtp) REVERT: T 59 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8050 (p0) REVERT: T 69 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.7101 (ttp-110) REVERT: U 21 ARG cc_start: 0.6785 (mmm160) cc_final: 0.6077 (mmt90) REVERT: V 10 LYS cc_start: 0.7924 (tppt) cc_final: 0.7305 (pttm) REVERT: V 47 VAL cc_start: 0.8192 (t) cc_final: 0.7855 (t) REVERT: V 50 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: W 30 SER cc_start: 0.9296 (t) cc_final: 0.8666 (p) REVERT: W 68 LYS cc_start: 0.8823 (tppp) cc_final: 0.8396 (tttm) REVERT: Y 4 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7723 (mppt) REVERT: Z 38 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6995 (mp0) REVERT: 0 33 SER cc_start: 0.7818 (m) cc_final: 0.7383 (t) REVERT: 2 37 LYS cc_start: 0.7889 (tttt) cc_final: 0.7295 (tttt) REVERT: 4 37 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: b 94 ARG cc_start: 0.6700 (ttp80) cc_final: 0.6409 (ttp-110) REVERT: b 99 MET cc_start: 0.8085 (ptm) cc_final: 0.7855 (ptm) REVERT: b 119 GLN cc_start: 0.8277 (pm20) cc_final: 0.7904 (pp30) REVERT: c 2 GLN cc_start: 0.7543 (pm20) cc_final: 0.7307 (pt0) REVERT: c 107 LYS cc_start: 0.8134 (mptt) cc_final: 0.7694 (mppt) REVERT: c 184 ASN cc_start: 0.7757 (t0) cc_final: 0.7367 (m-40) REVERT: e 65 LYS cc_start: 0.8264 (mttm) cc_final: 0.7947 (mtpt) REVERT: e 94 PHE cc_start: 0.8166 (t80) cc_final: 0.7705 (t80) REVERT: e 134 ASN cc_start: 0.8365 (m-40) cc_final: 0.8080 (m-40) REVERT: f 79 ARG cc_start: 0.7162 (ttm-80) cc_final: 0.6777 (ttt-90) REVERT: h 12 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7646 (mtt-85) REVERT: h 48 PHE cc_start: 0.6683 (p90) cc_final: 0.6211 (p90) REVERT: h 100 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8872 (pp) REVERT: h 116 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7631 (mtt90) REVERT: i 5 TYR cc_start: 0.7954 (m-80) cc_final: 0.7589 (m-80) REVERT: i 30 ASN cc_start: 0.8017 (m-40) cc_final: 0.7631 (t0) REVERT: j 7 ARG cc_start: 0.7047 (mmt180) cc_final: 0.6557 (mmt-90) REVERT: j 19 ASP cc_start: 0.8299 (t0) cc_final: 0.8062 (t0) REVERT: j 37 ARG cc_start: 0.5289 (mmp80) cc_final: 0.4723 (mmt90) REVERT: j 62 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7338 (mtp85) REVERT: k 33 ILE cc_start: 0.9044 (tp) cc_final: 0.8618 (mt) REVERT: k 84 MET cc_start: 0.7630 (mmm) cc_final: 0.7329 (mmm) REVERT: m 16 ILE cc_start: 0.8258 (mp) cc_final: 0.8047 (pt) REVERT: m 77 LYS cc_start: 0.8511 (ptpt) cc_final: 0.8052 (ptpp) REVERT: m 90 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6756 (t-90) REVERT: n 6 LYS cc_start: 0.7984 (tptt) cc_final: 0.7596 (mttp) REVERT: p 1 MET cc_start: 0.6205 (ptp) cc_final: 0.5494 (ttt) REVERT: q 4 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6626 (tp) REVERT: r 50 TYR cc_start: 0.8432 (m-80) cc_final: 0.8116 (m-80) REVERT: s 47 THR cc_start: 0.7597 (p) cc_final: 0.7359 (t) REVERT: t 84 LYS cc_start: 0.7409 (ttpt) cc_final: 0.6126 (mptt) REVERT: u 44 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6776 (ptt90) REVERT: w 47 LEU cc_start: 0.8150 (tt) cc_final: 0.7938 (mt) REVERT: w 70 MET cc_start: 0.7194 (pmm) cc_final: 0.6188 (ptt) REVERT: 7 97 MET cc_start: 0.4842 (mmt) cc_final: 0.4332 (mmm) REVERT: 7 137 MET cc_start: 0.6510 (mmm) cc_final: 0.5788 (ptt) outliers start: 171 outliers final: 124 residues processed: 1389 average time/residue: 1.3155 time to fit residues: 3123.5985 Evaluate side-chains 1366 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1228 time to evaluate : 8.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 LYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 24 GLU Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 126 THR Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 612 optimal weight: 10.0000 chunk 985 optimal weight: 8.9990 chunk 601 optimal weight: 0.0070 chunk 467 optimal weight: 7.9990 chunk 685 optimal weight: 10.0000 chunk 1034 optimal weight: 10.0000 chunk 951 optimal weight: 6.9990 chunk 823 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 636 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 49 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 97 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN O 104 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 2 26 ASN ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN k 63 GLN k 118 ASN l 4 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 159812 Z= 0.322 Angle : 0.701 16.843 239016 Z= 0.352 Chirality : 0.038 0.320 30547 Planarity : 0.005 0.083 12841 Dihedral : 23.570 179.939 79850 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.11 % Favored : 88.67 % Rotamer: Outliers : 4.01 % Allowed : 24.24 % Favored : 71.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.53 (0.10), residues: 5834 helix: -0.99 (0.13), residues: 1617 sheet: -1.32 (0.16), residues: 982 loop : -2.20 (0.10), residues: 3235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 212 HIS 0.008 0.002 HIS M 13 PHE 0.035 0.002 PHE u 36 TYR 0.043 0.003 TYR O 99 ARG 0.018 0.001 ARG K 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11668 Ramachandran restraints generated. 5834 Oldfield, 0 Emsley, 5834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1247 time to evaluate : 6.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8422 (mt-10) REVERT: C 268 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7236 (ttt-90) REVERT: D 18 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7571 (p0) REVERT: E 25 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7332 (mt-10) REVERT: E 30 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8762 (tm-30) REVERT: E 80 SER cc_start: 0.8458 (t) cc_final: 0.8167 (p) REVERT: E 131 THR cc_start: 0.7962 (p) cc_final: 0.7676 (p) REVERT: F 59 ILE cc_start: 0.7635 (mp) cc_final: 0.7429 (mp) REVERT: F 94 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8142 (mtt180) REVERT: F 176 PHE cc_start: 0.7146 (t80) cc_final: 0.6909 (t80) REVERT: G 126 THR cc_start: 0.7794 (m) cc_final: 0.7369 (p) REVERT: J 80 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7482 (t-90) REVERT: K 1 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6230 (mtp) REVERT: M 6 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7353 (ttp80) REVERT: M 110 GLU cc_start: 0.6332 (tm-30) cc_final: 0.6077 (tm-30) REVERT: N 13 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7954 (p0) REVERT: N 107 ASN cc_start: 0.8883 (t0) cc_final: 0.8642 (t0) REVERT: O 53 THR cc_start: 0.8494 (p) cc_final: 0.8222 (p) REVERT: Q 73 ILE cc_start: 0.8802 (tt) cc_final: 0.8574 (tt) REVERT: R 73 LYS cc_start: 0.8428 (tppt) cc_final: 0.8184 (tptt) REVERT: R 98 ILE cc_start: 0.8149 (mm) cc_final: 0.7870 (mm) REVERT: S 18 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7417 (ttp80) REVERT: S 86 MET cc_start: 0.8436 (mtp) cc_final: 0.8233 (mtp) REVERT: T 1 MET cc_start: 0.3883 (mmm) cc_final: 0.3211 (mmm) REVERT: T 30 ILE cc_start: 0.8599 (tt) cc_final: 0.8263 (pt) REVERT: T 59 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8148 (p0) REVERT: T 69 ARG cc_start: 0.7336 (ttp-110) cc_final: 0.7021 (ttp-110) REVERT: U 21 ARG cc_start: 0.6868 (mmm160) cc_final: 0.6169 (mmt-90) REVERT: V 10 LYS cc_start: 0.8097 (tppt) cc_final: 0.7429 (pttm) REVERT: V 47 VAL cc_start: 0.8387 (t) cc_final: 0.7993 (t) REVERT: V 50 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: W 30 SER cc_start: 0.9298 (t) cc_final: 0.8821 (p) REVERT: W 68 LYS cc_start: 0.8815 (tppp) cc_final: 0.8455 (ttmm) REVERT: X 43 LYS cc_start: 0.7893 (mttm) cc_final: 0.7612 (mttp) REVERT: Y 4 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7790 (mppt) REVERT: Z 38 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6956 (mp0) REVERT: 0 33 SER cc_start: 0.8208 (m) cc_final: 0.7734 (t) REVERT: 3 5 THR cc_start: 0.9121 (m) cc_final: 0.8746 (p) REVERT: 4 3 VAL cc_start: 0.8848 (m) cc_final: 0.8525 (p) REVERT: 4 18 LYS cc_start: 0.8186 (tptm) cc_final: 0.7918 (tppt) REVERT: 4 37 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: 6 25 ARG cc_start: 0.6638 (ttp-170) cc_final: 0.6143 (ttp-170) REVERT: b 94 ARG cc_start: 0.6855 (ttp80) cc_final: 0.6557 (ttp-110) REVERT: b 99 MET cc_start: 0.8220 (ptm) cc_final: 0.7753 (ptm) REVERT: b 119 GLN cc_start: 0.8213 (pm20) cc_final: 0.7533 (pp30) REVERT: b 153 MET cc_start: 0.8836 (mtp) cc_final: 0.8563 (mtp) REVERT: c 135 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7270 (ttm-80) REVERT: d 177 MET cc_start: 0.5797 (mmm) cc_final: 0.5247 (mmm) REVERT: f 1 MET cc_start: 0.5808 (mmm) cc_final: 0.5307 (tpt) REVERT: h 12 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7777 (mtt-85) REVERT: h 48 PHE cc_start: 0.7182 (p90) cc_final: 0.6662 (p90) REVERT: h 57 GLU cc_start: 0.8273 (pm20) cc_final: 0.7998 (pm20) REVERT: h 100 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8901 (pp) REVERT: i 30 ASN cc_start: 0.8069 (m-40) cc_final: 0.7653 (t0) REVERT: j 7 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6736 (mmt-90) REVERT: j 62 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7306 (mtp85) REVERT: j 73 LEU cc_start: 0.7484 (tp) cc_final: 0.7274 (tp) REVERT: j 90 LEU cc_start: 0.7001 (mt) cc_final: 0.6705 (tp) REVERT: k 33 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8980 (tp) REVERT: m 90 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6860 (t-90) REVERT: n 6 LYS cc_start: 0.8043 (tptt) cc_final: 0.7616 (mttm) REVERT: p 1 MET cc_start: 0.6510 (ptp) cc_final: 0.5966 (ttt) REVERT: q 4 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6259 (tp) REVERT: q 43 LEU cc_start: 0.7637 (mt) cc_final: 0.7434 (mp) REVERT: s 54 ARG cc_start: 0.8268 (ptp-170) cc_final: 0.8041 (ptm160) REVERT: s 56 HIS cc_start: 0.7818 (m90) cc_final: 0.7489 (m170) REVERT: t 84 LYS cc_start: 0.7563 (ttpt) cc_final: 0.6212 (mptt) REVERT: u 44 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6703 (ptt90) REVERT: w 47 LEU cc_start: 0.8351 (tt) cc_final: 0.8062 (mt) REVERT: w 70 MET cc_start: 0.7201 (pmm) cc_final: 0.6869 (pmm) REVERT: 7 97 MET cc_start: 0.5540 (mmt) cc_final: 0.5009 (mmm) REVERT: 7 137 MET cc_start: 0.6710 (mmm) cc_final: 0.5906 (ptt) outliers start: 194 outliers final: 159 residues processed: 1348 average time/residue: 1.3357 time to fit residues: 3105.1801 Evaluate side-chains 1395 residues out of total 4862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1222 time to evaluate : 5.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 133 LYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 48 MET Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 24 GLU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 26 CYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 90 HIS Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain u residue 30 GLU Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain w residue 15 ILE Chi-restraints excluded: chain w residue 24 VAL Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 75 LEU Chi-restraints excluded: chain w residue 86 ASN Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 114 ILE Chi-restraints excluded: chain w residue 123 ILE Chi-restraints excluded: chain w residue 126 THR Chi-restraints excluded: chain w residue 129 ASN Chi-restraints excluded: chain w residue 161 VAL Chi-restraints excluded: chain w residue 180 SER Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 124 VAL Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 172 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1038 random chunks: chunk 654 optimal weight: 10.0000 chunk 877 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 759 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 824 optimal weight: 6.9990 chunk 345 optimal weight: 0.8980 chunk 846 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN l 4 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125996 restraints weight = 287957.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128545 restraints weight = 136105.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128635 restraints weight = 75354.123| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.238 159812 Z= 0.345 Angle : 0.734 59.200 239016 Z= 0.378 Chirality : 0.039 1.190 30547 Planarity : 0.006 0.234 12841 Dihedral : 23.570 179.949 79850 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.04 % Favored : 88.72 % Rotamer: Outliers : 4.72 % Allowed : 24.06 % Favored : 71.22 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.56 (0.10), residues: 5834 helix: -1.02 (0.13), residues: 1616 sheet: -1.33 (0.16), residues: 982 loop : -2.23 (0.10), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 80 HIS 0.018 0.002 HIS M 13 PHE 0.086 0.002 PHE m 62 TYR 0.039 0.003 TYR O 99 ARG 0.063 0.001 ARG m 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43930.73 seconds wall clock time: 764 minutes 57.49 seconds (45897.49 seconds total)