Starting phenix.real_space_refine on Sun Feb 25 02:54:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enu_3903/02_2024/6enu_3903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enu_3903/02_2024/6enu_3903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enu_3903/02_2024/6enu_3903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enu_3903/02_2024/6enu_3903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enu_3903/02_2024/6enu_3903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enu_3903/02_2024/6enu_3903_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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 4613 5.49 5 S 155 5.16 5 C 73892 2.51 5 N 27276 2.21 5 O 40539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 64": "OD1" <-> "OD2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "w PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 146475 Number of models: 1 Model: "" Number of chains: 58 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': 102, 'rna2p_pyr': 52, 'rna3p_pur': 772, 'rna3p_pyr': 613} Link IDs: {'rna2p': 154, 'rna3p': 1384} 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: "v" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} 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': 101, 'rna3p_pur': 1426, 'rna3p_pyr': 1111} Link IDs: {'rna2p': 334, 'rna3p': 2536} 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: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} 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: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: "x" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 62} 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: "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': 1, 'PTRANS': 8, 'TRANS': 178} 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: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "x" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 57.28, per 1000 atoms: 0.39 Number of scatterers: 146475 At special positions: 0 Unit cell: (267.748, 277.504, 227.64, 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 155 16.00 P 4613 15.00 O 40539 8.00 N 27276 7.00 C 73892 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: 57.75 Conformation dependent library (CDL) restraints added in 7.0 seconds 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11186 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: 178 helices and 79 sheets defined 37.0% alpha, 19.4% beta 1333 base pairs and 2700 stacking pairs defined. Time for finding SS restraints: 77.45 Creating SS restraints... Processing helix chain 'b' and resid 41 through 63 removed outlier: 3.722A pdb=" N THR b 45 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 4.313A pdb=" N GLU b 51 " --> pdb=" O PRO b 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG b 62 " --> pdb=" O LYS b 58 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS b 63 " --> pdb=" O ILE b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 87 removed outlier: 6.263A pdb=" N SER b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 5.138A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG b 112 " --> pdb=" O GLN b 108 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLN b 119 " --> pdb=" O ASP b 115 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.860A pdb=" N GLU b 139 " --> pdb=" O MET b 135 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.587A pdb=" N GLU b 174 " --> pdb=" O ILE b 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA b 175 " --> pdb=" O ALA b 171 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 196 removed outlier: 4.836A pdb=" N VAL b 195 " --> pdb=" O ASP b 191 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP b 196 " --> pdb=" O PRO b 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 191 through 196' Processing helix chain 'b' and resid 207 through 225 removed outlier: 4.214A pdb=" N LEU b 211 " --> pdb=" O ARG b 207 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR b 212 " --> pdb=" O ALA b 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU b 222 " --> pdb=" O ALA b 218 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.865A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU c 11 " --> pdb=" O ASN c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 4.164A pdb=" N ASN c 31 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP c 35 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS c 44 " --> pdb=" O GLN c 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.049A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 5.129A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.800A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.525A pdb=" N ALA c 132 " --> pdb=" O MET c 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.738A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG d 13 " --> pdb=" O LYS d 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.567A pdb=" N VAL d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY d 65 " --> pdb=" O ARG d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.647A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 96 removed outlier: 3.859A pdb=" N LEU d 89 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 removed outlier: 3.537A pdb=" N GLY d 105 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 120 removed outlier: 3.532A pdb=" N GLN d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 6.536A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU d 158 " --> pdb=" O VAL d 154 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.036A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER d 204 " --> pdb=" O VAL d 200 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.798A pdb=" N LYS e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN e 69 " --> pdb=" O LYS e 65 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.758A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 147 removed outlier: 3.772A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU e 144 " --> pdb=" O ILE e 140 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN e 147 " --> pdb=" O LEU e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 removed outlier: 3.721A pdb=" N ALA e 153 " --> pdb=" O PRO e 149 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS e 155 " --> pdb=" O MET e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 removed outlier: 4.058A pdb=" N GLY e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 removed outlier: 4.565A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.772A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.979A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.760A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS g 24 " --> pdb=" O GLU g 20 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.702A pdb=" N SER g 40 " --> pdb=" O SER g 36 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA g 50 " --> pdb=" O LEU g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.603A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE g 61 " --> pdb=" O GLU g 57 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.410A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG g 101 " --> pdb=" O ALA g 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.965A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA g 127 " --> pdb=" O LEU g 123 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN g 129 " --> pdb=" O ASP g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.918A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.669A pdb=" N ALA h 19 " --> pdb=" O ASN h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.812A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY h 119 " --> pdb=" O ALA h 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 44 through 55 removed outlier: 4.386A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN i 49 " --> pdb=" O MET i 45 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.550A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 44 through 55' Processing helix chain 'i' and resid 70 through 87 removed outlier: 3.525A pdb=" N ARG i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 101 removed outlier: 4.861A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG i 98 " --> pdb=" O ARG i 94 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.685A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 4.431A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.904A pdb=" N SER k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.917A 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 59 removed outlier: 4.235A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 75 removed outlier: 4.329A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.104A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN k 100 " --> pdb=" O ILE k 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 removed outlier: 3.975A pdb=" N LEU l 6 " --> pdb=" O THR l 2 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL l 7 " --> pdb=" O VAL l 3 " (cutoff:3.500A) removed outlier: 4.157A 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: 4.855A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 20 removed outlier: 4.029A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.779A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA m 35 " --> pdb=" O ALA m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.220A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.711A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA m 60 " --> pdb=" O ARG m 56 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.903A pdb=" N ARG m 69 " --> pdb=" O GLU m 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG m 70 " --> pdb=" O GLY m 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER m 73 " --> pdb=" O ARG m 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 removed outlier: 3.753A pdb=" N ARG m 91 " --> pdb=" O GLY m 87 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG m 92 " --> pdb=" O LEU m 88 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY m 93 " --> pdb=" O ARG m 89 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 removed outlier: 3.787A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU n 15 " --> pdb=" O LYS n 11 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS n 18 " --> pdb=" O ALA n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 23 through 31 removed outlier: 4.500A pdb=" N LYS n 27 " --> pdb=" O ARG n 23 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA n 28 " --> pdb=" O ALA n 24 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER n 31 " --> pdb=" O LYS n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 52 removed outlier: 3.670A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA n 44 " --> pdb=" O ASP n 40 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.882A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.070A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 46 removed outlier: 3.633A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA o 43 " --> pdb=" O GLN o 39 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS o 45 " --> pdb=" O HIS o 41 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS o 46 " --> pdb=" O PHE o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 4.331A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN o 61 " --> pdb=" O ARG o 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG o 71 " --> pdb=" O ASP o 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.704A pdb=" N LEU o 80 " --> pdb=" O ARG o 76 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU o 82 " --> pdb=" O THR o 78 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 64 removed outlier: 4.616A pdb=" N ALA p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY p 62 " --> pdb=" O ALA p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.981A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU p 77 " --> pdb=" O ALA p 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 17 removed outlier: 4.753A pdb=" N GLY r 16 " --> pdb=" O PHE r 12 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL r 17 " --> pdb=" O THR r 13 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.917A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.631A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) removed outlier: 3.730A 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 47 through 65 removed outlier: 3.501A pdb=" N GLN r 51 " --> pdb=" O ARG r 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG r 52 " --> pdb=" O ALA r 48 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR r 63 " --> pdb=" O LYS r 59 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 25 removed outlier: 4.186A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.508A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.963A 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 40 removed outlier: 4.817A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG t 17 " --> pdb=" O SER t 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE t 38 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 removed outlier: 3.800A pdb=" N GLN t 47 " --> pdb=" O LYS t 43 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE t 50 " --> pdb=" O ALA t 46 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.532A pdb=" N ARG t 59 " --> pdb=" O PRO t 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN t 60 " --> pdb=" O ILE t 56 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA t 61 " --> pdb=" O VAL t 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 5.943A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN t 77 " --> pdb=" O ARG t 73 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.662A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 33 removed outlier: 4.581A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) removed outlier: 7.079A 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 36 through 61 Proline residue: u 40 - end of helix removed outlier: 3.604A pdb=" N LYS u 45 " --> pdb=" O THR u 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG u 54 " --> pdb=" O SER u 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 removed outlier: 3.525A pdb=" N ARG C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 15' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.524A 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: 4.149A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.915A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.128A 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 259 through 267 removed outlier: 6.439A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.162A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.547A pdb=" N VAL D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.699A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.325A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 removed outlier: 3.912A pdb=" N GLY D 44 " --> pdb=" O ASP D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 39 through 44' Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.630A pdb=" N ALA E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.753A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.534A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.620A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.672A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 4.023A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'F' and resid 1 through 10 removed outlier: 3.784A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.104A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.032A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 60 removed outlier: 3.640A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.815A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.820A 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: 3.949A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.874A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 3.738A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.692A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.521A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 4.024A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 6.302A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 74 removed outlier: 4.788A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 4.704A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.071A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.577A pdb=" N ASP J 71 " --> pdb=" O ASN J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.589A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.769A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.946A 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 123 removed outlier: 3.696A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.250A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.558A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.792A 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 74 removed outlier: 4.240A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 removed outlier: 4.253A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.693A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 5.461A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.631A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.588A pdb=" N PHE M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.873A 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 32 removed outlier: 3.648A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 3.676A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.066A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.524A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.564A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.534A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.588A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.092A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.701A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.630A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.312A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.072A 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: 3.805A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.833A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 72 removed outlier: 3.887A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 3.698A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY Q 81 " --> pdb=" O LYS Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.653A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 15 through 25 removed outlier: 3.531A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.532A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.948A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 11 removed outlier: 3.836A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.946A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.511A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.740A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.037A 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: 3.768A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.752A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.155A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.695A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 removed outlier: 3.521A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.620A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.568A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 35 removed outlier: 3.511A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 4.769A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.628A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 20 removed outlier: 4.715A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 removed outlier: 3.781A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 25 removed outlier: 4.014A pdb=" N ALA 2 23 " --> pdb=" O ARG 2 19 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.547A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.540A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 removed outlier: 4.993A 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: 5.159A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '6' and resid 43 through 53 removed outlier: 4.305A pdb=" N LYS 6 47 " --> pdb=" O PHE 6 43 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG 6 49 " --> pdb=" O THR 6 45 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL 6 51 " --> pdb=" O LYS 6 47 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 43 through 53' Processing helix chain '6' and resid 55 through 65 removed outlier: 4.323A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 15 removed outlier: 5.946A pdb=" N VAL 7 10 " --> pdb=" O LYS 7 6 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE 7 11 " --> pdb=" O ARG 7 7 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG 7 12 " --> pdb=" O MET 7 8 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS 7 14 " --> pdb=" O VAL 7 10 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL 7 15 " --> pdb=" O ILE 7 11 " (cutoff:3.500A) Processing helix chain '7' and resid 24 through 30 removed outlier: 4.043A pdb=" N ALA 7 28 " --> pdb=" O ASN 7 24 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU 7 29 " --> pdb=" O GLU 7 25 " (cutoff:3.500A) Processing helix chain '7' and resid 81 through 91 removed outlier: 4.744A pdb=" N GLU 7 85 " --> pdb=" O GLY 7 81 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA 7 87 " --> pdb=" O ASN 7 83 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS 7 88 " --> pdb=" O ALA 7 84 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA 7 89 " --> pdb=" O GLU 7 85 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA 7 90 " --> pdb=" O ALA 7 86 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY 7 91 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 96 through 107 removed outlier: 6.928A pdb=" N LEU 7 100 " --> pdb=" O GLY 7 96 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA 7 101 " --> pdb=" O MET 7 97 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN 7 103 " --> pdb=" O ASP 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 117 through 126 removed outlier: 5.236A pdb=" N ARG 7 122 " --> pdb=" O PRO 7 118 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL 7 123 " --> pdb=" O ASP 7 119 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY 7 125 " --> pdb=" O MET 7 121 " (cutoff:3.500A) removed outlier: 3.981A 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 158 removed outlier: 3.591A pdb=" N ASN 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA 7 158 " --> pdb=" O LYS 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 201 removed outlier: 3.703A pdb=" N LYS 7 186 " --> pdb=" O ALA 7 182 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU 7 187 " --> pdb=" O ASP 7 183 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN 7 188 " --> pdb=" O LYS 7 184 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 7 191 " --> pdb=" O GLU 7 187 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU 7 193 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL 7 194 " --> pdb=" O GLU 7 190 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA 7 195 " --> pdb=" O ALA 7 191 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU 7 196 " --> pdb=" O LEU 7 192 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS 7 200 " --> pdb=" O LEU 7 196 " (cutoff:3.500A) Proline residue: 7 201 - end of helix Processing helix chain 'w' and resid 96 through 101 removed outlier: 3.528A pdb=" N GLY w 101 " --> pdb=" O ALA w 97 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 30 through 33 removed outlier: 3.915A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 88 through 92 removed outlier: 3.536A pdb=" N LEU b 67 " --> pdb=" O ALA b 159 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.630A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 163 through 169 removed outlier: 3.565A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 140 through 143 removed outlier: 4.268A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 11 through 15 removed outlier: 3.812A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.159A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU e 123 " --> pdb=" O GLN e 96 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.613A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 39 through 42 removed outlier: 5.515A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 71 through 78 removed outlier: 6.981A pdb=" N THR g 71 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.254A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR h 61 " --> pdb=" O ASP h 47 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.688A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.511A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR i 65 " --> pdb=" O ARG i 17 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.353A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER j 101 " --> pdb=" O ARG j 7 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.683A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'k' and resid 41 through 44 removed outlier: 3.754A pdb=" N GLY k 42 " --> pdb=" O ILE k 33 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 28 through 31 removed outlier: 4.998A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.561A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.987A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 6 through 10 removed outlier: 6.721A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 's' and resid 29 through 33 removed outlier: 4.683A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 1 through 4 Processing sheet with id= 24, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.804A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.382A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.557A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.664A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.088A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 179 through 182 Processing sheet with id= 30, first strand: chain 'D' and resid 24 through 29 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.555A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.918A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.508A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 14 through 19 removed outlier: 6.210A pdb=" N GLN G 21 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY G 30 " --> pdb=" O GLY G 27 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 93 through 98 removed outlier: 7.232A pdb=" N ASN G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 112 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.569A pdb=" N LYS G 133 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 88 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS G 85 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 2 through 5 removed outlier: 5.685A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 114 through 117 removed outlier: 5.520A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 40, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.313A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.968A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.747A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'L' and resid 120 through 123 Processing sheet with id= 44, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.723A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.467A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.596A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.581A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA O 37 " --> pdb=" O ALA O 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 37 through 45 removed outlier: 6.382A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.781A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.649A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.066A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 57 through 60 removed outlier: 4.950A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.504A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.169A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 4 through 8 removed outlier: 4.825A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 81 through 88 removed outlier: 4.246A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.386A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'U' and resid 39 through 44 removed outlier: 4.523A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.860A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'W' and resid 34 through 37 removed outlier: 4.045A pdb=" N SER W 35 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'W' and resid 45 through 48 removed outlier: 6.371A pdb=" N ILE W 82 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS W 78 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL W 71 " --> pdb=" O LYS W 78 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE W 80 " --> pdb=" O PHE W 69 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE W 69 " --> pdb=" O ILE W 80 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL W 67 " --> pdb=" O ILE W 82 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA W 84 " --> pdb=" O GLY W 65 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY W 65 " --> pdb=" O ALA W 84 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X' and resid 11 through 18 removed outlier: 4.146A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 64, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.038A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '0' and resid 27 through 30 removed outlier: 6.249A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '1' and resid 18 through 23 removed outlier: 6.227A pdb=" N HIS 1 18 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE 1 47 " --> pdb=" O SER 1 13 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '3' and resid 21 through 24 removed outlier: 5.584A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 69, first strand: chain '6' and resid 11 through 16 removed outlier: 3.724A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '7' and resid 59 through 65 removed outlier: 7.592A pdb=" N VAL 7 59 " --> pdb=" O ASP 7 166 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP 7 166 " --> pdb=" O VAL 7 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG 7 164 " --> pdb=" O GLY 7 61 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR 7 63 " --> pdb=" O ARG 7 162 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN 7 160 " --> pdb=" O LEU 7 65 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '7' and resid 75 through 78 Processing sheet with id= 72, first strand: chain '7' and resid 170 through 177 removed outlier: 4.624A pdb=" N ILE 7 170 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL 7 42 " --> pdb=" O GLY 7 176 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN 7 47 " --> pdb=" O VAL 7 212 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL 7 212 " --> pdb=" O ASN 7 47 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER 7 213 " --> pdb=" O ASP 7 225 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA 7 223 " --> pdb=" O SER 7 215 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR 7 217 " --> pdb=" O GLY 7 221 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY 7 221 " --> pdb=" O THR 7 217 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'w' and resid 2 through 5 removed outlier: 6.482A pdb=" N ALA w 2 " --> pdb=" O GLY w 64 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA w 62 " --> pdb=" O TYR w 4 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'w' and resid 12 through 16 removed outlier: 4.597A pdb=" N LEU w 13 " --> pdb=" O VAL w 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL w 24 " --> pdb=" O LEU w 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS w 42 " --> pdb=" O GLU w 25 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'w' and resid 81 through 86 removed outlier: 6.407A pdb=" N TRP w 82 " --> pdb=" O SER w 94 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER w 94 " --> pdb=" O TRP w 82 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE w 84 " --> pdb=" O GLN w 92 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN w 92 " --> pdb=" O PHE w 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN w 86 " --> pdb=" O PHE w 90 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'w' and resid 113 through 117 Processing sheet with id= 77, first strand: chain 'w' and resid 130 through 134 removed outlier: 4.704A pdb=" N VAL w 173 " --> pdb=" O VAL w 187 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER w 185 " --> pdb=" O LYS w 175 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'w' and resid 152 through 156 removed outlier: 4.583A pdb=" N ALA w 160 " --> pdb=" O LEU w 156 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'w' and resid 39 through 44 removed outlier: 3.788A pdb=" N VAL w 52 " --> pdb=" O LEU w 43 " (cutoff:3.500A) 1556 hydrogen bonds defined for protein. 4587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3277 hydrogen bonds 5174 hydrogen bond angles 0 basepair planarities 1333 basepair parallelities 2700 stacking parallelities Total time for adding SS restraints: 256.88 Time building geometry restraints manager: 62.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 15063 1.31 - 1.44: 69415 1.44 - 1.57: 65018 1.57 - 1.70: 9218 1.70 - 1.83: 278 Bond restraints: 158992 Sorted by residual: bond pdb=" O3' C x 74 " pdb=" P C x 75 " ideal model delta sigma weight residual 1.607 1.473 0.134 1.50e-02 4.44e+03 8.01e+01 bond pdb=" N ALA w 147 " pdb=" CA ALA w 147 " ideal model delta sigma weight residual 1.457 1.562 -0.105 1.29e-02 6.01e+03 6.59e+01 bond pdb=" C ILE s 39 " pdb=" N PHE s 40 " ideal model delta sigma weight residual 1.330 1.224 0.107 1.37e-02 5.33e+03 6.07e+01 bond pdb=" C LYS X 9 " pdb=" N ARG X 10 " ideal model delta sigma weight residual 1.327 1.202 0.125 1.71e-02 3.42e+03 5.35e+01 bond pdb=" NZ KEO w 34 " pdb=" C05 KEO w 34 " ideal model delta sigma weight residual 1.349 1.446 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 158987 not shown) Histogram of bond angle deviations from ideal: 74.09 - 87.65: 4 87.65 - 101.21: 1843 101.21 - 114.77: 128822 114.77 - 128.33: 100103 128.33 - 141.90: 6752 Bond angle restraints: 237524 Sorted by residual: angle pdb=" O3' A x 73 " pdb=" P C x 74 " pdb=" OP1 C x 74 " ideal model delta sigma weight residual 108.00 74.09 33.91 3.00e+00 1.11e-01 1.28e+02 angle pdb=" O3' A x 73 " pdb=" P C x 74 " pdb=" OP2 C x 74 " ideal model delta sigma weight residual 108.00 75.92 32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C GLY 7 132 " pdb=" N PRO 7 133 " pdb=" CD PRO 7 133 " ideal model delta sigma weight residual 125.00 85.44 39.56 4.10e+00 5.95e-02 9.31e+01 angle pdb=" C ASN 7 139 " pdb=" N PRO 7 140 " pdb=" CD PRO 7 140 " ideal model delta sigma weight residual 125.00 86.17 38.83 4.10e+00 5.95e-02 8.97e+01 angle pdb=" N ARG 7 134 " pdb=" CA ARG 7 134 " pdb=" C ARG 7 134 " ideal model delta sigma weight residual 111.14 102.28 8.86 1.08e+00 8.57e-01 6.73e+01 ... (remaining 237519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 89841 35.97 - 71.93: 10638 71.93 - 107.90: 1233 107.90 - 143.87: 18 143.87 - 179.83: 44 Dihedral angle restraints: 101774 sinusoidal: 84429 harmonic: 17345 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 -113.27 -66.73 0 5.00e+00 4.00e-02 1.78e+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 -117.39 -62.61 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA ASN f 52 " pdb=" C ASN f 52 " pdb=" N LYS f 53 " pdb=" CA LYS f 53 " ideal model delta harmonic sigma weight residual -180.00 -118.67 -61.33 0 5.00e+00 4.00e-02 1.50e+02 ... (remaining 101771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 30158 0.202 - 0.404: 157 0.404 - 0.607: 9 0.607 - 0.809: 0 0.809 - 1.011: 2 Chirality restraints: 30326 Sorted by residual: chirality pdb=" P C x 74 " pdb=" OP1 C x 74 " pdb=" OP2 C x 74 " pdb=" O5' C x 74 " both_signs ideal model delta sigma weight residual True 2.41 1.40 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" P C x 75 " pdb=" OP1 C x 75 " pdb=" OP2 C x 75 " pdb=" O5' C x 75 " both_signs ideal model delta sigma weight residual True 2.41 -1.40 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CG LEU w 107 " pdb=" CB LEU w 107 " pdb=" CD1 LEU w 107 " pdb=" CD2 LEU w 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 30323 not shown) Planarity restraints: 12959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 7 139 " 0.141 5.00e-02 4.00e+02 2.23e-01 7.98e+01 pdb=" N PRO 7 140 " -0.385 5.00e-02 4.00e+02 pdb=" CA PRO 7 140 " 0.152 5.00e-02 4.00e+02 pdb=" CD PRO 7 140 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 7 132 " -0.141 5.00e-02 4.00e+02 2.21e-01 7.82e+01 pdb=" N PRO 7 133 " 0.381 5.00e-02 4.00e+02 pdb=" CA PRO 7 133 " -0.151 5.00e-02 4.00e+02 pdb=" CD PRO 7 133 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET 7 137 " 0.111 5.00e-02 4.00e+02 1.74e-01 4.87e+01 pdb=" N PRO 7 138 " -0.302 5.00e-02 4.00e+02 pdb=" CA PRO 7 138 " 0.108 5.00e-02 4.00e+02 pdb=" CD PRO 7 138 " 0.083 5.00e-02 4.00e+02 ... (remaining 12956 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 7 1.79 - 2.57: 1270 2.57 - 3.34: 157051 3.34 - 4.12: 481752 4.12 - 4.90: 701694 Nonbonded interactions: 1341774 Sorted by model distance: nonbonded pdb=" ND2 ASN 7 139 " pdb=" CG2 THR 7 146 " model vdw 1.009 3.540 nonbonded pdb=" N3 A A2169 " pdb=" NH2 ARG 7 134 " model vdw 1.325 2.600 nonbonded pdb=" C PRO A3001 " pdb=" N PRO x 101 " model vdw 1.341 3.350 nonbonded pdb=" N2 G x 52 " pdb=" O2 C x 62 " model vdw 1.398 2.496 nonbonded pdb=" O3' A x 76 " pdb=" C PRO x 101 " model vdw 1.629 3.270 ... (remaining 1341769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 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: 0.220 Extract box with map and model: 15.730 Check model and map are aligned: 1.640 Set scattering table: 1.060 Process input model: 557.680 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.420 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 585.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 158992 Z= 0.460 Angle : 1.008 39.564 237524 Z= 0.520 Chirality : 0.053 1.011 30326 Planarity : 0.008 0.223 12959 Dihedral : 23.072 179.833 90585 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.76 % Favored : 88.51 % Rotamer: Outliers : 1.19 % Allowed : 3.64 % Favored : 95.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.01 % Twisted General : 0.56 % 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: -4.85 (0.08), residues: 5987 helix: -4.33 (0.06), residues: 1678 sheet: -2.39 (0.14), residues: 1097 loop : -2.91 (0.09), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP C 212 HIS 0.033 0.003 HIS k 117 PHE 0.036 0.004 PHE b 31 TYR 0.035 0.004 TYR H 25 ARG 0.021 0.002 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2009 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1950 time to evaluate : 6.426 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: symmetry clash revert: symmetry clash REVERT: b 41 ASN cc_start: 0.7277 (t0) cc_final: 0.7070 (t0) REVERT: b 193 ASP cc_start: 0.6423 (t70) cc_final: 0.6199 (t70) REVERT: c 120 THR cc_start: 0.8496 (m) cc_final: 0.8237 (m) REVERT: c 141 MET cc_start: 0.8085 (mmm) cc_final: 0.7752 (mmm) REVERT: d 88 ASN cc_start: 0.8497 (m-40) cc_final: 0.8273 (m110) REVERT: e 69 ASN cc_start: 0.8156 (t160) cc_final: 0.7758 (t0) REVERT: e 152 VAL cc_start: 0.8102 (m) cc_final: 0.7849 (t) REVERT: f 9 MET cc_start: 0.8122 (mtm) cc_final: 0.7879 (mtm) REVERT: g 66 GLU cc_start: 0.7139 (pt0) cc_final: 0.6937 (pt0) REVERT: g 75 LYS cc_start: 0.7317 (ptmt) cc_final: 0.7044 (pttm) REVERT: g 100 MET cc_start: 0.8088 (mtm) cc_final: 0.7649 (mtt) REVERT: g 105 GLU cc_start: 0.5970 (tp30) cc_final: 0.5518 (tp30) REVERT: h 61 THR cc_start: 0.8074 (m) cc_final: 0.7798 (p) REVERT: j 45 ARG cc_start: 0.6260 (mtp85) cc_final: 0.6049 (mtp85) REVERT: k 56 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8158 (ttpt) REVERT: k 64 VAL cc_start: 0.9213 (p) cc_final: 0.8818 (t) REVERT: m 80 MET cc_start: 0.7201 (mtm) cc_final: 0.6783 (ttp) REVERT: n 75 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7931 (ttm170) REVERT: p 17 TYR cc_start: 0.8524 (m-80) cc_final: 0.8136 (m-80) REVERT: s 78 THR cc_start: 0.8536 (p) cc_final: 0.8274 (m) REVERT: t 7 LYS cc_start: 0.8760 (ptpt) cc_final: 0.8436 (ptpt) REVERT: t 56 ILE cc_start: 0.9129 (tp) cc_final: 0.8744 (tp) REVERT: C 81 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7700 (mm-30) REVERT: C 149 LYS cc_start: 0.9041 (tptm) cc_final: 0.8790 (tptm) REVERT: C 159 THR cc_start: 0.9006 (m) cc_final: 0.8741 (p) REVERT: C 255 LYS cc_start: 0.8811 (mttp) cc_final: 0.8331 (mmmt) REVERT: E 4 VAL cc_start: 0.8302 (m) cc_final: 0.8009 (p) REVERT: E 24 ASN cc_start: 0.8889 (t0) cc_final: 0.8684 (t0) REVERT: E 43 THR cc_start: 0.8197 (p) cc_final: 0.7928 (p) REVERT: E 155 GLU cc_start: 0.5944 (tp30) cc_final: 0.5543 (tp30) REVERT: E 165 HIS cc_start: 0.6496 (t-170) cc_final: 0.6248 (t70) REVERT: E 170 ARG cc_start: 0.8396 (mmt90) cc_final: 0.8024 (mtp85) REVERT: E 185 LYS cc_start: 0.8354 (mmtp) cc_final: 0.7822 (mmtt) REVERT: F 47 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7247 (tptt) REVERT: F 72 SER cc_start: 0.7278 (t) cc_final: 0.7030 (p) REVERT: F 104 THR cc_start: 0.8571 (m) cc_final: 0.8127 (p) REVERT: F 129 MET cc_start: 0.7293 (ptp) cc_final: 0.6845 (ptp) REVERT: G 36 LEU cc_start: 0.8289 (mt) cc_final: 0.8083 (mt) REVERT: G 66 THR cc_start: 0.8399 (m) cc_final: 0.8140 (m) REVERT: G 121 THR cc_start: 0.7898 (p) cc_final: 0.7674 (t) REVERT: G 142 GLN cc_start: 0.8149 (tp40) cc_final: 0.7875 (mm-40) REVERT: K 20 MET cc_start: 0.8692 (ttp) cc_final: 0.8384 (ttp) REVERT: K 51 LYS cc_start: 0.8188 (mttp) cc_final: 0.7937 (mtmt) REVERT: K 59 LYS cc_start: 0.8429 (mttt) cc_final: 0.8102 (mttt) REVERT: K 106 GLU cc_start: 0.6079 (mp0) cc_final: 0.5794 (mp0) REVERT: L 76 GLU cc_start: 0.7289 (pt0) cc_final: 0.7075 (pt0) REVERT: M 45 GLN cc_start: 0.8607 (mt0) cc_final: 0.8386 (mt0) REVERT: N 116 VAL cc_start: 0.8620 (t) cc_final: 0.8410 (t) REVERT: P 2 ASN cc_start: 0.8539 (m-40) cc_final: 0.8139 (m-40) REVERT: Q 51 GLN cc_start: 0.8471 (mt0) cc_final: 0.8256 (mt0) REVERT: R 27 ILE cc_start: 0.8650 (mm) cc_final: 0.8448 (mm) REVERT: S 15 GLN cc_start: 0.8186 (tt0) cc_final: 0.7774 (tt0) REVERT: S 92 ARG cc_start: 0.7637 (ptp90) cc_final: 0.7435 (ptm-80) REVERT: T 59 ASN cc_start: 0.8829 (p0) cc_final: 0.8550 (p0) REVERT: T 70 HIS cc_start: 0.6924 (t70) cc_final: 0.6621 (t-170) REVERT: T 74 ILE cc_start: 0.7568 (pt) cc_final: 0.7226 (mp) REVERT: U 36 GLU cc_start: 0.6677 (pm20) cc_final: 0.6438 (pm20) REVERT: W 11 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7007 (mtm-85) REVERT: W 32 LEU cc_start: 0.9156 (mt) cc_final: 0.8703 (mt) REVERT: W 35 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8543 (m) REVERT: W 44 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8257 (ttmm) REVERT: 0 16 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7870 (mtt180) REVERT: 3 48 MET cc_start: 0.7870 (mmm) cc_final: 0.7564 (mmm) REVERT: 3 56 LEU cc_start: 0.8924 (mt) cc_final: 0.8488 (mt) REVERT: 6 56 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.6845 (mmm160) REVERT: w 4 TYR cc_start: 0.7921 (m-80) cc_final: 0.7547 (m-80) REVERT: w 29 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: w 53 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7006 (mt-10) REVERT: w 63 GLU cc_start: 0.6271 (tp30) cc_final: 0.6055 (tp30) REVERT: w 78 ASP cc_start: 0.7648 (t0) cc_final: 0.7426 (t0) outliers start: 59 outliers final: 27 residues processed: 1989 average time/residue: 1.4166 time to fit residues: 4684.5364 Evaluate side-chains 1460 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1430 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 41 ARG Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 121 MET Chi-restraints excluded: chain 7 residue 137 MET Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 29 PHE Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 107 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 881 optimal weight: 0.9980 chunk 791 optimal weight: 4.9990 chunk 439 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 533 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 818 optimal weight: 2.9990 chunk 316 optimal weight: 10.0000 chunk 497 optimal weight: 6.9990 chunk 609 optimal weight: 10.0000 chunk 948 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 23 ASN b 35 ASN b 167 HIS c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 197 HIS e 69 ASN f 11 HIS f 55 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN i 49 GLN j 15 HIS j 64 GLN l 111 GLN n 3 GLN n 60 GLN o 37 HIS o 39 GLN o 50 HIS p 63 GLN q 30 HIS q 44 HIS r 51 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS s 68 HIS t 12 GLN t 19 HIS t 51 ASN C 36 ASN C 114 GLN C 162 GLN D 32 ASN D 49 GLN D 94 GLN D 130 GLN D 150 GLN D 164 GLN E 136 GLN E 156 ASN E 163 ASN F 26 GLN G 63 GLN G 115 GLN G 138 GLN J 40 HIS J 58 ASN K 88 ASN K 93 GLN M 22 GLN N 9 GLN N 18 GLN N 31 HIS N 107 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN P 6 GLN P 11 GLN Q 43 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN S 7 HIS T 15 HIS U 65 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 3 42 HIS ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN 6 20 ASN 7 139 ASN w 71 ASN w 87 ASN ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 158992 Z= 0.257 Angle : 0.665 28.140 237524 Z= 0.346 Chirality : 0.041 1.924 30326 Planarity : 0.006 0.145 12959 Dihedral : 23.775 178.761 78802 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.09 % Favored : 90.60 % Rotamer: Outliers : 3.94 % Allowed : 12.80 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.01 % Twisted General : 0.34 % 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: -3.81 (0.09), residues: 5987 helix: -2.89 (0.09), residues: 1735 sheet: -2.07 (0.15), residues: 1066 loop : -2.47 (0.10), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 212 HIS 0.010 0.002 HIS 3 30 PHE 0.022 0.002 PHE b 31 TYR 0.025 0.002 TYR g 84 ARG 0.008 0.001 ARG f 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1494 time to evaluate : 6.394 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: b 94 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8008 (ttt180) REVERT: e 25 LYS cc_start: 0.8852 (tptm) cc_final: 0.8519 (tptt) REVERT: e 53 ARG cc_start: 0.8392 (tpp80) cc_final: 0.8147 (mmt90) REVERT: e 59 ILE cc_start: 0.9019 (pp) cc_final: 0.8647 (mt) REVERT: e 67 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7431 (mtt-85) REVERT: f 68 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6582 (mm110) REVERT: g 100 MET cc_start: 0.8188 (mtm) cc_final: 0.7952 (mtt) REVERT: g 137 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: g 139 ASP cc_start: 0.7463 (m-30) cc_final: 0.7183 (m-30) REVERT: h 98 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7632 (pp) REVERT: j 10 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8245 (pp) REVERT: j 45 ARG cc_start: 0.6404 (mtp85) cc_final: 0.6195 (ttt90) REVERT: j 47 GLU cc_start: 0.7195 (tt0) cc_final: 0.6975 (tt0) REVERT: k 84 MET cc_start: 0.7615 (mmm) cc_final: 0.7036 (mtt) REVERT: l 110 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7514 (mmmt) REVERT: m 71 GLU cc_start: 0.7659 (tp30) cc_final: 0.7411 (tp30) REVERT: n 15 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8352 (tt) REVERT: n 75 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7996 (ttm170) REVERT: o 56 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8625 (mt) REVERT: p 12 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8748 (ttpp) REVERT: p 17 TYR cc_start: 0.8740 (m-80) cc_final: 0.8383 (m-80) REVERT: t 56 ILE cc_start: 0.9090 (tp) cc_final: 0.8699 (tp) REVERT: t 84 LYS cc_start: 0.7143 (ttmm) cc_final: 0.6762 (ttmm) REVERT: C 255 LYS cc_start: 0.8728 (mttp) cc_final: 0.8296 (mmmt) REVERT: E 4 VAL cc_start: 0.8393 (m) cc_final: 0.7962 (p) REVERT: E 155 GLU cc_start: 0.5824 (tp30) cc_final: 0.5547 (tp30) REVERT: E 165 HIS cc_start: 0.6563 (t-170) cc_final: 0.6357 (t70) REVERT: E 170 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7902 (mtp85) REVERT: F 6 TYR cc_start: 0.8423 (t80) cc_final: 0.7960 (t80) REVERT: F 47 LYS cc_start: 0.7860 (ptmt) cc_final: 0.7659 (tptt) REVERT: F 129 MET cc_start: 0.7253 (ptp) cc_final: 0.6799 (ptp) REVERT: G 142 GLN cc_start: 0.8071 (tp40) cc_final: 0.7755 (tp40) REVERT: K 51 LYS cc_start: 0.8148 (mttp) cc_final: 0.7770 (mttp) REVERT: K 59 LYS cc_start: 0.8412 (mttt) cc_final: 0.8076 (mttt) REVERT: K 106 GLU cc_start: 0.6240 (mp0) cc_final: 0.6002 (mp0) REVERT: L 76 GLU cc_start: 0.7524 (pt0) cc_final: 0.7310 (pt0) REVERT: Q 36 GLN cc_start: 0.8244 (tt0) cc_final: 0.8024 (tt0) REVERT: Q 101 ASP cc_start: 0.8005 (t0) cc_final: 0.7780 (t70) REVERT: R 27 ILE cc_start: 0.8484 (mm) cc_final: 0.7653 (mm) REVERT: R 60 LYS cc_start: 0.8072 (tttm) cc_final: 0.7779 (tmtt) REVERT: S 59 GLU cc_start: 0.6964 (pt0) cc_final: 0.6654 (pt0) REVERT: T 59 ASN cc_start: 0.8762 (p0) cc_final: 0.8365 (p0) REVERT: U 5 ARG cc_start: 0.7536 (ptp-170) cc_final: 0.7216 (ptp-170) REVERT: W 11 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6858 (mtm-85) REVERT: W 35 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8680 (p) REVERT: W 44 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8229 (ttmm) REVERT: W 68 LYS cc_start: 0.8349 (tppt) cc_final: 0.8028 (tppt) REVERT: W 70 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7518 (tt0) REVERT: 0 30 ASP cc_start: 0.8377 (t70) cc_final: 0.8119 (t0) REVERT: 2 44 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7150 (p) REVERT: 3 56 LEU cc_start: 0.8752 (mt) cc_final: 0.8547 (mt) REVERT: 7 105 LYS cc_start: 0.7291 (mtpp) cc_final: 0.7000 (mttp) outliers start: 195 outliers final: 117 residues processed: 1591 average time/residue: 1.3715 time to fit residues: 3715.3943 Evaluate side-chains 1471 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1345 time to evaluate : 6.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 109 LYS Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 42 LYS Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain T residue 26 LYS Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 6 residue 62 LYS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain 7 residue 212 VAL Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 93 LEU Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 138 THR Chi-restraints excluded: chain w residue 139 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 526 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 789 optimal weight: 9.9990 chunk 645 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 949 optimal weight: 3.9990 chunk 1026 optimal weight: 0.0770 chunk 845 optimal weight: 4.9990 chunk 941 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 761 optimal weight: 9.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN c 189 HIS ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 151 GLN ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN j 64 GLN l 111 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 13 HIS s 13 HIS s 56 HIS E 163 ASN F 26 GLN G 44 HIS P 6 GLN R 18 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS X 33 HIS Z 8 GLN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 4 13 ASN 6 20 ASN 7 155 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 158992 Z= 0.266 Angle : 0.634 26.442 237524 Z= 0.329 Chirality : 0.040 2.001 30326 Planarity : 0.005 0.119 12959 Dihedral : 23.627 179.522 78763 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.62 % Favored : 90.06 % Rotamer: Outliers : 5.26 % Allowed : 14.96 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.31 % 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: -3.13 (0.10), residues: 5987 helix: -1.86 (0.11), residues: 1752 sheet: -1.83 (0.14), residues: 1134 loop : -2.29 (0.10), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 212 HIS 0.010 0.002 HIS 3 30 PHE 0.027 0.002 PHE b 31 TYR 0.022 0.002 TYR g 84 ARG 0.009 0.001 ARG o 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1658 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1398 time to evaluate : 6.426 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 35 ASP cc_start: 0.8168 (t0) cc_final: 0.7755 (t0) REVERT: c 63 ILE cc_start: 0.8370 (tp) cc_final: 0.8116 (tt) REVERT: c 199 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (t) REVERT: d 183 ARG cc_start: 0.7440 (ppt170) cc_final: 0.7154 (ppt170) REVERT: e 13 LYS cc_start: 0.8106 (mttp) cc_final: 0.7794 (mmtm) REVERT: e 25 LYS cc_start: 0.8879 (tptm) cc_final: 0.8459 (tptt) REVERT: e 59 ILE cc_start: 0.9128 (pp) cc_final: 0.8691 (mt) REVERT: e 60 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: g 100 MET cc_start: 0.8176 (mtm) cc_final: 0.7846 (mtt) REVERT: g 137 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: h 98 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7685 (pp) REVERT: j 45 ARG cc_start: 0.6702 (mtp85) cc_final: 0.6443 (ptm160) REVERT: k 84 MET cc_start: 0.7473 (mmm) cc_final: 0.7213 (mtt) REVERT: l 111 GLN cc_start: 0.8377 (mt0) cc_final: 0.8171 (mt0) REVERT: m 29 SER cc_start: 0.8655 (t) cc_final: 0.8364 (m) REVERT: m 69 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7360 (mtt-85) REVERT: m 71 GLU cc_start: 0.7718 (tp30) cc_final: 0.7446 (tp30) REVERT: m 80 MET cc_start: 0.7262 (mtm) cc_final: 0.6883 (mtp) REVERT: m 82 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8314 (tt) REVERT: n 15 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8411 (tt) REVERT: p 12 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8717 (ttmt) REVERT: p 17 TYR cc_start: 0.8777 (m-80) cc_final: 0.8575 (m-80) REVERT: s 17 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7875 (mtpp) REVERT: s 31 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7526 (mtp-110) REVERT: t 56 ILE cc_start: 0.9041 (tp) cc_final: 0.8772 (tp) REVERT: D 92 VAL cc_start: 0.9000 (t) cc_final: 0.8744 (p) REVERT: E 4 VAL cc_start: 0.8298 (m) cc_final: 0.7902 (p) REVERT: E 145 ASP cc_start: 0.6267 (t70) cc_final: 0.6039 (t70) REVERT: E 170 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7771 (mtp85) REVERT: F 47 LYS cc_start: 0.8141 (ptmt) cc_final: 0.7691 (tptt) REVERT: F 129 MET cc_start: 0.7224 (ptp) cc_final: 0.6684 (ptp) REVERT: G 148 ARG cc_start: 0.8309 (ttt90) cc_final: 0.7863 (ttt180) REVERT: K 30 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8121 (ttt180) REVERT: K 51 LYS cc_start: 0.8140 (mttp) cc_final: 0.7755 (mttp) REVERT: K 59 LYS cc_start: 0.8424 (mttt) cc_final: 0.8067 (mttt) REVERT: K 66 LYS cc_start: 0.8673 (mttp) cc_final: 0.8314 (mttt) REVERT: N 56 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8234 (mmmm) REVERT: Q 100 PHE cc_start: 0.7478 (m-80) cc_final: 0.7258 (m-10) REVERT: R 10 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: S 59 GLU cc_start: 0.7018 (pt0) cc_final: 0.6795 (pt0) REVERT: T 37 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6767 (p0) REVERT: T 59 ASN cc_start: 0.8766 (p0) cc_final: 0.8375 (p0) REVERT: U 5 ARG cc_start: 0.7446 (ptp-170) cc_final: 0.7004 (mtt180) REVERT: W 11 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6908 (mtm-85) REVERT: W 39 ARG cc_start: 0.8477 (mmm160) cc_final: 0.8125 (mmm160) REVERT: W 44 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8145 (ttmm) REVERT: Y 31 GLN cc_start: 0.8280 (mp10) cc_final: 0.7802 (mp10) REVERT: 0 30 ASP cc_start: 0.8493 (t70) cc_final: 0.8236 (t0) REVERT: 2 44 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7177 (p) REVERT: 3 56 LEU cc_start: 0.8576 (mt) cc_final: 0.8294 (mt) REVERT: 7 99 ASP cc_start: 0.6152 (m-30) cc_final: 0.5870 (m-30) REVERT: 7 105 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6781 (mttp) outliers start: 260 outliers final: 171 residues processed: 1535 average time/residue: 1.4054 time to fit residues: 3666.7595 Evaluate side-chains 1498 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1317 time to evaluate : 5.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 938 optimal weight: 0.8980 chunk 714 optimal weight: 5.9990 chunk 492 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 453 optimal weight: 10.0000 chunk 637 optimal weight: 8.9990 chunk 953 optimal weight: 9.9990 chunk 1009 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 903 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 169 HIS c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 197 HIS e 11 GLN f 55 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN h 66 GLN j 64 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN D 150 GLN E 62 GLN E 163 ASN K 93 GLN L 54 GLN M 22 GLN N 107 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN P 11 GLN U 45 GLN U 68 ASN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 4 13 ASN 6 20 ASN 7 165 ASN 7 168 ASN ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 158992 Z= 0.501 Angle : 0.802 28.506 237524 Z= 0.406 Chirality : 0.048 1.899 30326 Planarity : 0.007 0.106 12959 Dihedral : 23.743 179.414 78760 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.59 % Favored : 89.04 % Rotamer: Outliers : 6.69 % Allowed : 16.68 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.36 % 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: -2.99 (0.10), residues: 5987 helix: -1.61 (0.12), residues: 1739 sheet: -1.82 (0.15), residues: 1110 loop : -2.25 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP n 42 HIS 0.015 0.002 HIS 3 30 PHE 0.024 0.003 PHE i 38 TYR 0.036 0.003 TYR g 84 ARG 0.010 0.001 ARG 4 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1706 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1375 time to evaluate : 6.492 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: c 35 ASP cc_start: 0.8276 (t0) cc_final: 0.8002 (t0) REVERT: c 138 GLN cc_start: 0.7398 (mt0) cc_final: 0.7106 (mp10) REVERT: c 141 MET cc_start: 0.8199 (mmm) cc_final: 0.7966 (mmp) REVERT: d 28 ASP cc_start: 0.5067 (OUTLIER) cc_final: 0.4529 (p0) REVERT: e 59 ILE cc_start: 0.9145 (pp) cc_final: 0.8757 (mt) REVERT: e 60 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7753 (mm-40) REVERT: f 2 ARG cc_start: 0.5649 (mtp-110) cc_final: 0.5405 (mtp-110) REVERT: g 6 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6575 (pp) REVERT: h 98 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7605 (pp) REVERT: k 84 MET cc_start: 0.7454 (mmm) cc_final: 0.7138 (mtt) REVERT: l 51 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8234 (t) REVERT: m 26 LYS cc_start: 0.8838 (tptt) cc_final: 0.8593 (tptm) REVERT: m 29 SER cc_start: 0.8776 (t) cc_final: 0.8460 (m) REVERT: m 69 ARG cc_start: 0.7575 (mtt-85) cc_final: 0.7339 (mtt-85) REVERT: m 71 GLU cc_start: 0.7736 (tp30) cc_final: 0.7453 (tp30) REVERT: m 80 MET cc_start: 0.7589 (mtm) cc_final: 0.7236 (mtp) REVERT: p 12 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8815 (ttmt) REVERT: p 63 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7544 (mm-40) REVERT: s 17 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8050 (mtpp) REVERT: s 31 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7626 (mtp-110) REVERT: t 56 ILE cc_start: 0.9022 (tp) cc_final: 0.8771 (tp) REVERT: C 180 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6552 (mpp) REVERT: E 4 VAL cc_start: 0.8266 (m) cc_final: 0.7891 (p) REVERT: E 19 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.6901 (t80) REVERT: E 163 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8288 (t0) REVERT: F 47 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7718 (tptt) REVERT: F 62 GLN cc_start: 0.8559 (pm20) cc_final: 0.8193 (pt0) REVERT: F 129 MET cc_start: 0.7358 (ptp) cc_final: 0.6902 (ptp) REVERT: F 132 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6737 (mtp-110) REVERT: H 90 LEU cc_start: 0.6226 (tp) cc_final: 0.5954 (tp) REVERT: K 29 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.7207 (t-90) REVERT: K 51 LYS cc_start: 0.8049 (mttp) cc_final: 0.7696 (mttp) REVERT: K 66 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8370 (mttt) REVERT: K 106 GLU cc_start: 0.6999 (mp0) cc_final: 0.6794 (mp0) REVERT: Q 100 PHE cc_start: 0.7642 (m-80) cc_final: 0.7294 (m-10) REVERT: U 5 ARG cc_start: 0.7536 (ptp-170) cc_final: 0.7219 (mtt180) REVERT: W 11 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7061 (mtm-85) REVERT: W 39 ARG cc_start: 0.8593 (mmm160) cc_final: 0.8339 (mmm160) REVERT: W 44 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8224 (ttmm) REVERT: X 75 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7050 (mm-30) REVERT: Y 5 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7047 (mt-10) REVERT: Z 5 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8272 (mmmm) REVERT: 0 30 ASP cc_start: 0.8544 (t70) cc_final: 0.8236 (t0) REVERT: 1 49 LYS cc_start: 0.8500 (mttp) cc_final: 0.8172 (mmtm) REVERT: 4 32 LYS cc_start: 0.8288 (mtpt) cc_final: 0.8071 (mttt) REVERT: 6 63 ARG cc_start: 0.6961 (mtt180) cc_final: 0.6629 (mtp85) REVERT: w 177 ASP cc_start: 0.7978 (p0) cc_final: 0.7698 (p0) outliers start: 331 outliers final: 236 residues processed: 1555 average time/residue: 1.3732 time to fit residues: 3654.8597 Evaluate side-chains 1567 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1320 time to evaluate : 6.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 153 VAL Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 29 PHE Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 138 THR Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 170 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 840 optimal weight: 0.9980 chunk 572 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 751 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 861 optimal weight: 0.8980 chunk 697 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 515 optimal weight: 8.9990 chunk 905 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN d 195 ASN e 11 GLN e 72 ASN e 96 GLN f 55 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 17 GLN h 20 ASN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN n 3 GLN C 162 GLN D 150 GLN E 163 ASN J 58 ASN J 136 GLN N 107 ASN O 38 GLN P 11 GLN Q 19 GLN Q 36 GLN Q 51 GLN Q 55 GLN 0 4 GLN 3 27 ASN 4 13 ASN 6 20 ASN 7 155 ASN ** w 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 158992 Z= 0.175 Angle : 0.582 27.842 237524 Z= 0.301 Chirality : 0.037 1.986 30326 Planarity : 0.005 0.098 12959 Dihedral : 23.545 179.879 78760 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.72 % Favored : 91.03 % Rotamer: Outliers : 4.77 % Allowed : 19.78 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.50 % 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: -2.46 (0.10), residues: 5987 helix: -1.00 (0.12), residues: 1762 sheet: -1.46 (0.15), residues: 1093 loop : -2.08 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 169 HIS 0.010 0.001 HIS w 83 PHE 0.018 0.001 PHE f 8 TYR 0.023 0.001 TYR F 7 ARG 0.009 0.000 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1351 time to evaluate : 6.484 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: b 77 GLU cc_start: 0.6091 (pm20) cc_final: 0.5834 (pm20) REVERT: b 112 ARG cc_start: 0.7499 (mmm160) cc_final: 0.7120 (mmm160) REVERT: c 35 ASP cc_start: 0.8139 (t0) cc_final: 0.7695 (t0) REVERT: d 28 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.4193 (p0) REVERT: e 12 GLU cc_start: 0.7365 (pt0) cc_final: 0.6493 (pt0) REVERT: e 25 LYS cc_start: 0.8903 (tptm) cc_final: 0.8341 (tptt) REVERT: e 59 ILE cc_start: 0.9103 (pp) cc_final: 0.8726 (mt) REVERT: e 60 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7620 (mm-40) REVERT: e 76 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (p0) REVERT: h 98 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7492 (pp) REVERT: i 6 TYR cc_start: 0.7972 (t80) cc_final: 0.7699 (t80) REVERT: m 80 MET cc_start: 0.7431 (mtm) cc_final: 0.7048 (mtp) REVERT: o 56 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8551 (mt) REVERT: p 12 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8667 (ttmt) REVERT: p 63 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7399 (mm-40) REVERT: s 17 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8163 (mtpp) REVERT: s 31 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7561 (mtp-110) REVERT: t 26 MET cc_start: 0.8437 (tmm) cc_final: 0.7993 (tmm) REVERT: t 56 ILE cc_start: 0.8994 (tp) cc_final: 0.8730 (tp) REVERT: t 82 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7871 (mt) REVERT: D 1 MET cc_start: 0.5444 (tmm) cc_final: 0.5010 (tmm) REVERT: D 92 VAL cc_start: 0.9018 (t) cc_final: 0.8751 (p) REVERT: E 4 VAL cc_start: 0.8008 (m) cc_final: 0.7591 (p) REVERT: E 47 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8634 (ptpp) REVERT: E 163 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8163 (t0) REVERT: F 47 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7718 (tptt) REVERT: F 129 MET cc_start: 0.7202 (ptp) cc_final: 0.6740 (ptp) REVERT: G 70 LEU cc_start: 0.8013 (mp) cc_final: 0.7794 (mp) REVERT: J 99 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.7929 (mmm160) REVERT: K 51 LYS cc_start: 0.8153 (mttp) cc_final: 0.7794 (mttp) REVERT: K 59 LYS cc_start: 0.8427 (mttt) cc_final: 0.8168 (mttt) REVERT: K 66 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8230 (mttt) REVERT: Q 100 PHE cc_start: 0.7535 (m-80) cc_final: 0.7197 (m-10) REVERT: R 10 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8130 (mtmm) REVERT: T 37 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6733 (p0) REVERT: T 59 ASN cc_start: 0.8616 (p0) cc_final: 0.8283 (p0) REVERT: U 5 ARG cc_start: 0.7324 (ptp-170) cc_final: 0.7049 (mtt180) REVERT: U 86 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: W 11 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7070 (mtm-85) REVERT: W 25 ARG cc_start: 0.8100 (mmp80) cc_final: 0.7836 (mmt-90) REVERT: W 44 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8062 (ttmm) REVERT: X 21 LEU cc_start: 0.8957 (mt) cc_final: 0.8633 (mp) REVERT: Y 31 GLN cc_start: 0.8407 (mp10) cc_final: 0.7953 (mp10) REVERT: 0 30 ASP cc_start: 0.8513 (t70) cc_final: 0.8226 (t0) REVERT: 1 49 LYS cc_start: 0.8453 (mttp) cc_final: 0.8199 (mmtm) REVERT: w 177 ASP cc_start: 0.7665 (p0) cc_final: 0.7322 (p0) outliers start: 236 outliers final: 163 residues processed: 1475 average time/residue: 1.3763 time to fit residues: 3451.3351 Evaluate side-chains 1486 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1310 time to evaluate : 6.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 19 GLU Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 39 ILE Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 100 ILE Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 170 ILE Chi-restraints excluded: chain w residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 339 optimal weight: 10.0000 chunk 908 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 592 optimal weight: 30.0000 chunk 249 optimal weight: 4.9990 chunk 1010 optimal weight: 6.9990 chunk 838 optimal weight: 0.3980 chunk 467 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 530 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 20 ASN i 4 GLN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS l 111 GLN m 7 ASN n 3 GLN o 45 HIS E 163 ASN J 136 GLN N 107 ASN Q 19 GLN Q 36 GLN 0 4 GLN 3 27 ASN 4 13 ASN ** w 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 158992 Z= 0.263 Angle : 0.620 28.140 237524 Z= 0.319 Chirality : 0.039 1.957 30326 Planarity : 0.005 0.070 12959 Dihedral : 23.522 179.522 78758 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.97 % Favored : 89.78 % Rotamer: Outliers : 5.60 % Allowed : 19.70 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.24 % 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: -2.31 (0.10), residues: 5987 helix: -0.80 (0.12), residues: 1757 sheet: -1.44 (0.15), residues: 1144 loop : -2.00 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 169 HIS 0.010 0.001 HIS 3 30 PHE 0.020 0.002 PHE f 8 TYR 0.022 0.002 TYR u 37 ARG 0.008 0.001 ARG m 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1570 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1293 time to evaluate : 6.423 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: b 112 ARG cc_start: 0.7499 (mmm160) cc_final: 0.7102 (mmm160) REVERT: c 123 LEU cc_start: 0.8881 (mt) cc_final: 0.8448 (mp) REVERT: c 199 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8904 (t) REVERT: d 19 PHE cc_start: 0.8302 (m-80) cc_final: 0.8063 (m-80) REVERT: d 28 ASP cc_start: 0.5102 (OUTLIER) cc_final: 0.4197 (p0) REVERT: e 12 GLU cc_start: 0.7113 (pt0) cc_final: 0.6903 (mt-10) REVERT: e 59 ILE cc_start: 0.9103 (pp) cc_final: 0.8703 (mt) REVERT: e 60 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7790 (mm-40) REVERT: e 133 ILE cc_start: 0.8936 (tp) cc_final: 0.8542 (pt) REVERT: h 75 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: h 98 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7636 (pp) REVERT: i 11 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.6646 (tpt170) REVERT: k 80 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7233 (p0) REVERT: m 69 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7501 (mtt-85) REVERT: m 80 MET cc_start: 0.7519 (mtm) cc_final: 0.7166 (mtp) REVERT: m 82 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8340 (tt) REVERT: m 99 GLN cc_start: 0.8895 (mp10) cc_final: 0.8671 (mp10) REVERT: p 12 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8747 (ttmt) REVERT: p 63 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7405 (mm-40) REVERT: s 17 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8155 (mtpp) REVERT: s 31 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7659 (mtp-110) REVERT: t 26 MET cc_start: 0.8501 (tmm) cc_final: 0.8069 (tmm) REVERT: t 56 ILE cc_start: 0.9006 (tp) cc_final: 0.8760 (tp) REVERT: D 1 MET cc_start: 0.5699 (tmm) cc_final: 0.5369 (tmm) REVERT: D 92 VAL cc_start: 0.9010 (t) cc_final: 0.8773 (p) REVERT: E 4 VAL cc_start: 0.7992 (m) cc_final: 0.7567 (p) REVERT: E 163 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8108 (t0) REVERT: F 47 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7735 (tptt) REVERT: F 129 MET cc_start: 0.7304 (ptp) cc_final: 0.6805 (ptp) REVERT: H 90 LEU cc_start: 0.5916 (tp) cc_final: 0.5645 (tp) REVERT: J 99 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.7946 (mmm160) REVERT: K 29 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.7185 (t-90) REVERT: K 51 LYS cc_start: 0.8158 (mttp) cc_final: 0.7813 (mttp) REVERT: K 59 LYS cc_start: 0.8442 (mttt) cc_final: 0.8110 (mttt) REVERT: K 66 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8287 (mttt) REVERT: K 106 GLU cc_start: 0.6998 (mp0) cc_final: 0.6788 (mp0) REVERT: N 114 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: O 19 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8063 (tt0) REVERT: Q 50 ARG cc_start: 0.8797 (mpt180) cc_final: 0.8525 (mpt90) REVERT: Q 100 PHE cc_start: 0.7570 (m-80) cc_final: 0.7186 (m-10) REVERT: S 59 GLU cc_start: 0.7097 (pt0) cc_final: 0.6782 (pt0) REVERT: T 37 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6742 (p0) REVERT: T 59 ASN cc_start: 0.8760 (p0) cc_final: 0.8380 (p0) REVERT: U 5 ARG cc_start: 0.7408 (ptp-170) cc_final: 0.7129 (mtt180) REVERT: U 86 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.5646 (m-80) REVERT: V 71 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7726 (mmtt) REVERT: W 25 ARG cc_start: 0.8317 (mmp80) cc_final: 0.8033 (mmp80) REVERT: W 44 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8161 (ttmm) REVERT: X 21 LEU cc_start: 0.8998 (mt) cc_final: 0.8650 (mp) REVERT: 0 30 ASP cc_start: 0.8528 (t70) cc_final: 0.8251 (t0) REVERT: 1 49 LYS cc_start: 0.8488 (mttp) cc_final: 0.8242 (mmtm) REVERT: 6 56 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.6914 (mmm160) REVERT: w 177 ASP cc_start: 0.7743 (p0) cc_final: 0.7414 (p0) outliers start: 277 outliers final: 213 residues processed: 1455 average time/residue: 1.3462 time to fit residues: 3332.0167 Evaluate side-chains 1509 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1281 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 75 GLN Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 11 ARG Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 100 ILE Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 170 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 973 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 575 optimal weight: 8.9990 chunk 737 optimal weight: 3.9990 chunk 571 optimal weight: 8.9990 chunk 850 optimal weight: 6.9990 chunk 564 optimal weight: 7.9990 chunk 1006 optimal weight: 0.6980 chunk 629 optimal weight: 8.9990 chunk 613 optimal weight: 10.0000 chunk 464 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 20 ASN i 31 GLN l 71 HIS l 111 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN D 150 GLN E 163 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN N 107 ASN Q 19 GLN Q 51 GLN 0 3 GLN 3 27 ASN 4 13 ASN 7 110 ASN 7 155 ASN w 86 ASN ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 158992 Z= 0.415 Angle : 0.731 28.439 237524 Z= 0.373 Chirality : 0.045 1.919 30326 Planarity : 0.006 0.075 12959 Dihedral : 23.616 179.625 78754 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.82 % Favored : 88.89 % Rotamer: Outliers : 6.29 % Allowed : 19.98 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.40 (0.10), residues: 5987 helix: -0.91 (0.12), residues: 1760 sheet: -1.50 (0.15), residues: 1136 loop : -2.03 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 169 HIS 0.014 0.002 HIS 3 30 PHE 0.023 0.002 PHE f 8 TYR 0.036 0.002 TYR o 77 ARG 0.011 0.001 ARG m 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1299 time to evaluate : 8.720 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: b 112 ARG cc_start: 0.7474 (mmm160) cc_final: 0.7046 (mmm160) REVERT: c 138 GLN cc_start: 0.7436 (mt0) cc_final: 0.7165 (mp10) REVERT: c 199 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8890 (t) REVERT: e 59 ILE cc_start: 0.9081 (pp) cc_final: 0.8708 (mt) REVERT: e 67 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7262 (mmt90) REVERT: h 75 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: h 98 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7577 (pp) REVERT: j 5 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.3906 (ttt90) REVERT: k 80 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7252 (p0) REVERT: p 12 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8798 (ttmt) REVERT: p 63 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7541 (mm-40) REVERT: s 31 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7658 (mtp-110) REVERT: D 28 GLU cc_start: 0.7261 (tp30) cc_final: 0.7014 (tp30) REVERT: E 4 VAL cc_start: 0.8152 (m) cc_final: 0.7748 (p) REVERT: E 47 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8823 (ptpp) REVERT: F 47 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7798 (tptt) REVERT: F 71 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7718 (ttpp) REVERT: F 129 MET cc_start: 0.7344 (ptp) cc_final: 0.6907 (ptp) REVERT: J 99 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.7942 (mmm160) REVERT: K 29 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.7241 (t-90) REVERT: K 51 LYS cc_start: 0.8153 (mttp) cc_final: 0.7801 (mttp) REVERT: K 59 LYS cc_start: 0.8471 (mttt) cc_final: 0.8106 (mttt) REVERT: K 66 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8332 (mttt) REVERT: K 106 GLU cc_start: 0.6957 (mp0) cc_final: 0.6704 (mp0) REVERT: N 114 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: Q 50 ARG cc_start: 0.8823 (mpt180) cc_final: 0.8573 (mpt90) REVERT: Q 100 PHE cc_start: 0.7637 (m-80) cc_final: 0.7304 (m-10) REVERT: R 13 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7674 (ttp80) REVERT: T 37 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6889 (p0) REVERT: T 59 ASN cc_start: 0.8889 (p0) cc_final: 0.8622 (p0) REVERT: U 5 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7203 (mtt180) REVERT: V 71 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7741 (mmtt) REVERT: W 25 ARG cc_start: 0.8373 (mmp80) cc_final: 0.8140 (mmp80) REVERT: W 44 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8192 (ttmm) REVERT: W 70 GLU cc_start: 0.7580 (tt0) cc_final: 0.7362 (tt0) REVERT: Y 31 GLN cc_start: 0.8456 (mp10) cc_final: 0.8073 (mp10) REVERT: 0 30 ASP cc_start: 0.8576 (t70) cc_final: 0.8301 (t0) REVERT: 1 49 LYS cc_start: 0.8512 (mttp) cc_final: 0.8255 (mmtm) REVERT: w 177 ASP cc_start: 0.7886 (p0) cc_final: 0.7613 (p0) outliers start: 311 outliers final: 247 residues processed: 1475 average time/residue: 1.3668 time to fit residues: 3418.2839 Evaluate side-chains 1539 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1280 time to evaluate : 6.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 75 GLN Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 17 LYS Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 55 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 29 PHE Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 100 ILE Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 170 ILE Chi-restraints excluded: chain w residue 173 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 622 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 600 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 197 optimal weight: 0.2980 chunk 194 optimal weight: 5.9990 chunk 639 optimal weight: 6.9990 chunk 685 optimal weight: 0.9980 chunk 497 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 790 optimal weight: 20.0000 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN l 111 GLN C 162 GLN D 150 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 19 GLN Q 51 GLN 0 4 GLN 3 27 ASN 4 13 ASN ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 158992 Z= 0.307 Angle : 0.673 28.140 237524 Z= 0.347 Chirality : 0.042 1.943 30326 Planarity : 0.005 0.091 12959 Dihedral : 23.614 178.884 78754 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.46 % Favored : 89.29 % Rotamer: Outliers : 6.11 % Allowed : 20.65 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.27 % 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: -2.31 (0.10), residues: 5987 helix: -0.81 (0.12), residues: 1757 sheet: -1.46 (0.15), residues: 1124 loop : -1.99 (0.11), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 169 HIS 0.011 0.001 HIS p 59 PHE 0.021 0.002 PHE w 9 TYR 0.044 0.002 TYR o 77 ARG 0.011 0.001 ARG P 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1307 time to evaluate : 6.356 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: b 112 ARG cc_start: 0.7430 (mmm160) cc_final: 0.7003 (mmm160) REVERT: c 138 GLN cc_start: 0.7422 (mt0) cc_final: 0.7180 (mp10) REVERT: c 199 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8901 (t) REVERT: e 25 LYS cc_start: 0.8957 (tptm) cc_final: 0.8392 (tptt) REVERT: e 59 ILE cc_start: 0.9140 (pp) cc_final: 0.8707 (mt) REVERT: f 2 ARG cc_start: 0.5882 (mtp-110) cc_final: 0.5521 (mtp-110) REVERT: h 75 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: h 98 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7545 (pp) REVERT: k 80 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7210 (p0) REVERT: m 99 GLN cc_start: 0.8948 (mp10) cc_final: 0.8744 (mp10) REVERT: p 12 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8758 (ttmt) REVERT: p 63 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7496 (mm-40) REVERT: s 31 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7571 (mtp-110) REVERT: t 56 ILE cc_start: 0.9043 (tp) cc_final: 0.8780 (tp) REVERT: C 180 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6495 (mpp) REVERT: D 1 MET cc_start: 0.6425 (tmm) cc_final: 0.5804 (tmm) REVERT: D 165 MET cc_start: 0.8174 (ttp) cc_final: 0.7787 (ttp) REVERT: E 4 VAL cc_start: 0.8147 (m) cc_final: 0.7736 (p) REVERT: E 47 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8648 (ptpp) REVERT: F 71 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7765 (ttpp) REVERT: F 129 MET cc_start: 0.7372 (ptp) cc_final: 0.6931 (ptp) REVERT: J 99 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.7936 (mmm160) REVERT: K 29 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.7199 (t-90) REVERT: K 51 LYS cc_start: 0.8155 (mttp) cc_final: 0.7796 (mttp) REVERT: K 59 LYS cc_start: 0.8487 (mttt) cc_final: 0.8120 (mttt) REVERT: K 66 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8311 (mttt) REVERT: K 106 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: N 114 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: O 19 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8111 (tt0) REVERT: P 9 GLN cc_start: 0.8453 (mt0) cc_final: 0.8199 (mt0) REVERT: Q 50 ARG cc_start: 0.8771 (mpt180) cc_final: 0.8526 (mpt90) REVERT: Q 100 PHE cc_start: 0.7663 (m-80) cc_final: 0.7305 (m-10) REVERT: R 10 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8285 (mttp) REVERT: R 13 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7667 (ttp80) REVERT: S 59 GLU cc_start: 0.7170 (pt0) cc_final: 0.6834 (pt0) REVERT: T 37 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6850 (p0) REVERT: U 5 ARG cc_start: 0.7424 (ptp-170) cc_final: 0.7192 (mtt180) REVERT: V 71 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7715 (mmtt) REVERT: W 25 ARG cc_start: 0.8331 (mmp80) cc_final: 0.8100 (mmp80) REVERT: W 44 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8174 (ttmm) REVERT: W 70 GLU cc_start: 0.7611 (tt0) cc_final: 0.7379 (tt0) REVERT: X 21 LEU cc_start: 0.8998 (mt) cc_final: 0.8631 (mp) REVERT: Y 31 GLN cc_start: 0.8474 (mp10) cc_final: 0.8038 (mp10) REVERT: 0 30 ASP cc_start: 0.8566 (t70) cc_final: 0.8282 (t0) REVERT: 1 49 LYS cc_start: 0.8523 (mttp) cc_final: 0.8280 (mmtm) REVERT: 2 3 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7123 (mmp80) REVERT: 6 56 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.6772 (mmm160) REVERT: w 177 ASP cc_start: 0.7858 (p0) cc_final: 0.7621 (p0) outliers start: 302 outliers final: 257 residues processed: 1476 average time/residue: 1.4202 time to fit residues: 3580.4979 Evaluate side-chains 1558 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1286 time to evaluate : 6.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 81 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 17 ASP Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 75 GLN Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 117 GLN Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 26 ARG Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 19 GLU Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 55 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 58 ASP Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain 7 residue 210 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 100 ILE Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 170 ILE Chi-restraints excluded: chain w residue 173 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 915 optimal weight: 6.9990 chunk 964 optimal weight: 4.9990 chunk 879 optimal weight: 2.9990 chunk 937 optimal weight: 4.9990 chunk 963 optimal weight: 0.9990 chunk 564 optimal weight: 6.9990 chunk 408 optimal weight: 10.0000 chunk 736 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 847 optimal weight: 2.9990 chunk 886 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 11 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN l 111 GLN C 162 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 19 GLN Q 51 GLN 3 27 ASN 4 13 ASN ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 158992 Z= 0.231 Angle : 0.637 27.841 237524 Z= 0.330 Chirality : 0.040 1.965 30326 Planarity : 0.005 0.097 12959 Dihedral : 23.611 179.663 78754 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.19 % Favored : 89.58 % Rotamer: Outliers : 5.30 % Allowed : 21.44 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.02 % 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: -2.22 (0.10), residues: 5987 helix: -0.69 (0.12), residues: 1753 sheet: -1.44 (0.15), residues: 1128 loop : -1.95 (0.11), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 169 HIS 0.012 0.001 HIS p 59 PHE 0.020 0.002 PHE f 8 TYR 0.030 0.002 TYR F 142 ARG 0.016 0.001 ARG m 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1316 time to evaluate : 6.452 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: b 112 ARG cc_start: 0.7465 (mmm160) cc_final: 0.7049 (mmm160) REVERT: c 138 GLN cc_start: 0.7385 (mt0) cc_final: 0.7160 (mp10) REVERT: e 25 LYS cc_start: 0.8950 (tptm) cc_final: 0.8372 (tptt) REVERT: e 59 ILE cc_start: 0.9129 (pp) cc_final: 0.8657 (mt) REVERT: e 67 ARG cc_start: 0.7438 (mtt-85) cc_final: 0.7053 (mmt180) REVERT: f 2 ARG cc_start: 0.5955 (mtp-110) cc_final: 0.5589 (mtp-110) REVERT: h 75 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: h 98 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7477 (pp) REVERT: j 5 ARG cc_start: 0.4729 (OUTLIER) cc_final: 0.3866 (ttt90) REVERT: j 63 ASP cc_start: 0.6955 (m-30) cc_final: 0.6712 (m-30) REVERT: m 80 MET cc_start: 0.7455 (mtm) cc_final: 0.7169 (mtp) REVERT: m 82 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8323 (tt) REVERT: m 99 GLN cc_start: 0.8954 (mp10) cc_final: 0.8750 (mp10) REVERT: p 12 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8712 (ttmt) REVERT: p 63 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7529 (mm-40) REVERT: s 31 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7571 (mtp-110) REVERT: t 56 ILE cc_start: 0.9031 (tp) cc_final: 0.8791 (tp) REVERT: C 180 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6502 (mpp) REVERT: D 92 VAL cc_start: 0.9021 (t) cc_final: 0.8774 (p) REVERT: E 4 VAL cc_start: 0.8007 (m) cc_final: 0.7594 (p) REVERT: E 47 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8572 (ptpp) REVERT: F 71 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7700 (ttpp) REVERT: F 129 MET cc_start: 0.7309 (ptp) cc_final: 0.6858 (ptp) REVERT: J 99 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7925 (mmm160) REVERT: K 29 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7223 (t-90) REVERT: K 51 LYS cc_start: 0.8155 (mttp) cc_final: 0.7791 (mttp) REVERT: K 59 LYS cc_start: 0.8456 (mttt) cc_final: 0.8099 (mttt) REVERT: K 66 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8290 (mttt) REVERT: K 106 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: N 114 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: O 19 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8082 (tt0) REVERT: P 9 GLN cc_start: 0.8496 (mt0) cc_final: 0.8212 (mt0) REVERT: Q 100 PHE cc_start: 0.7642 (m-80) cc_final: 0.7204 (m-10) REVERT: R 10 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8260 (mttp) REVERT: S 59 GLU cc_start: 0.7209 (pt0) cc_final: 0.6898 (pt0) REVERT: T 37 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6827 (p0) REVERT: V 71 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7727 (mmtt) REVERT: W 25 ARG cc_start: 0.8318 (mmp80) cc_final: 0.8078 (mmp80) REVERT: W 44 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8159 (ttmm) REVERT: W 70 GLU cc_start: 0.7588 (tt0) cc_final: 0.7357 (tt0) REVERT: X 21 LEU cc_start: 0.8981 (mt) cc_final: 0.8622 (mp) REVERT: Y 31 GLN cc_start: 0.8479 (mp10) cc_final: 0.8020 (mp10) REVERT: Z 36 GLU cc_start: 0.6566 (tp30) cc_final: 0.6285 (tp30) REVERT: 0 30 ASP cc_start: 0.8562 (t70) cc_final: 0.8280 (t0) REVERT: 1 49 LYS cc_start: 0.8516 (mttp) cc_final: 0.8288 (mmtm) REVERT: 6 56 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.6769 (mmm160) REVERT: w 177 ASP cc_start: 0.7818 (p0) cc_final: 0.7503 (p0) outliers start: 262 outliers final: 231 residues processed: 1467 average time/residue: 1.3591 time to fit residues: 3387.5080 Evaluate side-chains 1544 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1299 time to evaluate : 6.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 81 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 75 GLN Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 19 GLU Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 55 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 137 MET Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain 7 residue 210 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 100 ILE Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 170 ILE Chi-restraints excluded: chain w residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 934 optimal weight: 8.9990 chunk 615 optimal weight: 10.0000 chunk 991 optimal weight: 8.9990 chunk 605 optimal weight: 8.9990 chunk 470 optimal weight: 20.0000 chunk 689 optimal weight: 10.0000 chunk 1040 optimal weight: 0.0980 chunk 957 optimal weight: 0.2980 chunk 828 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 639 optimal weight: 8.9990 overall best weight: 5.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 11 GLN e 72 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN C 162 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 19 GLN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 4 13 ASN ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 158992 Z= 0.413 Angle : 0.733 28.554 237524 Z= 0.374 Chirality : 0.045 1.913 30326 Planarity : 0.006 0.084 12959 Dihedral : 23.627 179.743 78754 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.99 % Favored : 88.71 % Rotamer: Outliers : 5.64 % Allowed : 21.42 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.50 % Twisted General : 0.31 % 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: -2.34 (0.10), residues: 5987 helix: -0.79 (0.12), residues: 1769 sheet: -1.48 (0.15), residues: 1136 loop : -2.04 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 169 HIS 0.013 0.002 HIS 3 30 PHE 0.025 0.002 PHE w 9 TYR 0.030 0.002 TYR g 84 ARG 0.015 0.001 ARG m 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11974 Ramachandran restraints generated. 5987 Oldfield, 0 Emsley, 5987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1576 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1297 time to evaluate : 6.605 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: b 8 MET cc_start: 0.6066 (tmm) cc_final: 0.5840 (tmm) REVERT: b 112 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7017 (mmm160) REVERT: c 138 GLN cc_start: 0.7463 (mt0) cc_final: 0.7186 (mp10) REVERT: c 199 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8885 (t) REVERT: d 104 MET cc_start: 0.8580 (mtm) cc_final: 0.8355 (mtt) REVERT: e 25 LYS cc_start: 0.8979 (tptm) cc_final: 0.8396 (tptt) REVERT: e 59 ILE cc_start: 0.9135 (pp) cc_final: 0.8731 (mt) REVERT: e 67 ARG cc_start: 0.7436 (mtt-85) cc_final: 0.6937 (mmt180) REVERT: e 91 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8377 (m) REVERT: f 40 GLU cc_start: 0.7180 (tt0) cc_final: 0.6958 (tt0) REVERT: f 62 MET cc_start: 0.7752 (tpp) cc_final: 0.7395 (tpp) REVERT: h 75 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: h 98 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7588 (pp) REVERT: h 113 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7652 (ttp-170) REVERT: j 5 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.4042 (ttt90) REVERT: j 63 ASP cc_start: 0.7041 (m-30) cc_final: 0.6805 (m-30) REVERT: k 80 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7184 (p0) REVERT: m 80 MET cc_start: 0.7442 (mtm) cc_final: 0.7141 (mtp) REVERT: p 12 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8748 (ttmt) REVERT: p 63 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7462 (mm-40) REVERT: q 5 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7268 (ttm-80) REVERT: s 17 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8008 (mtpp) REVERT: s 31 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7622 (mtp-110) REVERT: t 56 ILE cc_start: 0.8997 (tp) cc_final: 0.8739 (tp) REVERT: C 180 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6498 (mpp) REVERT: D 1 MET cc_start: 0.6658 (tmm) cc_final: 0.6242 (tmm) REVERT: D 28 GLU cc_start: 0.7240 (tp30) cc_final: 0.6948 (tp30) REVERT: E 4 VAL cc_start: 0.8045 (m) cc_final: 0.7640 (p) REVERT: E 47 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8747 (ptpp) REVERT: F 71 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7771 (ttpp) REVERT: F 129 MET cc_start: 0.7388 (ptp) cc_final: 0.6967 (ptp) REVERT: F 132 ARG cc_start: 0.7283 (mtp85) cc_final: 0.6663 (mtp-110) REVERT: F 139 GLU cc_start: 0.7498 (mp0) cc_final: 0.7214 (mp0) REVERT: K 29 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: K 51 LYS cc_start: 0.8196 (mttp) cc_final: 0.7927 (mtmt) REVERT: K 53 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7882 (mtpp) REVERT: K 59 LYS cc_start: 0.8480 (mttt) cc_final: 0.8108 (mttt) REVERT: K 66 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8467 (ttmt) REVERT: K 106 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: N 114 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: O 19 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8115 (tt0) REVERT: P 9 GLN cc_start: 0.8576 (mt0) cc_final: 0.8293 (mt0) REVERT: Q 50 ARG cc_start: 0.8818 (mpt180) cc_final: 0.8566 (mpt90) REVERT: Q 100 PHE cc_start: 0.7695 (m-80) cc_final: 0.7307 (m-10) REVERT: S 59 GLU cc_start: 0.7143 (pt0) cc_final: 0.6848 (pt0) REVERT: T 6 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7869 (mmm160) REVERT: U 5 ARG cc_start: 0.7778 (mtt180) cc_final: 0.6966 (mtt180) REVERT: V 71 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7716 (mmtt) REVERT: W 25 ARG cc_start: 0.8413 (mmp80) cc_final: 0.8187 (mmp80) REVERT: W 44 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8200 (ttmm) REVERT: W 70 GLU cc_start: 0.7634 (tt0) cc_final: 0.7349 (tt0) REVERT: Y 31 GLN cc_start: 0.8475 (mp10) cc_final: 0.7965 (mp10) REVERT: 0 3 GLN cc_start: 0.8710 (pt0) cc_final: 0.8473 (pt0) REVERT: 0 30 ASP cc_start: 0.8578 (t70) cc_final: 0.8314 (t0) REVERT: 1 49 LYS cc_start: 0.8547 (mttp) cc_final: 0.8306 (mmtm) REVERT: 2 3 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7026 (mmp80) REVERT: 7 97 MET cc_start: 0.3582 (mmp) cc_final: 0.3361 (mmp) REVERT: w 42 LYS cc_start: 0.8167 (mttp) cc_final: 0.7785 (mmtm) REVERT: w 177 ASP cc_start: 0.7895 (p0) cc_final: 0.7692 (p0) outliers start: 279 outliers final: 242 residues processed: 1460 average time/residue: 1.3590 time to fit residues: 3380.7403 Evaluate side-chains 1540 residues out of total 4973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1281 time to evaluate : 6.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 163 GLN Chi-restraints excluded: chain d residue 195 ASN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 75 GLN Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 35 ASP Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 52 ARG Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 5 ARG Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 55 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 119 ASP Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 173 THR Chi-restraints excluded: chain 7 residue 184 LYS Chi-restraints excluded: chain 7 residue 200 LYS Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 18 ASP Chi-restraints excluded: chain w residue 31 LYS Chi-restraints excluded: chain w residue 100 ILE Chi-restraints excluded: chain w residue 107 LEU Chi-restraints excluded: chain w residue 139 ASP Chi-restraints excluded: chain w residue 168 VAL Chi-restraints excluded: chain w residue 170 ILE Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 507 optimal weight: 6.9990 chunk 657 optimal weight: 10.0000 chunk 882 optimal weight: 0.5980 chunk 253 optimal weight: 0.2980 chunk 763 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 829 optimal weight: 0.9990 chunk 347 optimal weight: 10.0000 chunk 851 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 14 HIS c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN e 72 ASN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN C 162 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 19 GLN Q 51 GLN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 4 13 ASN ** w 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102931 restraints weight = 229857.927| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 0.94 r_work: 0.3022 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.116 158992 Z= 0.152 Angle : 0.629 27.110 237524 Z= 0.327 Chirality : 0.039 2.013 30326 Planarity : 0.005 0.134 12959 Dihedral : 23.678 179.469 78754 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.25 % Favored : 90.51 % Rotamer: Outliers : 3.82 % Allowed : 23.50 % Favored : 72.68 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.02 % 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: -2.09 (0.11), residues: 5987 helix: -0.52 (0.12), residues: 1761 sheet: -1.43 (0.15), residues: 1115 loop : -1.88 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP f 42 HIS 0.014 0.001 HIS p 59 PHE 0.021 0.002 PHE Y 26 TYR 0.037 0.002 TYR F 142 ARG 0.014 0.001 ARG m 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48351.43 seconds wall clock time: 839 minutes 54.92 seconds (50394.92 seconds total)