Starting phenix.real_space_refine on Tue Mar 19 15:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enf_3898/03_2024/6enf_3898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enf_3898/03_2024/6enf_3898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enf_3898/03_2024/6enf_3898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enf_3898/03_2024/6enf_3898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enf_3898/03_2024/6enf_3898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6enf_3898/03_2024/6enf_3898.pdb" } resolution = 3.2 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 4546 5.49 5 S 143 5.16 5 C 70578 2.51 5 N 26280 2.21 5 O 39250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 64": "OD1" <-> "OD2" Residue "W PHE 69": "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 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140797 Number of models: 1 Model: "" Number of chains: 53 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "A" Number of atoms: 60275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2807, 60275 Classifications: {'RNA': 2807} Modifications used: {'p5*END': 1, 'rna2p_pur': 226, 'rna2p_pyr': 97, 'rna3p_pur': 1399, 'rna3p_pyr': 1085} Link IDs: {'rna2p': 323, 'rna3p': 2483} Chain breaks: 2 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 52} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 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': 8, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 62} Time building chain proxies: 52.09, per 1000 atoms: 0.37 Number of scatterers: 140797 At special positions: 0 Unit cell: (268.832, 277.504, 220.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 P 4546 15.00 O 39250 8.00 N 26280 7.00 C 70578 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: 48.06 Conformation dependent library (CDL) restraints added in 5.4 seconds 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10156 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 70 sheets defined 32.0% alpha, 16.6% beta 1392 base pairs and 2440 stacking pairs defined. Time for finding SS restraints: 45.14 Creating SS restraints... Processing helix chain 'b' and resid 45 through 61 Processing helix chain 'b' and resid 77 through 84 Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.659A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN b 119 " --> pdb=" O ASP b 115 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.843A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.860A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA b 175 " --> pdb=" O ALA b 171 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 224 removed outlier: 3.905A pdb=" N LEU b 211 " --> pdb=" O ARG b 207 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR b 212 " --> pdb=" O ALA b 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU b 222 " --> pdb=" O ALA b 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 11 removed outlier: 3.871A pdb=" N LEU c 11 " --> pdb=" O GLY c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 46 removed outlier: 3.550A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP c 35 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 47 through 49 No H-bonds generated for 'chain 'c' and resid 47 through 49' Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.976A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 92 removed outlier: 3.668A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 124 removed outlier: 3.923A pdb=" N GLU c 124 " --> pdb=" O THR c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 145 removed outlier: 3.639A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA c 145 " --> pdb=" O MET c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 159 removed outlier: 4.092A pdb=" N ALA c 159 " --> pdb=" O LEU c 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 removed outlier: 3.668A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG d 13 " --> pdb=" O LYS d 9 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.628A pdb=" N VAL d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.502A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 95 removed outlier: 3.606A pdb=" N LEU d 89 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 109 through 119 Processing helix chain 'd' and resid 157 through 162 removed outlier: 3.540A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 190 removed outlier: 3.619A pdb=" N LEU d 190 " --> pdb=" O ARG d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 201 removed outlier: 4.085A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 205 removed outlier: 3.707A pdb=" N LYS d 205 " --> pdb=" O LEU d 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 202 through 205' Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.554A pdb=" N LYS e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 116 removed outlier: 3.698A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 145 removed outlier: 3.664A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 5.314A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.544A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 80 removed outlier: 3.659A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 28 removed outlier: 3.679A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.587A 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 46 removed outlier: 3.644A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 54 Processing helix chain 'g' and resid 56 through 66 removed outlier: 3.616A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE g 61 " --> pdb=" O GLU g 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 109 removed outlier: 4.272A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 125 removed outlier: 3.730A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 144 Processing helix chain 'h' and resid 4 through 18 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 112 through 119 removed outlier: 3.649A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY h 119 " --> pdb=" O ALA h 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 52 removed outlier: 3.818A pdb=" N GLU i 52 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.673A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 99 removed outlier: 5.146A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 33 removed outlier: 3.797A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 85 removed outlier: 3.711A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 71 removed outlier: 3.792A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 101 Processing helix chain 'l' and resid 4 through 9 removed outlier: 4.216A pdb=" N ARG l 8 " --> pdb=" O ASN l 4 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 118 removed outlier: 3.622A pdb=" N GLY l 117 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL l 118 " --> pdb=" O LYS l 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 114 through 118' Processing helix chain 'm' and resid 13 through 18 Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 48 through 57 removed outlier: 3.787A pdb=" N ILE m 52 " --> pdb=" O SER m 48 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 62 removed outlier: 3.590A pdb=" N PHE m 62 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 83 removed outlier: 4.027A pdb=" N ARG m 69 " --> pdb=" O GLU m 65 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG m 70 " --> pdb=" O GLY m 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER m 73 " --> pdb=" O ARG m 69 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 92 removed outlier: 3.537A pdb=" N ARG m 91 " --> pdb=" O GLY m 87 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG m 92 " --> pdb=" O LEU m 88 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 110 removed outlier: 3.611A pdb=" N LYS m 109 " --> pdb=" O ALA m 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 20 removed outlier: 3.718A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS n 18 " --> pdb=" O ALA n 14 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR n 19 " --> pdb=" O LEU n 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE n 20 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 23 through 27 removed outlier: 3.727A pdb=" N LYS n 27 " --> pdb=" O ALA n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.736A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA n 44 " --> pdb=" O ASP n 40 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 91 removed outlier: 3.633A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.631A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 39 Processing helix chain 'o' and resid 48 through 73 removed outlier: 4.025A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 82 removed outlier: 3.804A pdb=" N GLU o 82 " --> pdb=" O THR o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 64 removed outlier: 3.708A pdb=" N GLY p 62 " --> pdb=" O ALA p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 76 Processing helix chain 'r' and resid 11 through 15 removed outlier: 3.660A pdb=" N GLU r 15 " --> pdb=" O PHE r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 29 Processing helix chain 'r' and resid 30 through 32 No H-bonds generated for 'chain 'r' and resid 30 through 32' Processing helix chain 'r' and resid 47 through 62 removed outlier: 3.682A pdb=" N ARG r 52 " --> pdb=" O ALA r 48 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 22 removed outlier: 3.719A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 44 removed outlier: 3.816A pdb=" N ILE s 44 " --> pdb=" O PRO s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 74 removed outlier: 3.614A pdb=" N GLU s 72 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA s 74 " --> pdb=" O GLY s 71 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 41 removed outlier: 4.556A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS t 15 " --> pdb=" O ILE t 11 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET t 27 " --> pdb=" O ARG t 23 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS t 32 " --> pdb=" O ARG t 28 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS t 33 " --> pdb=" O THR t 29 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 60 removed outlier: 3.714A pdb=" N GLN t 47 " --> pdb=" O LYS t 43 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS t 48 " --> pdb=" O ALA t 44 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.504A pdb=" N ASP t 58 " --> pdb=" O GLN t 54 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN t 60 " --> pdb=" O ILE t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 86 removed outlier: 4.150A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 59 removed outlier: 3.571A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 196 through 202 removed outlier: 4.238A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.638A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.974A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.719A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.549A pdb=" N VAL E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.978A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.622A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.811A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.627A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 4.158A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.686A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.760A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.561A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.874A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 170 removed outlier: 3.837A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.523A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.814A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 4.119A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.990A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.603A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.604A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.621A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 107 removed outlier: 3.649A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'J' and resid 120 through 122 No H-bonds generated for 'chain 'J' and resid 120 through 122' Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.827A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.547A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.986A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.701A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 72 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.619A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.505A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 139 No H-bonds generated for 'chain 'L' and resid 137 through 139' Processing helix chain 'M' and resid 43 through 55 removed outlier: 3.749A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 58 No H-bonds generated for 'chain 'M' and resid 56 through 58' Processing helix chain 'M' and resid 109 through 122 removed outlier: 3.818A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.595A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 45 removed outlier: 3.634A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 55 removed outlier: 3.688A pdb=" N LEU N 51 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.538A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.678A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 removed outlier: 3.895A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 21 removed outlier: 3.710A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 67 through 83 removed outlier: 3.530A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.551A pdb=" N ALA O 107 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.594A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 removed outlier: 3.810A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 55' Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.501A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 20 removed outlier: 3.743A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.829A pdb=" N SER Q 28 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 69 removed outlier: 3.980A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 85 removed outlier: 3.831A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY Q 81 " --> pdb=" O LYS Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.669A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.669A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.749A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.946A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 56 removed outlier: 3.984A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 62 removed outlier: 3.763A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP S 62 " --> pdb=" O ALA S 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 57 through 62' Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 2 through 7 removed outlier: 3.979A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 25 removed outlier: 3.642A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 49 removed outlier: 3.692A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 22 Processing helix chain 'V' and resid 44 through 51 removed outlier: 4.016A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 removed outlier: 3.830A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 61 Processing helix chain 'X' and resid 62 through 73 Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.515A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 34 removed outlier: 3.563A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 61 removed outlier: 3.803A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.522A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 removed outlier: 3.508A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 removed outlier: 3.678A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 23 removed outlier: 3.528A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA 2 23 " --> pdb=" O ARG 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.721A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 removed outlier: 3.696A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 35 Processing helix chain '3' and resid 38 through 43 removed outlier: 3.663A pdb=" N LEU 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 61 Processing helix chain '4' and resid 30 through 34 Processing helix chain '6' and resid 47 through 52 removed outlier: 3.864A pdb=" N VAL 6 51 " --> pdb=" O LYS 6 47 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 47 through 52' Processing helix chain '6' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'b' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'b' and resid 89 through 91 removed outlier: 6.070A pdb=" N ILE b 66 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL b 91 " --> pdb=" O ILE b 66 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE b 68 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU b 67 " --> pdb=" O ALA b 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 184 through 186 Processing sheet with id=AA4, first strand: chain 'c' and resid 19 through 20 removed outlier: 7.011A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE c 56 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 163 through 170 Processing sheet with id=AA6, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AA7, first strand: chain 'e' and resid 13 through 14 Processing sheet with id=AA8, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AA9, first strand: chain 'e' and resid 84 through 85 removed outlier: 3.755A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 58 through 61 removed outlier: 3.590A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 72 through 77 Processing sheet with id=AB3, first strand: chain 'h' and resid 23 through 27 removed outlier: 3.707A pdb=" N THR h 61 " --> pdb=" O GLU h 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 75 through 76 removed outlier: 6.881A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 5 through 7 removed outlier: 6.525A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL i 66 " --> pdb=" O VAL i 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.599A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.599A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS n 97 " --> pdb=" O GLU j 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 40 through 44 removed outlier: 3.675A pdb=" N GLY k 42 " --> pdb=" O ILE k 33 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY k 18 " --> pdb=" O GLU k 82 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N MET k 84 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA k 20 " --> pdb=" O MET k 84 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LYS k 86 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE k 22 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU k 81 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR k 110 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL k 83 " --> pdb=" O THR k 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'l' and resid 34 through 39 removed outlier: 4.751A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.675A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 9 through 11 Processing sheet with id=AC4, first strand: chain 'q' and resid 6 through 7 removed outlier: 6.954A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 10 through 13 removed outlier: 6.981A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 's' and resid 30 through 32 Processing sheet with id=AC7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AC8, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC9, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.836A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.753A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG C 166 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 4 through 15 removed outlier: 4.156A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 77 through 83 removed outlier: 5.161A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.511A pdb=" N GLY D 163 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AD6, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.400A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.641A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU F 35 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP F 152 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.670A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AE1, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AE2, first strand: chain 'G' and resid 94 through 98 Processing sheet with id=AE3, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.643A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AE5, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.576A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.647A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 74 through 77 removed outlier: 3.546A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.739A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.436A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.523A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.627A pdb=" N THR N 36 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 47 through 50 removed outlier: 3.691A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.828A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.536A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.230A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 5 through 10 removed outlier: 5.662A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 82 through 83 Processing sheet with id=AF9, first strand: chain 'S' and resid 86 through 87 Processing sheet with id=AG1, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.602A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN T 59 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 67 through 70 removed outlier: 3.525A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.403A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AG5, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AG6, first strand: chain 'V' and resid 2 through 5 removed outlier: 6.257A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU V 42 " --> pdb=" O PHE V 26 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 22 through 23 removed outlier: 6.547A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 46 through 47 removed outlier: 7.003A pdb=" N HIS W 46 " --> pdb=" O ILE W 80 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 13 through 15 Processing sheet with id=AH1, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.714A pdb=" N VAL X 50 " --> pdb=" O HIS X 33 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.610A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '0' and resid 28 through 29 removed outlier: 3.512A pdb=" N HIS 0 37 " --> pdb=" O SER 0 28 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '1' and resid 19 through 24 removed outlier: 3.615A pdb=" N THR 1 22 " --> pdb=" O ILE 1 8 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 1 6 " --> pdb=" O LYS 1 24 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '3' and resid 14 through 15 removed outlier: 3.597A pdb=" N LYS 3 14 " --> pdb=" O LYS 3 22 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS 3 23 " --> pdb=" O ALA 3 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AH7, first strand: chain '6' and resid 22 through 25 removed outlier: 8.986A pdb=" N LEU 6 32 " --> pdb=" O GLU 6 11 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR 6 13 " --> pdb=" O LEU 6 32 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3534 hydrogen bonds 5612 hydrogen bond angles 0 basepair planarities 1392 basepair parallelities 2440 stacking parallelities Total time for adding SS restraints: 232.98 Time building geometry restraints manager: 52.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20101 1.33 - 1.45: 66292 1.45 - 1.58: 57360 1.58 - 1.70: 9082 1.70 - 1.82: 255 Bond restraints: 153090 Sorted by residual: bond pdb=" C LYS b 27 " pdb=" N PRO b 28 " ideal model delta sigma weight residual 1.334 1.380 -0.047 8.40e-03 1.42e+04 3.10e+01 bond pdb=" CA ILE 3 31 " pdb=" C ILE 3 31 " ideal model delta sigma weight residual 1.523 1.590 -0.067 1.27e-02 6.20e+03 2.76e+01 bond pdb=" O3' C x 74 " pdb=" P C x 75 " ideal model delta sigma weight residual 1.607 1.556 0.051 1.50e-02 4.44e+03 1.16e+01 bond pdb=" CA ALA W 63 " pdb=" C ALA W 63 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.14e+01 bond pdb=" O3' C x 34 " pdb=" P G x 35 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.50e-02 4.44e+03 9.67e+00 ... (remaining 153085 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.53: 27629 106.53 - 114.40: 97469 114.40 - 122.27: 71726 122.27 - 130.13: 30034 130.13 - 138.00: 2359 Bond angle restraints: 229217 Sorted by residual: angle pdb=" C VAL C 215 " pdb=" N ARG C 216 " pdb=" CA ARG C 216 " ideal model delta sigma weight residual 120.49 138.00 -17.51 1.42e+00 4.96e-01 1.52e+02 angle pdb=" C4' G x 35 " pdb=" C3' G x 35 " pdb=" O3' G x 35 " ideal model delta sigma weight residual 113.00 123.96 -10.96 1.50e+00 4.44e-01 5.34e+01 angle pdb=" N LEU g 29 " pdb=" CA LEU g 29 " pdb=" C LEU g 29 " ideal model delta sigma weight residual 114.75 105.92 8.83 1.26e+00 6.30e-01 4.91e+01 angle pdb=" C GLN f 17 " pdb=" N VAL f 18 " pdb=" CA VAL f 18 " ideal model delta sigma weight residual 120.24 124.47 -4.23 6.30e-01 2.52e+00 4.51e+01 angle pdb=" C GLU W 83 " pdb=" N ALA W 84 " pdb=" CA ALA W 84 " ideal model delta sigma weight residual 123.11 113.93 9.18 1.42e+00 4.96e-01 4.18e+01 ... (remaining 229212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 86850 35.94 - 71.88: 10011 71.88 - 107.82: 1188 107.82 - 143.76: 19 143.76 - 179.70: 39 Dihedral angle restraints: 98107 sinusoidal: 82360 harmonic: 15747 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 -110.03 -69.97 0 5.00e+00 4.00e-02 1.96e+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 -122.62 -57.38 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA LYS f 53 " pdb=" C LYS f 53 " pdb=" N LEU f 54 " pdb=" CA LEU f 54 " ideal model delta harmonic sigma weight residual 180.00 -130.78 -49.22 0 5.00e+00 4.00e-02 9.69e+01 ... (remaining 98104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 29106 0.146 - 0.292: 179 0.292 - 0.438: 19 0.438 - 0.583: 1 0.583 - 0.729: 1 Chirality restraints: 29306 Sorted by residual: chirality pdb=" C3' G x 35 " pdb=" C4' G x 35 " pdb=" O3' G x 35 " pdb=" C2' G x 35 " both_signs ideal model delta sigma weight residual False -2.48 -1.75 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA LYS W 68 " pdb=" N LYS W 68 " pdb=" C LYS W 68 " pdb=" CB LYS W 68 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA HIS W 57 " pdb=" N HIS W 57 " pdb=" C HIS W 57 " pdb=" CB HIS W 57 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 29303 not shown) Planarity restraints: 12136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS W 44 " -0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C LYS W 44 " 0.087 2.00e-02 2.50e+03 pdb=" O LYS W 44 " -0.033 2.00e-02 2.50e+03 pdb=" N PHE W 45 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY W 73 " -0.079 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO W 74 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO W 74 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO W 74 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 23 " -0.019 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C VAL W 23 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL W 23 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS W 24 " -0.023 2.00e-02 2.50e+03 ... (remaining 12133 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 11 1.97 - 2.71: 9673 2.71 - 3.44: 172306 3.44 - 4.17: 455573 4.17 - 4.90: 619063 Nonbonded interactions: 1256626 Sorted by model distance: nonbonded pdb=" N3 C B 12 " pdb=" C GLY W 73 " model vdw 1.244 3.350 nonbonded pdb=" N3 C B 12 " pdb=" O GLY W 73 " model vdw 1.381 3.120 nonbonded pdb=" C2 C B 12 " pdb=" O GLY W 73 " model vdw 1.410 3.260 nonbonded pdb=" N3 C B 12 " pdb=" N PRO W 74 " model vdw 1.425 3.200 nonbonded pdb=" N4 C B 12 " pdb=" CD PRO W 74 " model vdw 1.649 3.520 ... (remaining 1256621 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: 3.000 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: 0.120 Extract box with map and model: 14.330 Check model and map are aligned: 1.470 Set scattering table: 0.930 Process input model: 466.710 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.370 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 492.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 153090 Z= 0.183 Angle : 0.750 17.512 229217 Z= 0.382 Chirality : 0.037 0.729 29306 Planarity : 0.006 0.122 12136 Dihedral : 22.559 179.698 87948 Min Nonbonded Distance : 1.244 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.99 % Favored : 91.68 % Rotamer: Outliers : 0.53 % Allowed : 2.78 % Favored : 96.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.25 % 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: -4.83 (0.08), residues: 5435 helix: -4.39 (0.06), residues: 1555 sheet: -2.25 (0.15), residues: 922 loop : -2.87 (0.09), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 212 HIS 0.010 0.001 HIS k 117 PHE 0.024 0.002 PHE b 49 TYR 0.020 0.002 TYR N 112 ARG 0.008 0.001 ARG c 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1718 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1694 time to evaluate : 5.791 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 100 LEU cc_start: 0.7643 (mt) cc_final: 0.7207 (mt) REVERT: c 100 ILE cc_start: 0.8220 (pt) cc_final: 0.7854 (mt) REVERT: c 122 GLN cc_start: 0.7058 (mt0) cc_final: 0.6811 (mt0) REVERT: c 128 MET cc_start: 0.7060 (mmm) cc_final: 0.6554 (mtp) REVERT: e 102 THR cc_start: 0.6905 (m) cc_final: 0.6437 (m) REVERT: f 17 GLN cc_start: 0.7433 (mt0) cc_final: 0.7147 (mm-40) REVERT: g 58 LEU cc_start: 0.6613 (pp) cc_final: 0.6305 (pp) REVERT: g 147 ASN cc_start: 0.6194 (t0) cc_final: 0.5937 (t0) REVERT: h 21 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7962 (mmtt) REVERT: h 95 MET cc_start: 0.7898 (mtp) cc_final: 0.7675 (mtp) REVERT: i 35 GLU cc_start: 0.5971 (tp30) cc_final: 0.5578 (tp30) REVERT: k 26 PHE cc_start: 0.7724 (m-80) cc_final: 0.7448 (m-10) REVERT: n 53 ARG cc_start: 0.7308 (tpp80) cc_final: 0.7019 (ttm-80) REVERT: t 25 SER cc_start: 0.7680 (t) cc_final: 0.7410 (m) REVERT: C 89 ASN cc_start: 0.8551 (m110) cc_final: 0.7596 (p0) REVERT: C 254 LYS cc_start: 0.7528 (tptt) cc_final: 0.7084 (mmtt) REVERT: D 95 SER cc_start: 0.8198 (t) cc_final: 0.7876 (p) REVERT: D 131 ASP cc_start: 0.7187 (t70) cc_final: 0.6925 (t0) REVERT: D 197 THR cc_start: 0.8153 (m) cc_final: 0.7828 (p) REVERT: E 15 SER cc_start: 0.7634 (m) cc_final: 0.7321 (p) REVERT: E 35 TYR cc_start: 0.7950 (t80) cc_final: 0.6931 (t80) REVERT: E 158 PHE cc_start: 0.7626 (t80) cc_final: 0.7251 (t80) REVERT: E 171 ASP cc_start: 0.4817 (t70) cc_final: 0.4547 (t70) REVERT: E 185 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7621 (mmtm) REVERT: F 13 LYS cc_start: 0.7640 (ttpm) cc_final: 0.7425 (ttmm) REVERT: J 108 MET cc_start: 0.8228 (mtt) cc_final: 0.7902 (mtt) REVERT: K 99 ILE cc_start: 0.8118 (mt) cc_final: 0.7898 (mt) REVERT: L 27 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7788 (pp) REVERT: M 18 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7192 (mtm-85) REVERT: M 112 LEU cc_start: 0.7764 (tp) cc_final: 0.7562 (tp) REVERT: N 24 MET cc_start: 0.7611 (ttp) cc_final: 0.7281 (ttp) REVERT: P 30 TRP cc_start: 0.7791 (m100) cc_final: 0.7427 (m100) REVERT: P 71 ARG cc_start: 0.8333 (ttt180) cc_final: 0.8114 (ttt180) REVERT: Q 89 ILE cc_start: 0.7542 (mt) cc_final: 0.7268 (tt) REVERT: R 101 ILE cc_start: 0.7935 (mm) cc_final: 0.7705 (mm) REVERT: S 108 SER cc_start: 0.7916 (t) cc_final: 0.7633 (p) REVERT: T 29 THR cc_start: 0.8011 (m) cc_final: 0.7551 (m) REVERT: U 91 LYS cc_start: 0.6381 (ttmt) cc_final: 0.5490 (tptt) REVERT: V 78 GLN cc_start: 0.7812 (mt0) cc_final: 0.7357 (mt0) REVERT: W 66 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7375 (mtmt) REVERT: X 5 GLN cc_start: 0.8500 (mm110) cc_final: 0.7968 (mm-40) REVERT: X 36 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7628 (ttp-110) REVERT: X 49 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7345 (tpt-90) REVERT: Z 10 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7524 (mtp85) outliers start: 24 outliers final: 11 residues processed: 1709 average time/residue: 1.4383 time to fit residues: 3999.3806 Evaluate side-chains 1148 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1135 time to evaluate : 5.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 12 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain W residue 41 ARG Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 82 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 830 optimal weight: 7.9990 chunk 745 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 254 optimal weight: 0.8980 chunk 502 optimal weight: 10.9990 chunk 398 optimal weight: 10.0000 chunk 770 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 chunk 468 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 892 optimal weight: 7.9990 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 35 ASN b 169 HIS ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN c 68 HIS c 139 ASN d 40 HIS d 115 GLN d 151 GLN e 69 ASN f 55 HIS f 68 GLN g 27 ASN i 24 ASN ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 4 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 GLN n 43 ASN n 60 GLN o 36 ASN p 26 ASN p 29 ASN p 63 GLN p 79 ASN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN r 73 HIS s 13 HIS s 51 HIS s 68 HIS t 47 GLN t 54 GLN C 36 ASN C 196 ASN C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 150 GLN D 173 GLN E 62 GLN E 156 ASN E 195 GLN J 58 ASN K 88 ASN N 31 HIS O 98 GLN P 11 GLN Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 18 GLN R 43 ASN R 91 GLN S 7 HIS T 15 HIS U 39 ASN X 22 ASN Y 25 GLN Y 45 GLN Y 58 ASN 2 6 GLN 3 42 HIS Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 153090 Z= 0.396 Angle : 0.728 13.943 229217 Z= 0.372 Chirality : 0.042 0.319 29306 Planarity : 0.006 0.071 12136 Dihedral : 23.396 178.296 77112 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.67 % Favored : 91.09 % Rotamer: Outliers : 4.64 % Allowed : 11.55 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.10), residues: 5435 helix: -2.60 (0.10), residues: 1628 sheet: -1.77 (0.15), residues: 918 loop : -2.46 (0.10), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 212 HIS 0.016 0.002 HIS k 117 PHE 0.031 0.003 PHE C 66 TYR 0.023 0.002 TYR u 37 ARG 0.021 0.001 ARG i 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1245 time to evaluate : 5.911 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: b 36 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7507 (ttmm) REVERT: b 81 ASP cc_start: 0.6358 (m-30) cc_final: 0.6058 (m-30) REVERT: b 130 LYS cc_start: 0.6272 (mmmt) cc_final: 0.6061 (mtpp) REVERT: c 32 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7650 (tt) REVERT: c 42 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8179 (mp) REVERT: c 128 MET cc_start: 0.6779 (mmm) cc_final: 0.6179 (mtp) REVERT: d 56 GLU cc_start: 0.8210 (tp30) cc_final: 0.8005 (tp30) REVERT: d 104 MET cc_start: 0.8502 (mtt) cc_final: 0.8290 (mtt) REVERT: d 194 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7891 (tp) REVERT: e 25 LYS cc_start: 0.8757 (tptm) cc_final: 0.8461 (tptm) REVERT: e 96 GLN cc_start: 0.7810 (tt0) cc_final: 0.7507 (tt0) REVERT: g 142 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6688 (tpp-160) REVERT: h 9 MET cc_start: 0.8161 (ttt) cc_final: 0.7900 (ttt) REVERT: i 29 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7425 (mt) REVERT: i 56 MET cc_start: 0.6805 (tmm) cc_final: 0.6552 (tmm) REVERT: i 60 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6688 (pp) REVERT: i 118 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7381 (ttm170) REVERT: j 64 GLN cc_start: 0.8171 (mt0) cc_final: 0.7842 (mt0) REVERT: m 62 PHE cc_start: 0.5037 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: n 43 ASN cc_start: 0.7537 (m110) cc_final: 0.7194 (m-40) REVERT: n 62 ASN cc_start: 0.8505 (t0) cc_final: 0.8229 (t0) REVERT: p 12 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7542 (ttpp) REVERT: p 33 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8269 (mp) REVERT: s 13 HIS cc_start: 0.7424 (p-80) cc_final: 0.7183 (p-80) REVERT: C 73 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 250 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8440 (tm-30) REVERT: C 252 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8567 (mttt) REVERT: D 92 VAL cc_start: 0.7754 (t) cc_final: 0.7548 (m) REVERT: D 95 SER cc_start: 0.8307 (t) cc_final: 0.7986 (p) REVERT: D 178 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8576 (m) REVERT: E 141 MET cc_start: 0.7600 (mpp) cc_final: 0.6876 (mpp) REVERT: E 154 ASP cc_start: 0.4883 (p0) cc_final: 0.4498 (t0) REVERT: E 185 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8094 (mmtm) REVERT: F 13 LYS cc_start: 0.7921 (ttpm) cc_final: 0.7615 (ttmm) REVERT: F 119 LYS cc_start: 0.7249 (mtmm) cc_final: 0.6962 (mtmm) REVERT: G 151 ARG cc_start: 0.8412 (ttm170) cc_final: 0.7971 (tpp80) REVERT: J 102 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: K 67 LYS cc_start: 0.8838 (tptt) cc_final: 0.8598 (tptt) REVERT: L 27 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8084 (pp) REVERT: L 78 ARG cc_start: 0.7896 (mtp180) cc_final: 0.6959 (mtt90) REVERT: N 17 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7135 (ttm-80) REVERT: N 24 MET cc_start: 0.7665 (ttp) cc_final: 0.7462 (ttp) REVERT: R 101 ILE cc_start: 0.8176 (mm) cc_final: 0.7948 (mm) REVERT: S 108 SER cc_start: 0.8454 (t) cc_final: 0.8098 (p) REVERT: T 36 LYS cc_start: 0.7699 (tppt) cc_final: 0.7412 (tptm) REVERT: U 92 VAL cc_start: 0.7337 (m) cc_final: 0.7067 (t) REVERT: V 78 GLN cc_start: 0.8234 (mt0) cc_final: 0.7907 (mt0) REVERT: W 35 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8663 (m) REVERT: W 83 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: X 49 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7110 (tpt-90) REVERT: Y 14 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7461 (mm) REVERT: Y 21 LEU cc_start: 0.7654 (mt) cc_final: 0.7447 (mm) REVERT: 0 11 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8558 (mmtt) REVERT: 3 14 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8025 (mmmm) REVERT: 4 36 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7718 (ttp80) REVERT: 6 15 SER cc_start: 0.7794 (t) cc_final: 0.7334 (p) outliers start: 209 outliers final: 123 residues processed: 1353 average time/residue: 1.3734 time to fit residues: 3135.2455 Evaluate side-chains 1242 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1103 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 109 LYS Chi-restraints excluded: chain g residue 125 ASP Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 496 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 742 optimal weight: 7.9990 chunk 607 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 894 optimal weight: 3.9990 chunk 966 optimal weight: 2.9990 chunk 796 optimal weight: 3.9990 chunk 886 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 717 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN c 184 ASN c 189 HIS d 40 HIS d 70 GLN d 88 ASN d 125 ASN e 69 ASN g 85 GLN i 31 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 GLN n 43 ASN p 26 ASN q 30 HIS D 32 ASN E 195 GLN G 29 ASN G 44 HIS K 88 ASN M 45 GLN O 98 GLN Q 19 GLN Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN 0 18 HIS 2 26 ASN 3 27 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 153090 Z= 0.199 Angle : 0.562 12.867 229217 Z= 0.293 Chirality : 0.035 0.277 29306 Planarity : 0.005 0.064 12136 Dihedral : 23.289 178.359 77094 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.06 % Favored : 91.78 % Rotamer: Outliers : 4.06 % Allowed : 15.55 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 5435 helix: -1.53 (0.12), residues: 1620 sheet: -1.40 (0.16), residues: 923 loop : -2.16 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 212 HIS 0.011 0.001 HIS t 19 PHE 0.025 0.002 PHE b 49 TYR 0.018 0.001 TYR u 37 ARG 0.008 0.001 ARG j 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1189 time to evaluate : 5.714 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: b 36 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7327 (ttmm) REVERT: c 31 ASN cc_start: 0.7903 (t0) cc_final: 0.7530 (t0) REVERT: c 128 MET cc_start: 0.6791 (mmm) cc_final: 0.6155 (mtp) REVERT: c 184 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8456 (m-40) REVERT: d 75 TYR cc_start: 0.8537 (t80) cc_final: 0.8107 (t80) REVERT: d 186 GLU cc_start: 0.6958 (mp0) cc_final: 0.6585 (mp0) REVERT: d 194 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7862 (mt) REVERT: e 25 LYS cc_start: 0.8692 (tptm) cc_final: 0.8375 (tptm) REVERT: e 51 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8446 (ttmt) REVERT: e 69 ASN cc_start: 0.7314 (m-40) cc_final: 0.7047 (m110) REVERT: e 96 GLN cc_start: 0.7818 (tt0) cc_final: 0.7501 (tt0) REVERT: h 3 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7590 (mp10) REVERT: h 9 MET cc_start: 0.8143 (ttt) cc_final: 0.7905 (ttt) REVERT: h 98 LEU cc_start: 0.8388 (pp) cc_final: 0.8140 (pt) REVERT: i 60 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6686 (pp) REVERT: j 16 ARG cc_start: 0.6826 (mmt90) cc_final: 0.6543 (mmt90) REVERT: j 64 GLN cc_start: 0.8042 (mt0) cc_final: 0.7676 (mt0) REVERT: k 74 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7919 (mtmt) REVERT: m 65 GLU cc_start: 0.6119 (tp30) cc_final: 0.5881 (tm-30) REVERT: n 3 GLN cc_start: 0.8045 (mm110) cc_final: 0.7629 (mm110) REVERT: n 43 ASN cc_start: 0.7592 (m-40) cc_final: 0.7248 (m-40) REVERT: q 26 ARG cc_start: 0.7054 (mtm110) cc_final: 0.6842 (mtm110) REVERT: q 42 LYS cc_start: 0.8329 (mtpp) cc_final: 0.8103 (mtmm) REVERT: r 29 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7640 (mtpt) REVERT: C 73 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8433 (mm) REVERT: C 99 GLU cc_start: 0.6950 (tt0) cc_final: 0.6653 (tt0) REVERT: C 101 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7635 (mtp85) REVERT: C 132 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7535 (ttt180) REVERT: D 95 SER cc_start: 0.8203 (t) cc_final: 0.7905 (p) REVERT: E 141 MET cc_start: 0.7524 (mpp) cc_final: 0.6861 (mpp) REVERT: E 154 ASP cc_start: 0.4816 (p0) cc_final: 0.4593 (t0) REVERT: E 185 LYS cc_start: 0.8323 (mmtp) cc_final: 0.7850 (mmtm) REVERT: J 102 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6739 (mt-10) REVERT: K 31 ARG cc_start: 0.7834 (mpt90) cc_final: 0.7499 (mtt90) REVERT: K 45 GLU cc_start: 0.7166 (tt0) cc_final: 0.6593 (tt0) REVERT: K 88 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7815 (t0) REVERT: L 27 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8316 (pp) REVERT: L 78 ARG cc_start: 0.7720 (mtp180) cc_final: 0.6905 (mtt90) REVERT: L 129 LYS cc_start: 0.7875 (tppt) cc_final: 0.7034 (ttpp) REVERT: M 51 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7559 (mtp85) REVERT: N 17 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7848 (ttp-110) REVERT: N 21 PHE cc_start: 0.8753 (m-10) cc_final: 0.8534 (m-10) REVERT: N 24 MET cc_start: 0.7648 (ttp) cc_final: 0.7280 (mtp) REVERT: P 105 LYS cc_start: 0.8211 (mttt) cc_final: 0.7698 (mttm) REVERT: R 6 GLN cc_start: 0.7704 (tt0) cc_final: 0.7394 (mm-40) REVERT: S 48 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8286 (ttmm) REVERT: S 108 SER cc_start: 0.8504 (t) cc_final: 0.8201 (p) REVERT: T 24 MET cc_start: 0.7752 (mmt) cc_final: 0.7246 (mmm) REVERT: V 78 GLN cc_start: 0.8174 (mt0) cc_final: 0.7752 (mt0) REVERT: W 50 ASN cc_start: 0.8556 (m-40) cc_final: 0.8300 (m-40) REVERT: W 68 LYS cc_start: 0.8658 (tmmt) cc_final: 0.7661 (tptp) REVERT: X 49 ARG cc_start: 0.7377 (ttt180) cc_final: 0.7145 (tpt-90) REVERT: Y 14 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7345 (mm) REVERT: Z 10 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7215 (mtp85) REVERT: 0 11 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8493 (mmtt) REVERT: 3 14 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8039 (mmmm) REVERT: 3 51 LYS cc_start: 0.7495 (tmtt) cc_final: 0.7202 (tmtt) REVERT: 6 15 SER cc_start: 0.7666 (t) cc_final: 0.7370 (p) outliers start: 183 outliers final: 120 residues processed: 1274 average time/residue: 1.3308 time to fit residues: 2851.6728 Evaluate side-chains 1214 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1083 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 184 ASN Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 109 LYS Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 6 residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 883 optimal weight: 7.9990 chunk 672 optimal weight: 10.0000 chunk 464 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 897 optimal weight: 4.9990 chunk 950 optimal weight: 0.8980 chunk 468 optimal weight: 10.0000 chunk 850 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 HIS d 135 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 24 ASN i 31 GLN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 11 HIS n 43 ASN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 HIS p 79 ASN r 30 ASN t 67 HIS C 85 ASN C 133 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN F 4 HIS G 29 ASN K 88 ASN O 98 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 HIS 0 18 HIS 1 25 ASN 3 27 ASN 4 33 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 153090 Z= 0.479 Angle : 0.830 14.528 229217 Z= 0.421 Chirality : 0.047 0.347 29306 Planarity : 0.007 0.100 12136 Dihedral : 23.595 179.966 77091 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.36 % Favored : 89.40 % Rotamer: Outliers : 6.24 % Allowed : 16.66 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.10), residues: 5435 helix: -1.57 (0.12), residues: 1663 sheet: -1.49 (0.15), residues: 960 loop : -2.23 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.014 0.002 HIS 3 30 PHE 0.033 0.003 PHE s 40 TYR 0.029 0.003 TYR C 95 ARG 0.011 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1129 time to evaluate : 5.884 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 112 ARG cc_start: 0.7582 (tpt170) cc_final: 0.7304 (mmm160) REVERT: c 32 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7461 (tt) REVERT: c 42 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8112 (mp) REVERT: d 58 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: d 75 TYR cc_start: 0.8648 (t80) cc_final: 0.8280 (t80) REVERT: d 186 GLU cc_start: 0.7425 (mp0) cc_final: 0.7109 (mp0) REVERT: d 194 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7824 (mt) REVERT: e 25 LYS cc_start: 0.8772 (tptm) cc_final: 0.8496 (tptm) REVERT: e 96 GLN cc_start: 0.7878 (tt0) cc_final: 0.7562 (tt0) REVERT: f 14 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: g 3 ARG cc_start: 0.7601 (ptt180) cc_final: 0.7373 (ptt90) REVERT: g 47 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: h 4 ASP cc_start: 0.8671 (t0) cc_final: 0.8132 (t0) REVERT: i 60 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6422 (pp) REVERT: j 69 THR cc_start: 0.8455 (m) cc_final: 0.8168 (t) REVERT: k 30 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8460 (mp) REVERT: k 33 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8010 (mp) REVERT: k 74 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8165 (mtmm) REVERT: l 55 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7498 (ttt90) REVERT: m 16 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7781 (mp) REVERT: n 3 GLN cc_start: 0.7964 (mm110) cc_final: 0.7612 (mm110) REVERT: n 89 MET cc_start: 0.8392 (mmm) cc_final: 0.8170 (mmt) REVERT: p 33 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8090 (mt) REVERT: q 26 ARG cc_start: 0.7208 (mtm110) cc_final: 0.7004 (mtm110) REVERT: q 50 ASN cc_start: 0.4979 (OUTLIER) cc_final: 0.4145 (t0) REVERT: q 64 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8006 (ttp-170) REVERT: r 29 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7794 (mtpt) REVERT: t 52 GLU cc_start: 0.6984 (tp30) cc_final: 0.6704 (tp30) REVERT: u 33 ARG cc_start: 0.6298 (ttm110) cc_final: 0.6065 (ttm110) REVERT: C 4 LYS cc_start: 0.7736 (tttp) cc_final: 0.7446 (tttm) REVERT: C 22 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7231 (mm-30) REVERT: C 70 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6772 (mttt) REVERT: C 73 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8479 (mm) REVERT: C 81 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7141 (mt-10) REVERT: C 132 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7161 (ttp80) REVERT: C 250 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8315 (tm-30) REVERT: D 1 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.4927 (mmp) REVERT: E 141 MET cc_start: 0.7560 (mpp) cc_final: 0.6812 (mpp) REVERT: E 185 LYS cc_start: 0.8530 (mmtp) cc_final: 0.7974 (mmtm) REVERT: E 199 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7041 (ttp) REVERT: G 172 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6267 (tm-30) REVERT: K 31 ARG cc_start: 0.7952 (mpt90) cc_final: 0.7637 (mtt90) REVERT: K 64 ARG cc_start: 0.9127 (mtm-85) cc_final: 0.8810 (mtt180) REVERT: K 88 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7525 (t0) REVERT: L 27 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8785 (pp) REVERT: L 78 ARG cc_start: 0.7915 (mtp180) cc_final: 0.6732 (mtt90) REVERT: L 129 LYS cc_start: 0.8299 (tppt) cc_final: 0.7473 (ttpp) REVERT: M 51 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7593 (mtp85) REVERT: M 119 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8257 (mt) REVERT: N 17 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6715 (ttm-80) REVERT: N 24 MET cc_start: 0.7594 (ttp) cc_final: 0.7265 (mtp) REVERT: N 30 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7339 (ptm160) REVERT: P 30 TRP cc_start: 0.7786 (m100) cc_final: 0.7445 (m100) REVERT: P 105 LYS cc_start: 0.8385 (mttt) cc_final: 0.7841 (mttm) REVERT: Q 89 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7366 (tt) REVERT: R 21 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7888 (mtp180) REVERT: S 48 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (ttmm) REVERT: T 24 MET cc_start: 0.7612 (mmt) cc_final: 0.7373 (mmm) REVERT: U 18 LYS cc_start: 0.7462 (ttpt) cc_final: 0.7126 (tttt) REVERT: U 72 PHE cc_start: 0.8355 (t80) cc_final: 0.8145 (t80) REVERT: V 78 GLN cc_start: 0.8306 (mt0) cc_final: 0.7998 (mt0) REVERT: W 17 GLU cc_start: 0.6192 (mt-10) cc_final: 0.5932 (mt-10) REVERT: W 50 ASN cc_start: 0.8649 (m-40) cc_final: 0.8412 (m110) REVERT: W 68 LYS cc_start: 0.8735 (tmmt) cc_final: 0.8007 (tptp) REVERT: 3 14 LYS cc_start: 0.8521 (mmtp) cc_final: 0.8039 (mmmm) outliers start: 281 outliers final: 188 residues processed: 1296 average time/residue: 1.3240 time to fit residues: 2879.5207 Evaluate side-chains 1313 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1100 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 109 LYS Chi-restraints excluded: chain g residue 125 ASP Chi-restraints excluded: chain h residue 30 LYS Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 71 VAL Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 44 GLU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 791 optimal weight: 3.9990 chunk 539 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 707 optimal weight: 0.6980 chunk 392 optimal weight: 10.0000 chunk 810 optimal weight: 0.0870 chunk 656 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 485 optimal weight: 10.0000 chunk 852 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 overall best weight: 3.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN c 122 GLN d 40 HIS e 60 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN t 54 GLN t 67 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 165 HIS F 4 HIS K 88 ASN O 98 GLN Q 43 GLN R 18 GLN U 39 ASN 0 18 HIS 1 25 ASN 4 33 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 153090 Z= 0.247 Angle : 0.612 13.150 229217 Z= 0.319 Chirality : 0.038 0.294 29306 Planarity : 0.005 0.061 12136 Dihedral : 23.377 179.185 77089 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.56 % Favored : 91.24 % Rotamer: Outliers : 5.35 % Allowed : 19.12 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.42 (0.11), residues: 5435 helix: -1.01 (0.12), residues: 1633 sheet: -1.36 (0.16), residues: 976 loop : -2.06 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 212 HIS 0.011 0.001 HIS 3 30 PHE 0.022 0.002 PHE R 93 TYR 0.017 0.002 TYR C 95 ARG 0.010 0.001 ARG e 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1119 time to evaluate : 5.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 32 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7516 (tt) REVERT: c 42 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8219 (mp) REVERT: c 46 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8213 (mt) REVERT: d 75 TYR cc_start: 0.8589 (t80) cc_final: 0.8282 (t80) REVERT: d 110 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7614 (ttm170) REVERT: d 115 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: d 194 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7873 (mt) REVERT: e 25 LYS cc_start: 0.8702 (tptm) cc_final: 0.8316 (tptm) REVERT: e 96 GLN cc_start: 0.7777 (tt0) cc_final: 0.7427 (tt0) REVERT: f 62 MET cc_start: 0.7434 (mmm) cc_final: 0.7186 (mmm) REVERT: h 76 ARG cc_start: 0.7918 (tpt170) cc_final: 0.7705 (tpt170) REVERT: i 21 LYS cc_start: 0.7223 (tmtt) cc_final: 0.6787 (tptp) REVERT: k 33 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8158 (mp) REVERT: l 28 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.6774 (mm-40) REVERT: l 55 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7445 (ttt90) REVERT: n 3 GLN cc_start: 0.7939 (mm110) cc_final: 0.7565 (mm110) REVERT: p 53 ASP cc_start: 0.6536 (t70) cc_final: 0.6296 (t0) REVERT: q 5 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7448 (ttm110) REVERT: q 39 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7626 (mmm160) REVERT: q 64 ARG cc_start: 0.8369 (ttp80) cc_final: 0.7986 (ttp-170) REVERT: r 29 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7795 (mtmm) REVERT: C 4 LYS cc_start: 0.7715 (tttp) cc_final: 0.7413 (tttm) REVERT: C 22 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 73 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8514 (mm) REVERT: C 132 ARG cc_start: 0.7874 (ttp-110) cc_final: 0.7052 (ttp80) REVERT: C 166 ARG cc_start: 0.6349 (ttm-80) cc_final: 0.6001 (ttm-80) REVERT: D 1 MET cc_start: 0.5230 (ppp) cc_final: 0.4583 (mmt) REVERT: E 141 MET cc_start: 0.7463 (mpp) cc_final: 0.6739 (mpp) REVERT: E 185 LYS cc_start: 0.8393 (mmtp) cc_final: 0.7851 (mmtm) REVERT: E 199 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6920 (ttp) REVERT: F 163 GLU cc_start: 0.6827 (pm20) cc_final: 0.6325 (pm20) REVERT: J 61 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7581 (mmtt) REVERT: K 31 ARG cc_start: 0.7863 (mpt90) cc_final: 0.7449 (mtt90) REVERT: K 64 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8716 (mtt180) REVERT: K 88 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7505 (t0) REVERT: K 111 LYS cc_start: 0.8756 (tppt) cc_final: 0.8388 (tptt) REVERT: L 27 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8655 (pp) REVERT: L 78 ARG cc_start: 0.7825 (mtp180) cc_final: 0.6809 (mtt90) REVERT: L 100 ILE cc_start: 0.8295 (pt) cc_final: 0.8077 (pt) REVERT: L 129 LYS cc_start: 0.8001 (tppt) cc_final: 0.7359 (ttpp) REVERT: M 51 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7575 (mtp85) REVERT: N 24 MET cc_start: 0.7584 (ttp) cc_final: 0.7254 (mtp) REVERT: N 72 ASP cc_start: 0.6682 (t70) cc_final: 0.6447 (t70) REVERT: P 105 LYS cc_start: 0.8370 (mttt) cc_final: 0.7821 (mttm) REVERT: Q 89 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7304 (tt) REVERT: S 48 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8277 (ttmm) REVERT: T 24 MET cc_start: 0.7621 (mmt) cc_final: 0.7274 (mmm) REVERT: U 18 LYS cc_start: 0.7424 (ttpt) cc_final: 0.7118 (tttt) REVERT: U 72 PHE cc_start: 0.8150 (t80) cc_final: 0.7823 (t80) REVERT: V 78 GLN cc_start: 0.8254 (mt0) cc_final: 0.7903 (mt0) REVERT: W 17 GLU cc_start: 0.6273 (mt-10) cc_final: 0.6024 (mt-10) REVERT: W 50 ASN cc_start: 0.8638 (m-40) cc_final: 0.8388 (m110) REVERT: W 68 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8130 (tptp) REVERT: W 70 GLU cc_start: 0.6107 (mt-10) cc_final: 0.5781 (mt-10) REVERT: Y 14 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7399 (mm) REVERT: Z 10 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7220 (mtp85) REVERT: 3 14 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8023 (mmmm) REVERT: 6 15 SER cc_start: 0.7724 (t) cc_final: 0.7431 (p) outliers start: 241 outliers final: 175 residues processed: 1249 average time/residue: 1.2996 time to fit residues: 2723.8670 Evaluate side-chains 1275 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1083 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 125 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 28 GLN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 319 optimal weight: 9.9990 chunk 855 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 557 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 951 optimal weight: 5.9990 chunk 789 optimal weight: 0.1980 chunk 440 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 314 optimal weight: 0.6980 chunk 499 optimal weight: 20.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN e 88 HIS f 55 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 GLN r 30 ASN t 67 HIS D 36 GLN D 49 GLN K 88 ASN Q 19 GLN U 39 ASN Y 45 GLN 0 18 HIS 4 33 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 153090 Z= 0.292 Angle : 0.647 13.098 229217 Z= 0.335 Chirality : 0.039 0.300 29306 Planarity : 0.005 0.065 12136 Dihedral : 23.392 178.838 77089 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.92 % Favored : 89.88 % Rotamer: Outliers : 6.35 % Allowed : 19.44 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 5435 helix: -0.85 (0.13), residues: 1632 sheet: -1.29 (0.16), residues: 972 loop : -1.99 (0.11), residues: 2831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 212 HIS 0.013 0.001 HIS 3 30 PHE 0.024 0.002 PHE R 93 TYR 0.018 0.002 TYR C 95 ARG 0.010 0.001 ARG j 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1104 time to evaluate : 5.755 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: b 112 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7228 (mmm160) REVERT: b 139 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5925 (mp0) REVERT: b 160 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8469 (tt) REVERT: b 222 GLU cc_start: 0.7192 (tp30) cc_final: 0.6935 (tm-30) REVERT: c 32 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7476 (tt) REVERT: c 42 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8205 (mp) REVERT: c 124 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: d 43 ARG cc_start: 0.6786 (mpt180) cc_final: 0.6092 (mtt180) REVERT: d 58 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: d 75 TYR cc_start: 0.8638 (t80) cc_final: 0.8313 (t80) REVERT: d 110 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7729 (ttm170) REVERT: d 194 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7792 (mt) REVERT: e 25 LYS cc_start: 0.8716 (tptm) cc_final: 0.8320 (tptm) REVERT: e 29 ILE cc_start: 0.8186 (pt) cc_final: 0.7826 (mp) REVERT: e 96 GLN cc_start: 0.7823 (tt0) cc_final: 0.7471 (tt0) REVERT: e 147 ASN cc_start: 0.8282 (p0) cc_final: 0.7979 (p0) REVERT: e 151 MET cc_start: 0.6760 (mmm) cc_final: 0.6336 (mpp) REVERT: f 14 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: g 47 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: j 69 THR cc_start: 0.8446 (m) cc_final: 0.8118 (t) REVERT: k 33 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8122 (mp) REVERT: l 28 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.6903 (mm-40) REVERT: l 55 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7477 (ttt90) REVERT: n 3 GLN cc_start: 0.7914 (mm110) cc_final: 0.7604 (mm110) REVERT: n 19 TYR cc_start: 0.7037 (m-10) cc_final: 0.6556 (m-10) REVERT: p 33 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7917 (mt) REVERT: q 5 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7421 (ttm110) REVERT: q 50 ASN cc_start: 0.4881 (OUTLIER) cc_final: 0.3901 (t0) REVERT: r 29 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7616 (mtmm) REVERT: t 52 GLU cc_start: 0.6929 (tp30) cc_final: 0.6655 (tp30) REVERT: C 4 LYS cc_start: 0.7736 (tttp) cc_final: 0.7433 (tttm) REVERT: C 22 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 73 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8506 (mm) REVERT: C 132 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7191 (ttp80) REVERT: C 166 ARG cc_start: 0.6434 (ttm-80) cc_final: 0.6068 (ttm-80) REVERT: C 216 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: C 250 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8267 (tm-30) REVERT: D 1 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4851 (mmt) REVERT: D 74 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: E 141 MET cc_start: 0.7332 (mpp) cc_final: 0.6664 (mpp) REVERT: E 185 LYS cc_start: 0.8414 (mmtp) cc_final: 0.7850 (mmtm) REVERT: F 4 HIS cc_start: 0.6624 (t70) cc_final: 0.6356 (t-170) REVERT: F 163 GLU cc_start: 0.6905 (pm20) cc_final: 0.6363 (pm20) REVERT: G 172 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: J 53 TYR cc_start: 0.8633 (m-80) cc_final: 0.8109 (m-80) REVERT: J 61 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7502 (mmtt) REVERT: K 31 ARG cc_start: 0.7942 (mpt90) cc_final: 0.7571 (mtt90) REVERT: K 64 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8777 (mtt180) REVERT: K 111 LYS cc_start: 0.8764 (tppt) cc_final: 0.8365 (tptt) REVERT: L 27 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8723 (pp) REVERT: L 78 ARG cc_start: 0.7727 (mtp180) cc_final: 0.6765 (mtt90) REVERT: L 100 ILE cc_start: 0.8450 (pt) cc_final: 0.8224 (pt) REVERT: L 129 LYS cc_start: 0.8088 (tppt) cc_final: 0.7414 (ttpp) REVERT: M 51 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7542 (mtp85) REVERT: M 104 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: N 24 MET cc_start: 0.7572 (ttp) cc_final: 0.7268 (mtp) REVERT: N 72 ASP cc_start: 0.6700 (t70) cc_final: 0.6460 (t70) REVERT: N 97 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8315 (mt) REVERT: P 105 LYS cc_start: 0.8411 (mttt) cc_final: 0.7870 (mttm) REVERT: Q 89 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7384 (tt) REVERT: R 2 TYR cc_start: 0.8265 (p90) cc_final: 0.7887 (p90) REVERT: S 48 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8302 (ttmm) REVERT: U 18 LYS cc_start: 0.7505 (ttpt) cc_final: 0.7221 (tttt) REVERT: U 72 PHE cc_start: 0.8232 (t80) cc_final: 0.7838 (t80) REVERT: W 17 GLU cc_start: 0.6169 (mt-10) cc_final: 0.5918 (mt-10) REVERT: W 50 ASN cc_start: 0.8630 (m-40) cc_final: 0.8381 (m110) REVERT: W 68 LYS cc_start: 0.8808 (tmmt) cc_final: 0.8135 (tptp) REVERT: W 70 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5713 (mt-10) REVERT: Y 14 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7279 (mm) REVERT: 3 14 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8070 (mmmm) REVERT: 6 15 SER cc_start: 0.7741 (t) cc_final: 0.7443 (p) outliers start: 286 outliers final: 214 residues processed: 1269 average time/residue: 1.3061 time to fit residues: 2794.4360 Evaluate side-chains 1313 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1072 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 174 GLU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 124 GLU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 98 ASP Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain d residue 198 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 125 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 28 GLN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 916 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 541 optimal weight: 10.0000 chunk 694 optimal weight: 0.5980 chunk 538 optimal weight: 8.9990 chunk 800 optimal weight: 0.0070 chunk 531 optimal weight: 10.0000 chunk 947 optimal weight: 2.9990 chunk 592 optimal weight: 10.0000 chunk 577 optimal weight: 8.9990 chunk 437 optimal weight: 10.0000 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 17 HIS b 50 ASN c 18 ASN c 122 GLN c 184 ASN d 40 HIS e 60 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN i 24 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 ASN r 30 ASN t 67 HIS D 49 GLN G 29 ASN O 98 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 153090 Z= 0.210 Angle : 0.583 12.248 229217 Z= 0.304 Chirality : 0.036 0.283 29306 Planarity : 0.005 0.068 12136 Dihedral : 23.341 177.687 77089 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.70 % Favored : 91.06 % Rotamer: Outliers : 5.55 % Allowed : 20.59 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.07 (0.11), residues: 5435 helix: -0.61 (0.13), residues: 1638 sheet: -1.15 (0.16), residues: 966 loop : -1.92 (0.11), residues: 2831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 212 HIS 0.015 0.001 HIS f 55 PHE 0.024 0.002 PHE R 93 TYR 0.015 0.002 TYR F 7 ARG 0.008 0.001 ARG j 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1111 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 139 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: b 160 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8461 (tt) REVERT: c 32 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7528 (tt) REVERT: c 40 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: c 42 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8170 (mp) REVERT: d 43 ARG cc_start: 0.6877 (mpt180) cc_final: 0.6193 (mtt180) REVERT: d 75 TYR cc_start: 0.8626 (t80) cc_final: 0.8335 (t80) REVERT: d 110 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7596 (ttm170) REVERT: d 115 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: d 127 ARG cc_start: 0.6626 (mtp85) cc_final: 0.6402 (mtm110) REVERT: d 194 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7867 (mt) REVERT: e 25 LYS cc_start: 0.8742 (tptm) cc_final: 0.8329 (tptm) REVERT: e 29 ILE cc_start: 0.8242 (pt) cc_final: 0.7863 (mp) REVERT: e 96 GLN cc_start: 0.7813 (tt0) cc_final: 0.7457 (tt0) REVERT: e 144 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6746 (tp30) REVERT: e 151 MET cc_start: 0.6728 (mmm) cc_final: 0.6317 (mpp) REVERT: f 14 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: g 47 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: i 31 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7247 (mm-40) REVERT: j 69 THR cc_start: 0.8474 (m) cc_final: 0.8141 (t) REVERT: k 33 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8102 (mp) REVERT: l 28 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6736 (mm-40) REVERT: m 16 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7649 (mp) REVERT: m 28 ARG cc_start: 0.6630 (tpt90) cc_final: 0.6409 (tpt90) REVERT: n 3 GLN cc_start: 0.7907 (mm110) cc_final: 0.7581 (mm110) REVERT: n 19 TYR cc_start: 0.6769 (m-10) cc_final: 0.6240 (m-10) REVERT: n 43 ASN cc_start: 0.7604 (m-40) cc_final: 0.7124 (m-40) REVERT: n 92 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: p 1 MET cc_start: 0.6393 (tpt) cc_final: 0.6143 (tpt) REVERT: p 33 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7944 (mt) REVERT: q 5 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7396 (ttm110) REVERT: q 56 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7415 (p0) REVERT: q 64 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8069 (ttp-170) REVERT: r 29 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (mtmm) REVERT: C 4 LYS cc_start: 0.7737 (tttp) cc_final: 0.7438 (tttm) REVERT: C 12 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7556 (mmp-170) REVERT: C 22 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6981 (mm-30) REVERT: C 70 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6992 (mttt) REVERT: C 73 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8487 (mm) REVERT: C 132 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7327 (ttp80) REVERT: C 166 ARG cc_start: 0.6397 (ttm-80) cc_final: 0.6021 (ttm-80) REVERT: D 1 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4823 (mmt) REVERT: D 74 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: D 184 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6894 (mtp180) REVERT: E 141 MET cc_start: 0.7120 (mpp) cc_final: 0.6598 (mpp) REVERT: F 4 HIS cc_start: 0.6703 (t70) cc_final: 0.6451 (t-170) REVERT: F 163 GLU cc_start: 0.6877 (pm20) cc_final: 0.6321 (pm20) REVERT: G 172 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: K 64 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8731 (mtt180) REVERT: K 111 LYS cc_start: 0.8740 (tppt) cc_final: 0.8394 (tptt) REVERT: L 27 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8670 (pp) REVERT: L 78 ARG cc_start: 0.7639 (mtp180) cc_final: 0.6695 (mtt90) REVERT: L 100 ILE cc_start: 0.8491 (pt) cc_final: 0.8288 (pt) REVERT: L 129 LYS cc_start: 0.7957 (tppt) cc_final: 0.7341 (ttpp) REVERT: M 51 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7501 (mtp85) REVERT: N 24 MET cc_start: 0.7567 (ttp) cc_final: 0.7278 (mtp) REVERT: N 72 ASP cc_start: 0.6658 (t70) cc_final: 0.6420 (t70) REVERT: O 3 LYS cc_start: 0.7369 (ttpt) cc_final: 0.7049 (tttt) REVERT: P 105 LYS cc_start: 0.8347 (mttt) cc_final: 0.7783 (mttm) REVERT: Q 89 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7284 (tt) REVERT: S 48 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (ttmm) REVERT: U 18 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7177 (tttt) REVERT: U 72 PHE cc_start: 0.8190 (t80) cc_final: 0.7809 (t80) REVERT: W 17 GLU cc_start: 0.6091 (mt-10) cc_final: 0.5847 (mt-10) REVERT: W 50 ASN cc_start: 0.8608 (m-40) cc_final: 0.8351 (m110) REVERT: W 68 LYS cc_start: 0.8788 (tmmt) cc_final: 0.8051 (tptp) REVERT: W 78 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8139 (mtmt) REVERT: X 45 PHE cc_start: 0.8020 (m-80) cc_final: 0.7711 (m-80) REVERT: Y 14 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7508 (mm) REVERT: 3 14 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8055 (mmmm) REVERT: 6 15 SER cc_start: 0.7692 (t) cc_final: 0.7427 (p) outliers start: 250 outliers final: 189 residues processed: 1251 average time/residue: 1.3787 time to fit residues: 2936.8566 Evaluate side-chains 1287 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1070 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 184 ASN Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 176 LYS Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 125 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 28 GLN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 586 optimal weight: 8.9990 chunk 378 optimal weight: 10.0000 chunk 565 optimal weight: 10.0000 chunk 285 optimal weight: 0.4980 chunk 186 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 602 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 468 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 744 optimal weight: 0.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN e 81 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN i 24 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 117 HIS ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN r 73 HIS t 67 HIS G 72 ASN J 135 GLN O 98 GLN O 116 GLN P 11 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 153090 Z= 0.376 Angle : 0.716 12.554 229217 Z= 0.367 Chirality : 0.042 0.314 29306 Planarity : 0.006 0.086 12136 Dihedral : 23.440 179.928 77087 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.71 % Favored : 89.07 % Rotamer: Outliers : 5.95 % Allowed : 21.28 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.25 (0.11), residues: 5435 helix: -0.81 (0.13), residues: 1642 sheet: -1.27 (0.16), residues: 973 loop : -2.00 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 212 HIS 0.013 0.002 HIS b 17 PHE 0.025 0.002 PHE R 93 TYR 0.019 0.002 TYR u 37 ARG 0.010 0.001 ARG k 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1098 time to evaluate : 5.716 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: b 112 ARG cc_start: 0.7557 (tpt170) cc_final: 0.7247 (mmm160) REVERT: b 160 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8543 (tt) REVERT: b 222 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6665 (tm-30) REVERT: b 224 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5772 (ptm160) REVERT: c 9 ILE cc_start: 0.8834 (tt) cc_final: 0.8619 (tp) REVERT: c 32 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7439 (tt) REVERT: c 40 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (pt0) REVERT: c 42 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8086 (mp) REVERT: d 43 ARG cc_start: 0.6976 (mpt180) cc_final: 0.6320 (mtt180) REVERT: d 58 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: d 110 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: d 194 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7801 (mt) REVERT: e 25 LYS cc_start: 0.8762 (tptm) cc_final: 0.8350 (tptm) REVERT: e 70 MET cc_start: 0.7732 (mmt) cc_final: 0.7485 (mmt) REVERT: e 96 GLN cc_start: 0.7892 (tt0) cc_final: 0.7541 (tt0) REVERT: e 144 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: e 147 ASN cc_start: 0.8532 (p0) cc_final: 0.8218 (p0) REVERT: e 151 MET cc_start: 0.6927 (mmm) cc_final: 0.6485 (mpp) REVERT: f 14 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: g 47 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6741 (pm20) REVERT: g 85 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7418 (mp10) REVERT: j 69 THR cc_start: 0.8461 (m) cc_final: 0.8165 (t) REVERT: k 33 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8011 (mp) REVERT: l 28 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7002 (mm-40) REVERT: m 16 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7692 (mp) REVERT: n 3 GLN cc_start: 0.7927 (mm110) cc_final: 0.7610 (mm110) REVERT: n 19 TYR cc_start: 0.6854 (m-10) cc_final: 0.6411 (m-10) REVERT: p 33 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7813 (mp) REVERT: q 5 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7512 (ttm110) REVERT: q 50 ASN cc_start: 0.5264 (OUTLIER) cc_final: 0.3872 (t0) REVERT: q 64 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8009 (ttp-170) REVERT: r 29 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7651 (mtpt) REVERT: t 52 GLU cc_start: 0.6921 (tp30) cc_final: 0.6662 (tp30) REVERT: C 4 LYS cc_start: 0.7751 (tttp) cc_final: 0.7458 (tttm) REVERT: C 12 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7586 (mmp-170) REVERT: C 22 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7093 (mm-30) REVERT: C 70 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7042 (mttt) REVERT: C 71 ASP cc_start: 0.7437 (p0) cc_final: 0.6891 (p0) REVERT: C 73 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (mm) REVERT: C 132 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7470 (ttp80) REVERT: C 166 ARG cc_start: 0.6476 (ttm-80) cc_final: 0.6071 (ttm-80) REVERT: C 250 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8254 (tm-30) REVERT: D 1 MET cc_start: 0.5499 (ppp) cc_final: 0.4905 (mmt) REVERT: D 74 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: D 184 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6923 (mtp180) REVERT: E 141 MET cc_start: 0.7220 (mpp) cc_final: 0.6645 (mpp) REVERT: F 4 HIS cc_start: 0.6791 (t70) cc_final: 0.6491 (t-170) REVERT: F 163 GLU cc_start: 0.6848 (pm20) cc_final: 0.6296 (pm20) REVERT: G 94 ARG cc_start: 0.6794 (mmp80) cc_final: 0.6543 (mmp80) REVERT: G 172 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: J 53 TYR cc_start: 0.8665 (m-80) cc_final: 0.8194 (m-80) REVERT: L 27 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8809 (pp) REVERT: L 78 ARG cc_start: 0.7744 (mtp180) cc_final: 0.6657 (mtt90) REVERT: L 129 LYS cc_start: 0.8053 (tppt) cc_final: 0.7446 (ttpp) REVERT: M 51 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7525 (mtp85) REVERT: N 24 MET cc_start: 0.7534 (ttp) cc_final: 0.7246 (mtp) REVERT: N 72 ASP cc_start: 0.6741 (t70) cc_final: 0.6478 (t70) REVERT: N 97 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8367 (mt) REVERT: O 33 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6589 (mtm-85) REVERT: P 105 LYS cc_start: 0.8478 (mttt) cc_final: 0.8015 (mttm) REVERT: Q 89 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7433 (tt) REVERT: S 48 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8311 (ttmm) REVERT: U 18 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7243 (tttt) REVERT: U 72 PHE cc_start: 0.8377 (t80) cc_final: 0.7983 (t80) REVERT: W 17 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5942 (mt-10) REVERT: W 50 ASN cc_start: 0.8637 (m-40) cc_final: 0.8390 (m110) REVERT: W 68 LYS cc_start: 0.8819 (tmmt) cc_final: 0.8121 (tptt) REVERT: W 70 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5450 (mm-30) REVERT: X 27 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.6756 (ttp-170) REVERT: Y 14 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7302 (mm) REVERT: 3 14 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8079 (mmmm) REVERT: 6 15 SER cc_start: 0.7918 (t) cc_final: 0.7519 (p) outliers start: 268 outliers final: 210 residues processed: 1261 average time/residue: 1.3826 time to fit residues: 2950.3552 Evaluate side-chains 1308 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1069 time to evaluate : 5.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 174 GLU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 125 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 28 GLN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 861 optimal weight: 0.9990 chunk 907 optimal weight: 6.9990 chunk 828 optimal weight: 9.9990 chunk 882 optimal weight: 1.9990 chunk 531 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 chunk 693 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 797 optimal weight: 1.9990 chunk 835 optimal weight: 7.9990 chunk 879 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN c 122 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 40 HIS e 60 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN i 24 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN t 67 HIS G 29 ASN O 38 GLN O 98 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 153090 Z= 0.165 Angle : 0.566 12.697 229217 Z= 0.296 Chirality : 0.035 0.277 29306 Planarity : 0.004 0.072 12136 Dihedral : 23.339 177.410 77087 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.19 % Favored : 91.61 % Rotamer: Outliers : 4.29 % Allowed : 23.35 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 5435 helix: -0.41 (0.13), residues: 1630 sheet: -1.10 (0.16), residues: 993 loop : -1.84 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 247 HIS 0.020 0.001 HIS b 17 PHE 0.025 0.001 PHE V 91 TYR 0.014 0.001 TYR i 6 ARG 0.011 0.000 ARG u 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1088 time to evaluate : 5.750 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: b 112 ARG cc_start: 0.7493 (tpt170) cc_final: 0.7192 (mmm160) REVERT: b 160 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (tt) REVERT: b 224 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5729 (ptm160) REVERT: c 32 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7493 (tt) REVERT: c 42 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8141 (mp) REVERT: d 43 ARG cc_start: 0.6837 (mpt180) cc_final: 0.6049 (mtt180) REVERT: d 58 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: d 75 TYR cc_start: 0.8605 (t80) cc_final: 0.8327 (t80) REVERT: d 110 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: d 127 ARG cc_start: 0.6721 (mtp85) cc_final: 0.6434 (mtm110) REVERT: e 25 LYS cc_start: 0.8737 (tptm) cc_final: 0.8303 (tptm) REVERT: e 29 ILE cc_start: 0.8216 (pt) cc_final: 0.7797 (mp) REVERT: e 96 GLN cc_start: 0.7759 (tt0) cc_final: 0.7403 (tt0) REVERT: e 151 MET cc_start: 0.6887 (mmm) cc_final: 0.6463 (mpp) REVERT: f 14 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: j 69 THR cc_start: 0.8446 (m) cc_final: 0.8107 (t) REVERT: k 33 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8114 (mp) REVERT: l 28 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6633 (mm-40) REVERT: n 3 GLN cc_start: 0.7886 (mm110) cc_final: 0.7555 (mm110) REVERT: n 19 TYR cc_start: 0.6583 (m-10) cc_final: 0.6210 (m-10) REVERT: n 97 LYS cc_start: 0.8237 (pttt) cc_final: 0.7931 (pttp) REVERT: o 61 GLN cc_start: 0.7923 (mt0) cc_final: 0.7638 (mt0) REVERT: q 56 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7492 (p0) REVERT: q 64 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8044 (ttp-170) REVERT: r 60 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7093 (mtt180) REVERT: t 52 GLU cc_start: 0.6739 (tp30) cc_final: 0.6458 (tp30) REVERT: u 6 ARG cc_start: 0.6227 (tpp-160) cc_final: 0.6025 (tpp-160) REVERT: C 4 LYS cc_start: 0.7734 (tttp) cc_final: 0.7434 (tttm) REVERT: C 12 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7517 (mmp-170) REVERT: C 22 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6898 (mm-30) REVERT: C 70 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6765 (mtmt) REVERT: C 132 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7254 (ttp80) REVERT: C 166 ARG cc_start: 0.6505 (ttm-80) cc_final: 0.6097 (ttm-80) REVERT: D 1 MET cc_start: 0.5427 (ppp) cc_final: 0.4888 (mmt) REVERT: D 74 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7492 (tp30) REVERT: D 184 ARG cc_start: 0.7183 (mtp85) cc_final: 0.6857 (mtp180) REVERT: E 141 MET cc_start: 0.7130 (mpp) cc_final: 0.6593 (mpp) REVERT: F 4 HIS cc_start: 0.6712 (t70) cc_final: 0.6432 (t-170) REVERT: F 163 GLU cc_start: 0.6913 (pm20) cc_final: 0.6360 (pm20) REVERT: G 172 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: K 111 LYS cc_start: 0.8755 (tppt) cc_final: 0.8381 (tptt) REVERT: L 27 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8737 (pp) REVERT: L 78 ARG cc_start: 0.7607 (mtp180) cc_final: 0.6675 (mtt90) REVERT: L 129 LYS cc_start: 0.7878 (tppt) cc_final: 0.7307 (ttpp) REVERT: M 51 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7481 (mtp85) REVERT: N 24 MET cc_start: 0.7617 (ttp) cc_final: 0.7317 (mtp) REVERT: N 30 ARG cc_start: 0.7607 (ptm160) cc_final: 0.7371 (ptm160) REVERT: N 72 ASP cc_start: 0.6624 (t70) cc_final: 0.6387 (t70) REVERT: N 97 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8344 (mt) REVERT: O 3 LYS cc_start: 0.7398 (ttpt) cc_final: 0.7148 (tttt) REVERT: O 33 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6664 (mtm180) REVERT: P 105 LYS cc_start: 0.8355 (mttt) cc_final: 0.7883 (mttm) REVERT: P 113 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6237 (pp) REVERT: S 48 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8242 (ttmm) REVERT: U 18 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7194 (tttt) REVERT: W 17 GLU cc_start: 0.6057 (mt-10) cc_final: 0.5817 (mt-10) REVERT: W 50 ASN cc_start: 0.8604 (m-40) cc_final: 0.8343 (m110) REVERT: W 68 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8095 (tptp) REVERT: X 27 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.6489 (ttp80) REVERT: Y 14 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7588 (mm) REVERT: 0 35 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: 3 14 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8047 (mmmm) REVERT: 6 15 SER cc_start: 0.7710 (t) cc_final: 0.7462 (p) outliers start: 193 outliers final: 143 residues processed: 1198 average time/residue: 1.3190 time to fit residues: 2651.6301 Evaluate side-chains 1229 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1064 time to evaluate : 5.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 28 GLN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 579 optimal weight: 8.9990 chunk 933 optimal weight: 0.9990 chunk 569 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 649 optimal weight: 10.0000 chunk 979 optimal weight: 10.0000 chunk 901 optimal weight: 0.0060 chunk 779 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 602 optimal weight: 10.0000 chunk 478 optimal weight: 8.9990 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN i 24 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN t 67 HIS ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 153090 Z= 0.343 Angle : 0.683 13.006 229217 Z= 0.351 Chirality : 0.041 0.308 29306 Planarity : 0.005 0.103 12136 Dihedral : 23.388 179.645 77087 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.43 % Favored : 89.35 % Rotamer: Outliers : 4.82 % Allowed : 22.68 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.11), residues: 5435 helix: -0.63 (0.13), residues: 1650 sheet: -1.23 (0.16), residues: 982 loop : -1.91 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 212 HIS 0.018 0.002 HIS b 17 PHE 0.024 0.002 PHE R 93 TYR 0.019 0.002 TYR u 37 ARG 0.011 0.001 ARG V 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10870 Ramachandran restraints generated. 5435 Oldfield, 0 Emsley, 5435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1065 time to evaluate : 5.468 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: b 112 ARG cc_start: 0.7542 (tpt170) cc_final: 0.7233 (mmm160) REVERT: b 160 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8532 (tt) REVERT: b 222 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6646 (tm-30) REVERT: b 224 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.5581 (ptm160) REVERT: c 32 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7484 (tt) REVERT: c 40 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7072 (pt0) REVERT: c 42 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8163 (mp) REVERT: d 43 ARG cc_start: 0.6753 (mpt180) cc_final: 0.6165 (mtt180) REVERT: d 58 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: d 110 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7726 (ttm170) REVERT: d 127 ARG cc_start: 0.6700 (mtp85) cc_final: 0.6402 (mtm110) REVERT: e 25 LYS cc_start: 0.8763 (tptm) cc_final: 0.8344 (tptm) REVERT: e 81 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6712 (mp-120) REVERT: e 96 GLN cc_start: 0.7884 (tt0) cc_final: 0.7533 (tt0) REVERT: e 144 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: e 151 MET cc_start: 0.6954 (mmm) cc_final: 0.6597 (mpp) REVERT: f 2 ARG cc_start: 0.7325 (mtp85) cc_final: 0.7071 (mtt180) REVERT: f 14 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: g 85 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7500 (mp10) REVERT: j 69 THR cc_start: 0.8475 (m) cc_final: 0.8167 (t) REVERT: k 33 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8104 (mp) REVERT: k 74 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8272 (mtpp) REVERT: l 28 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.6886 (mm-40) REVERT: m 16 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7656 (mp) REVERT: m 28 ARG cc_start: 0.6719 (tpt90) cc_final: 0.6493 (tpt90) REVERT: n 3 GLN cc_start: 0.7933 (mm110) cc_final: 0.7607 (mm110) REVERT: n 19 TYR cc_start: 0.6712 (m-10) cc_final: 0.6253 (m-10) REVERT: p 33 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8009 (mt) REVERT: p 63 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7534 (mm-40) REVERT: q 5 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7494 (ttm110) REVERT: q 27 PHE cc_start: 0.8252 (t80) cc_final: 0.7894 (t80) REVERT: q 50 ASN cc_start: 0.5289 (OUTLIER) cc_final: 0.3865 (t0) REVERT: q 56 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7556 (p0) REVERT: q 64 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7988 (ttp-170) REVERT: t 52 GLU cc_start: 0.6978 (tp30) cc_final: 0.6716 (tp30) REVERT: C 4 LYS cc_start: 0.7752 (tttp) cc_final: 0.7453 (tttm) REVERT: C 12 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7569 (mmp-170) REVERT: C 22 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7096 (mm-30) REVERT: C 71 ASP cc_start: 0.7426 (p0) cc_final: 0.6893 (p0) REVERT: C 166 ARG cc_start: 0.6460 (ttm-80) cc_final: 0.6041 (ttm-80) REVERT: C 250 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8254 (tm-30) REVERT: D 1 MET cc_start: 0.5506 (ppp) cc_final: 0.4864 (mmt) REVERT: D 74 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: D 184 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6951 (mtp180) REVERT: E 30 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: E 141 MET cc_start: 0.7103 (mpp) cc_final: 0.6547 (mpp) REVERT: E 155 GLU cc_start: 0.6852 (tp30) cc_final: 0.6482 (tp30) REVERT: F 4 HIS cc_start: 0.6829 (t70) cc_final: 0.6527 (t-170) REVERT: G 172 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: J 53 TYR cc_start: 0.8656 (m-80) cc_final: 0.8181 (m-80) REVERT: K 105 ARG cc_start: 0.6997 (ttp80) cc_final: 0.6755 (ttp80) REVERT: K 111 LYS cc_start: 0.8753 (tppt) cc_final: 0.8336 (tptt) REVERT: L 27 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8809 (pp) REVERT: L 78 ARG cc_start: 0.7756 (mtp180) cc_final: 0.6758 (mtt90) REVERT: L 129 LYS cc_start: 0.7966 (tppt) cc_final: 0.7372 (ttpp) REVERT: M 51 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7519 (mtp85) REVERT: N 24 MET cc_start: 0.7567 (ttp) cc_final: 0.7279 (mtp) REVERT: N 72 ASP cc_start: 0.6848 (t70) cc_final: 0.6545 (t70) REVERT: N 97 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8382 (mt) REVERT: O 33 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6564 (mtm-85) REVERT: P 105 LYS cc_start: 0.8474 (mttt) cc_final: 0.8002 (mttm) REVERT: S 48 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8307 (ttmm) REVERT: U 18 LYS cc_start: 0.7519 (ttpt) cc_final: 0.7201 (tttt) REVERT: W 17 GLU cc_start: 0.6157 (mt-10) cc_final: 0.5908 (mt-10) REVERT: W 50 ASN cc_start: 0.8611 (m-40) cc_final: 0.8369 (m110) REVERT: W 68 LYS cc_start: 0.8820 (tmmt) cc_final: 0.8143 (tptt) REVERT: W 70 GLU cc_start: 0.6025 (mt-10) cc_final: 0.5458 (mm-30) REVERT: X 27 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.6727 (ttp-170) REVERT: Y 14 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7292 (mm) REVERT: 3 14 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8075 (mmmm) REVERT: 6 15 SER cc_start: 0.7806 (t) cc_final: 0.7422 (p) outliers start: 217 outliers final: 179 residues processed: 1198 average time/residue: 1.3073 time to fit residues: 2642.5925 Evaluate side-chains 1259 residues out of total 4530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1054 time to evaluate : 5.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 14 GLN Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 73 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 68 ARG Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 28 GLN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 50 ASN Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 81 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 6 residue 17 SER Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 35 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 983 random chunks: chunk 619 optimal weight: 10.0000 chunk 830 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 719 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 781 optimal weight: 5.9990 chunk 326 optimal weight: 0.8980 chunk 802 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 18 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 40 HIS e 60 GLN e 88 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN i 24 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN t 67 HIS G 29 ASN K 88 ASN O 98 GLN ** U 39 ASN ** 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 = 0.3645 r_free = 0.3645 target = 0.146373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121640 restraints weight = 211443.387| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.82 r_work: 0.3175 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 153090 Z= 0.210 Angle : 0.596 13.301 229217 Z= 0.310 Chirality : 0.036 0.283 29306 Planarity : 0.005 0.091 12136 Dihedral : 23.356 177.764 77087 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.03 % Favored : 90.75 % Rotamer: Outliers : 4.42 % Allowed : 23.19 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.11), residues: 5435 helix: -0.45 (0.13), residues: 1650 sheet: -1.13 (0.16), residues: 984 loop : -1.84 (0.11), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 212 HIS 0.014 0.001 HIS t 19 PHE 0.023 0.002 PHE R 93 TYR 0.015 0.002 TYR u 37 ARG 0.011 0.001 ARG V 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40348.83 seconds wall clock time: 701 minutes 56.27 seconds (42116.27 seconds total)