Starting phenix.real_space_refine (version: dev) on Fri May 20 15:21:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/05_2022/6gxp_0083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/05_2022/6gxp_0083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/05_2022/6gxp_0083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/05_2022/6gxp_0083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/05_2022/6gxp_0083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/05_2022/6gxp_0083_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "k ARG 121": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "w PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 122": "NH1" <-> "NH2" Residue "w ARG 282": "NH1" <-> "NH2" Residue "w ARG 399": "NH1" <-> "NH2" Residue "w ARG 527": "NH1" <-> "NH2" Residue "z ARG 12": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 147637 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 62177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2896, 62177 Classifications: {'RNA': 2896} Modifications used: {'rna2p_pyr': 91, 'rna3p_pyr': 1133, 'p5*END': 1, 'rna3p_pur': 1465, 'rna2p_pur': 207} Link IDs: {'rna3p': 2597, 'rna2p': 298} 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: {'rna3p_pyr': 53, 'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 62, 'rna2p_pyr': 2} Link IDs: {'rna3p': 114, 'rna2p': 5} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} 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: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "a" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pyr': 44, 'rna3p_pyr': 621, 'p5*END': 1, 'rna3p_pur': 784, 'rna2p_pur': 90} Link IDs: {'rna3p': 1404, 'rna2p': 134} Chain breaks: 2 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: {'PTRANS': 7, '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: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 829 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "w" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3943 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 5, 'TRANS': 8} Chain: "w" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GCP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 57.48, per 1000 atoms: 0.39 Number of scatterers: 147637 At special positions: 0 Unit cell: (265.25, 275.86, 247.213, 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 169 16.00 P 4558 15.00 O 40581 8.00 N 27456 7.00 C 74873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 51.22 Conformation dependent library (CDL) restraints added in 5.8 seconds 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11758 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 188 helices and 68 sheets defined 37.6% alpha, 15.5% beta 1412 base pairs and 2536 stacking pairs defined. Time for finding SS restraints: 58.09 Creating SS restraints... Processing helix chain 'C' and resid 11 through 16 removed outlier: 4.424A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 16' Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.931A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.040A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.693A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.612A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.285A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.771A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.126A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 105' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.701A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.522A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.703A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.582A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.698A pdb=" N ARG E 21 " --> pdb=" O GLU E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 16 through 21' Processing helix chain 'F' and resid 1 through 20 removed outlier: 3.792A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 4.189A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.092A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 4.377A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.564A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.524A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.542A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG G 152 " --> pdb=" O ARG G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.751A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 6.039A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.519A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.850A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.167A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.965A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.228A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 4.870A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.693A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.541A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.453A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.119A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.781A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.651A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.202A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 93 through 99 removed outlier: 6.546A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 93 through 99' Processing helix chain 'L' and resid 128 through 139 removed outlier: 6.465A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.725A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.648A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.025A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.887A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG N 71 " --> pdb=" O PHE N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.632A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.588A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.922A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.602A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.770A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.536A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.588A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.939A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.611A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 71 removed outlier: 4.303A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.555A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.936A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.505A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.352A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 2 through 11 removed outlier: 3.897A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 65 through 70 removed outlier: 4.129A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.789A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 4.296A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.329A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 4.687A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.764A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 25 through 35 Processing helix chain 'Y' and resid 40 through 62 removed outlier: 4.130A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.533A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 20 removed outlier: 4.808A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 3.648A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.826A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 45 removed outlier: 3.925A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.566A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 3.650A pdb=" N ASP 5 7 " --> pdb=" O LEU 5 3 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 5 20 " --> pdb=" O SER 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 4.594A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA 5 48 " --> pdb=" O ALA 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 68 removed outlier: 4.077A pdb=" N GLY 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR 5 67 " --> pdb=" O ALA 5 63 " (cutoff:3.500A) Proline residue: 5 68 - end of helix No H-bonds generated for 'chain '5' and resid 62 through 68' Processing helix chain '5' and resid 71 through 76 removed outlier: 4.467A pdb=" N ALA 5 75 " --> pdb=" O CYS 5 71 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE 5 76 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 71 through 76' Processing helix chain '5' and resid 94 through 106 removed outlier: 3.935A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.577A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 3.731A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 75 through 86 removed outlier: 4.475A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 123 removed outlier: 3.810A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 168 through 179 removed outlier: 4.114A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.783A pdb=" N VAL b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY b 223 " --> pdb=" O THR b 219 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 153 removed outlier: 4.789A pdb=" N ASP b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET b 153 " --> pdb=" O ILE b 150 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.748A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 47 removed outlier: 5.333A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.732A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.708A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.511A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.710A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.773A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.631A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 removed outlier: 4.566A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 6.392A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.205A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.016A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.157A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 147 removed outlier: 5.337A pdb=" N ASN e 147 " --> pdb=" O LEU e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 removed outlier: 4.183A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS e 155 " --> pdb=" O MET e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 12 through 33 removed outlier: 4.213A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 67 through 81 removed outlier: 4.201A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.502A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET g 30 " --> pdb=" O VAL g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.811A pdb=" N PHE g 61 " --> pdb=" O GLU g 57 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU g 65 " --> pdb=" O PHE g 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.664A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.860A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 147 removed outlier: 3.816A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.593A pdb=" N ALA h 19 " --> pdb=" O ASN h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 removed outlier: 4.031A pdb=" N VAL h 33 " --> pdb=" O SER h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.612A pdb=" N ARG h 116 " --> pdb=" O ASP h 112 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY h 119 " --> pdb=" O ALA h 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 38 removed outlier: 3.824A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 45 through 55 Proline residue: i 50 - end of helix removed outlier: 5.530A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 5.922A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 101 removed outlier: 4.822A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 5.244A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.805A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.319A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 72 removed outlier: 3.565A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 6.204A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 removed outlier: 3.784A pdb=" N LEU l 6 " --> pdb=" O THR l 2 " (cutoff:3.500A) Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.917A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 4.141A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.738A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.155A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.507A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA m 60 " --> pdb=" O ARG m 56 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 removed outlier: 4.159A pdb=" N LYS m 109 " --> pdb=" O ALA m 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.834A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.264A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'n' and resid 25 through 31 removed outlier: 4.543A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 46 removed outlier: 3.527A pdb=" N GLN o 27 " --> pdb=" O SER o 23 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE o 42 " --> pdb=" O LEU o 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA o 43 " --> pdb=" O GLN o 39 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N HIS o 45 " --> pdb=" O HIS o 41 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS o 46 " --> pdb=" O PHE o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.749A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.850A pdb=" N ASN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 4.859A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY r 16 " --> pdb=" O PHE r 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 11 through 16' Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.072A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.978A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY r 45 " --> pdb=" O SER r 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 40 through 45' Processing helix chain 'r' and resid 47 through 65 removed outlier: 3.606A pdb=" N LEU r 64 " --> pdb=" O ARG r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.724A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 7 through 41 removed outlier: 3.706A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA t 21 " --> pdb=" O ARG t 17 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix removed outlier: 4.286A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 6.653A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 4.282A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 34 removed outlier: 5.383A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 26 through 34' Processing helix chain 'u' and resid 38 through 61 Processing helix chain 'w' and resid 4 through 14 removed outlier: 3.747A pdb=" N LYS w 12 " --> pdb=" O GLN w 8 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG w 13 " --> pdb=" O GLU w 9 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ARG w 14 " --> pdb=" O VAL w 10 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 38 removed outlier: 3.693A pdb=" N LEU w 35 " --> pdb=" O GLU w 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY w 37 " --> pdb=" O VAL w 33 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN w 38 " --> pdb=" O LEU w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 107 removed outlier: 3.981A pdb=" N TYR w 100 " --> pdb=" O SER w 96 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG w 101 " --> pdb=" O GLU w 97 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR w 104 " --> pdb=" O TYR w 100 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA w 105 " --> pdb=" O ARG w 101 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL w 106 " --> pdb=" O THR w 102 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP w 107 " --> pdb=" O LEU w 103 " (cutoff:3.500A) Processing helix chain 'w' and resid 120 through 134 removed outlier: 4.208A pdb=" N LEU w 132 " --> pdb=" O GLU w 128 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG w 133 " --> pdb=" O VAL w 129 " (cutoff:3.500A) Processing helix chain 'w' and resid 150 through 162 Processing helix chain 'w' and resid 212 through 220 Processing helix chain 'w' and resid 221 through 238 Processing helix chain 'w' and resid 242 through 249 removed outlier: 4.321A pdb=" N PHE w 246 " --> pdb=" O ASP w 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU w 247 " --> pdb=" O LYS w 243 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA w 248 " --> pdb=" O GLU w 244 " (cutoff:3.500A) Processing helix chain 'w' and resid 262 through 275 removed outlier: 5.392A pdb=" N ASP w 266 " --> pdb=" O ASN w 262 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS w 267 " --> pdb=" O PHE w 263 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET w 268 " --> pdb=" O GLY w 264 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU w 269 " --> pdb=" O VAL w 265 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP w 270 " --> pdb=" O ASP w 266 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY w 271 " --> pdb=" O HIS w 267 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 422 removed outlier: 4.926A pdb=" N VAL w 417 " --> pdb=" O LEU w 413 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU w 421 " --> pdb=" O VAL w 417 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU w 422 " --> pdb=" O GLN w 418 " (cutoff:3.500A) Processing helix chain 'w' and resid 445 through 454 removed outlier: 3.523A pdb=" N VAL w 449 " --> pdb=" O GLN w 445 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU w 453 " --> pdb=" O VAL w 449 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS w 454 " --> pdb=" O VAL w 450 " (cutoff:3.500A) Processing helix chain 'w' and resid 479 through 490 removed outlier: 6.759A pdb=" N GLU w 483 " --> pdb=" O ALA w 479 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU w 484 " --> pdb=" O LYS w 480 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE w 485 " --> pdb=" O LYS w 481 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN w 489 " --> pdb=" O PHE w 485 " (cutoff:3.500A) Processing helix chain 'w' and resid 507 through 518 removed outlier: 3.624A pdb=" N LEU w 511 " --> pdb=" O SER w 507 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR w 518 " --> pdb=" O ALA w 514 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.850A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN C 127 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.586A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 175 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 89 through 95 removed outlier: 5.581A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.334A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.521A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.898A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.662A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.612A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP F 152 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 10, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 11, first strand: chain 'G' and resid 81 through 88 removed outlier: 5.628A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.716A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 2 through 5 removed outlier: 5.203A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 76 through 81 removed outlier: 7.067A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 14 through 19 removed outlier: 3.808A pdb=" N LEU J 57 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.567A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 88 through 91 Processing sheet with id= 18, first strand: chain 'M' and resid 62 through 65 Processing sheet with id= 19, first strand: chain 'M' and resid 71 through 74 removed outlier: 4.089A pdb=" N LYS M 71 " --> pdb=" O VAL M 93 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 99 through 102 removed outlier: 6.543A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 32 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL M 131 " --> pdb=" O GLY M 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS M 34 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.615A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.859A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.451A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 56 through 63 removed outlier: 7.979A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG P 71 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.954A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 19 through 24 removed outlier: 4.206A pdb=" N LYS R 24 " --> pdb=" O TRP R 92 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP R 92 " --> pdb=" O LYS R 24 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 57 through 60 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'R' and resid 68 through 78 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'S' and resid 4 through 8 removed outlier: 5.102A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.627A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'U' and resid 39 through 44 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'U' and resid 81 through 86 removed outlier: 5.725A pdb=" N ARG U 81 " --> pdb=" O LYS U 96 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.702A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'W' and resid 41 through 44 removed outlier: 6.809A pdb=" N ILE W 78 " --> pdb=" O GLY W 44 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'W' and resid 46 through 50 removed outlier: 7.116A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY W 50 " --> pdb=" O THR W 54 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'X' and resid 11 through 15 Processing sheet with id= 37, first strand: chain 'X' and resid 33 through 39 Processing sheet with id= 38, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.398A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS Z 2 " --> pdb=" O ASP Z 39 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '1' and resid 19 through 23 removed outlier: 3.831A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '3' and resid 21 through 24 No H-bonds generated for sheet with id= 40 Processing sheet with id= 41, first strand: chain '4' and resid 14 through 19 removed outlier: 6.149A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN 4 37 " --> pdb=" O ILE 4 23 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL 4 25 " --> pdb=" O GLN 4 35 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'b' and resid 29 through 33 removed outlier: 7.504A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN b 41 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE b 39 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.722A pdb=" N LEU b 160 " --> pdb=" O PRO b 181 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.399A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN c 99 " --> pdb=" O ILE c 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL c 65 " --> pdb=" O GLN c 99 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.793A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.998A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TRP d 169 " --> pdb=" O LYS d 182 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 16 through 23 removed outlier: 3.998A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'e' and resid 93 through 97 Processing sheet with id= 49, first strand: chain 'f' and resid 43 through 47 removed outlier: 6.186A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 72 through 76 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.613A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.708A pdb=" N ILE h 100 " --> pdb=" O VAL h 128 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.612A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA i 15 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU i 62 " --> pdb=" O LYS i 26 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 44 through 52 removed outlier: 6.709A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.687A pdb=" N ASN k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'l' and resid 34 through 40 removed outlier: 4.557A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 80 through 84 removed outlier: 4.850A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG l 93 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.807A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'q' and resid 6 through 10 removed outlier: 3.924A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 19 through 27 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 's' and resid 29 through 32 removed outlier: 4.155A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS s 51 " --> pdb=" O THR s 32 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'w' and resid 16 through 20 removed outlier: 5.060A pdb=" N ALA w 17 " --> pdb=" O CYS w 108 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU w 110 " --> pdb=" O ALA w 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE w 113 " --> pdb=" O PHE w 140 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'w' and resid 72 through 76 removed outlier: 4.127A pdb=" N SER w 73 " --> pdb=" O ASP w 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET w 75 " --> pdb=" O LEU w 86 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'w' and resid 180 through 185 removed outlier: 6.434A pdb=" N LYS w 180 " --> pdb=" O TYR w 193 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU w 189 " --> pdb=" O HIS w 184 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'w' and resid 281 through 284 removed outlier: 3.702A pdb=" N ARG w 282 " --> pdb=" O VAL w 289 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG w 287 " --> pdb=" O THR w 284 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'w' and resid 315 through 318 removed outlier: 5.546A pdb=" N ALA w 316 " --> pdb=" O GLY w 366 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N MET w 318 " --> pdb=" O ILE w 364 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE w 364 " --> pdb=" O MET w 318 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'w' and resid 328 through 334 removed outlier: 4.581A pdb=" N MET w 329 " --> pdb=" O ILE w 342 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE w 342 " --> pdb=" O MET w 329 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'w' and resid 424 through 429 removed outlier: 8.994A pdb=" N ALA w 424 " --> pdb=" O VAL w 441 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL w 441 " --> pdb=" O ALA w 424 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN w 426 " --> pdb=" O GLY w 439 " (cutoff:3.500A) 1734 hydrogen bonds defined for protein. 5142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3582 hydrogen bonds 5702 hydrogen bond angles 0 basepair planarities 1412 basepair parallelities 2536 stacking parallelities Total time for adding SS restraints: 254.71 Time building geometry restraints manager: 56.40 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: 24254 1.33 - 1.46: 66211 1.46 - 1.58: 60188 1.58 - 1.70: 9108 1.70 - 1.82: 304 Bond restraints: 160065 Sorted by residual: bond pdb=" C ILE k 115 " pdb=" N PRO k 116 " ideal model delta sigma weight residual 1.335 1.221 0.114 1.19e-02 7.06e+03 9.12e+01 bond pdb=" C3B GCP w 601 " pdb=" PB GCP w 601 " ideal model delta sigma weight residual 1.807 1.639 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" C3B GCP w 601 " pdb=" PG GCP w 601 " ideal model delta sigma weight residual 1.871 1.708 0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" CA PRO k 116 " pdb=" CB PRO k 116 " ideal model delta sigma weight residual 1.534 1.420 0.113 1.40e-02 5.10e+03 6.56e+01 bond pdb=" C1' A a 716 " pdb=" N9 A a 716 " ideal model delta sigma weight residual 1.475 1.592 -0.117 1.50e-02 4.44e+03 6.13e+01 ... (remaining 160060 not shown) Histogram of bond angle deviations from ideal: 96.10 - 104.12: 16300 104.12 - 112.14: 91705 112.14 - 120.16: 69924 120.16 - 128.18: 53400 128.18 - 136.20: 7380 Bond angle restraints: 238709 Sorted by residual: angle pdb=" N PRO k 116 " pdb=" CA PRO k 116 " pdb=" C PRO k 116 " ideal model delta sigma weight residual 113.84 132.40 -18.56 1.30e+00 5.92e-01 2.04e+02 angle pdb=" C ILE k 115 " pdb=" N PRO k 116 " pdb=" CA PRO k 116 " ideal model delta sigma weight residual 119.56 109.86 9.70 1.02e+00 9.61e-01 9.04e+01 angle pdb=" N GLY c 95 " pdb=" CA GLY c 95 " pdb=" C GLY c 95 " ideal model delta sigma weight residual 115.32 103.13 12.19 1.38e+00 5.25e-01 7.80e+01 angle pdb=" N PHE w 77 " pdb=" CA PHE w 77 " pdb=" C PHE w 77 " ideal model delta sigma weight residual 109.81 126.74 -16.93 2.21e+00 2.05e-01 5.87e+01 angle pdb=" N ALA g 64 " pdb=" CA ALA g 64 " pdb=" C ALA g 64 " ideal model delta sigma weight residual 114.75 105.28 9.47 1.26e+00 6.30e-01 5.65e+01 ... (remaining 238704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 83203 35.97 - 71.95: 2462 71.95 - 107.92: 202 107.92 - 143.89: 28 143.89 - 179.87: 41 Dihedral angle restraints: 85936 sinusoidal: 67713 harmonic: 18223 Sorted by residual: dihedral pdb=" CA ASP G 46 " pdb=" C ASP G 46 " pdb=" N ASN G 47 " pdb=" CA ASN G 47 " ideal model delta harmonic sigma weight residual -180.00 -117.93 -62.07 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA LYS q 68 " pdb=" C LYS q 68 " pdb=" N THR q 69 " pdb=" CA THR q 69 " ideal model delta harmonic sigma weight residual -180.00 -121.13 -58.87 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA ALA m 4 " pdb=" C ALA m 4 " pdb=" N GLY m 5 " pdb=" CA GLY m 5 " ideal model delta harmonic sigma weight residual -180.00 -121.18 -58.82 0 5.00e+00 4.00e-02 1.38e+02 ... (remaining 85933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 30221 0.152 - 0.304: 164 0.304 - 0.456: 20 0.456 - 0.608: 1 0.608 - 0.760: 4 Chirality restraints: 30410 Sorted by residual: chirality pdb=" CA ILE k 115 " pdb=" N ILE k 115 " pdb=" C ILE k 115 " pdb=" CB ILE k 115 " both_signs ideal model delta sigma weight residual False 2.43 1.67 0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CA PRO k 116 " pdb=" N PRO k 116 " pdb=" C PRO k 116 " pdb=" CB PRO k 116 " both_signs ideal model delta sigma weight residual False 2.72 2.01 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA PHE w 77 " pdb=" N PHE w 77 " pdb=" C PHE w 77 " pdb=" CB PHE w 77 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 30407 not shown) Planarity restraints: 13334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR q 69 " 0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C THR q 69 " -0.087 2.00e-02 2.50e+03 pdb=" O THR q 69 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS q 70 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE k 115 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO k 116 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO k 116 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO k 116 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE k 115 " 0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C ILE k 115 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE k 115 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO k 116 " 0.026 2.00e-02 2.50e+03 ... (remaining 13331 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 19 2.27 - 2.92: 53472 2.92 - 3.58: 218667 3.58 - 4.24: 438355 4.24 - 4.90: 583933 Nonbonded interactions: 1294446 Sorted by model distance: nonbonded pdb=" OP2 A a 676 " pdb=" O THR k 113 " model vdw 1.608 3.040 nonbonded pdb=" N7 A A1913 " pdb=" N7 G a1494 " model vdw 1.944 3.200 nonbonded pdb=" N7 A A1913 " pdb=" C8 G a1494 " model vdw 2.050 3.340 nonbonded pdb=" O2' A A1912 " pdb=" N3 G a1494 " model vdw 2.100 2.520 nonbonded pdb=" O4 U A2457 " pdb=" O6 G A2494 " model vdw 2.126 3.040 ... (remaining 1294441 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4558 5.49 5 S 169 5.16 5 C 74873 2.51 5 N 27456 2.21 5 O 40581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 19.360 Check model and map are aligned: 1.580 Convert atoms to be neutral: 0.920 Process input model: 519.570 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 550.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 0.168 160065 Z= 0.201 Angle : 0.804 18.556 238709 Z= 0.422 Chirality : 0.039 0.760 30410 Planarity : 0.006 0.110 13334 Dihedral : 13.998 179.867 74178 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.34 % Favored : 91.17 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.41 % 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: -4.12 (0.08), residues: 6286 helix: -2.82 (0.08), residues: 1876 sheet: -2.29 (0.15), residues: 987 loop : -2.87 (0.09), residues: 3423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2639 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 2625 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 2634 average time/residue: 1.5885 time to fit residues: 6858.9284 Evaluate side-chains 1535 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1534 time to evaluate : 6.624 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9737 time to fit residues: 10.2936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 903 optimal weight: 7.9990 chunk 811 optimal weight: 5.9990 chunk 450 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 547 optimal weight: 30.0000 chunk 433 optimal weight: 20.0000 chunk 838 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 509 optimal weight: 6.9990 chunk 624 optimal weight: 0.8980 chunk 971 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 134 HIS D 150 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS M 3 GLN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN R 18 GLN R 91 GLN S 7 HIS T 15 HIS U 53 GLN U 73 ASN W 8 ASN X 22 ASN Y 15 ASN Y 58 ASN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS 0 18 HIS 2 26 ASN 3 42 HIS ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 88 HIS c 101 ASN c 139 ASN ** d 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN e 134 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN i 3 ASN i 4 GLN i 125 GLN j 99 GLN ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 45 ASN m 99 GLN ** o 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 HIS o 49 HIS p 26 ASN p 63 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS w 311 HIS ** w 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 445 GLN ** w 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 15 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.153 160065 Z= 0.241 Angle : 0.647 15.026 238709 Z= 0.335 Chirality : 0.035 0.400 30410 Planarity : 0.006 0.113 13334 Dihedral : 14.635 179.475 61719 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.16 % Favored : 91.50 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.38 % 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: -2.87 (0.09), residues: 6286 helix: -0.99 (0.11), residues: 1950 sheet: -2.07 (0.15), residues: 1020 loop : -2.45 (0.10), residues: 3316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1916 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1905 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 1912 average time/residue: 1.4474 time to fit residues: 4663.9536 Evaluate side-chains 1400 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1400 time to evaluate : 6.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 540 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 808 optimal weight: 3.9990 chunk 661 optimal weight: 30.0000 chunk 268 optimal weight: 20.0000 chunk 973 optimal weight: 20.0000 chunk 1051 optimal weight: 30.0000 chunk 866 optimal weight: 10.0000 chunk 965 optimal weight: 50.0000 chunk 331 optimal weight: 9.9990 chunk 780 optimal weight: 20.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 150 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS G 142 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN N 62 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN Q 55 GLN S 7 HIS ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Y 20 ASN Y 27 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS 1 18 HIS 2 26 ASN 3 23 HIS ** 3 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN ** d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 HIS d 151 GLN f 11 HIS ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 3 ASN j 70 HIS ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 76 HIS ** m 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 HIS ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 85 ASN ** w 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 426 GLN ** w 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.114 160065 Z= 0.407 Angle : 0.882 17.143 238709 Z= 0.446 Chirality : 0.045 0.424 30410 Planarity : 0.008 0.107 13334 Dihedral : 15.905 179.996 61719 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 39.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.13 % Favored : 89.56 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.39 % 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: -2.62 (0.10), residues: 6286 helix: -0.74 (0.11), residues: 1966 sheet: -2.05 (0.15), residues: 1011 loop : -2.29 (0.10), residues: 3309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1688 time to evaluate : 6.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 1703 average time/residue: 1.4339 time to fit residues: 4149.8418 Evaluate side-chains 1288 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1277 time to evaluate : 6.513 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 1.1209 time to fit residues: 30.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 961 optimal weight: 8.9990 chunk 731 optimal weight: 40.0000 chunk 505 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 464 optimal weight: 6.9990 chunk 653 optimal weight: 20.0000 chunk 976 optimal weight: 9.9990 chunk 1034 optimal weight: 8.9990 chunk 510 optimal weight: 8.9990 chunk 925 optimal weight: 10.0000 chunk 278 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 47 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN H 66 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS S 40 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN V 44 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 HIS e 77 ASN f 3 HIS ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN j 99 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN o 36 ASN ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS ** q 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 510 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.121 160065 Z= 0.258 Angle : 0.665 14.170 238709 Z= 0.342 Chirality : 0.037 0.386 30410 Planarity : 0.006 0.100 13334 Dihedral : 15.784 179.217 61719 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.94 % Favored : 90.79 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.10), residues: 6286 helix: -0.32 (0.11), residues: 1963 sheet: -1.76 (0.16), residues: 921 loop : -2.13 (0.10), residues: 3402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1638 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1626 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 1634 average time/residue: 1.4300 time to fit residues: 3966.7323 Evaluate side-chains 1250 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1246 time to evaluate : 6.294 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.0884 time to fit residues: 15.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 861 optimal weight: 10.0000 chunk 587 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 770 optimal weight: 50.0000 chunk 426 optimal weight: 0.0020 chunk 882 optimal weight: 0.0980 chunk 714 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 528 optimal weight: 30.0000 chunk 928 optimal weight: 40.0000 chunk 260 optimal weight: 20.0000 overall best weight: 7.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN e 77 ASN ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN j 99 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 HIS ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 ASN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 369 ASN ** w 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 160065 Z= 0.243 Angle : 0.652 13.340 238709 Z= 0.336 Chirality : 0.037 0.402 30410 Planarity : 0.006 0.103 13334 Dihedral : 15.841 179.849 61719 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.04 % Favored : 89.74 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.10), residues: 6286 helix: -0.23 (0.11), residues: 1972 sheet: -1.75 (0.16), residues: 946 loop : -2.10 (0.10), residues: 3368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1594 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1589 time to evaluate : 6.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 1592 average time/residue: 1.4229 time to fit residues: 3880.5122 Evaluate side-chains 1234 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1233 time to evaluate : 6.619 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2399 time to fit residues: 9.6886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 347 optimal weight: 20.0000 chunk 931 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 607 optimal weight: 30.0000 chunk 255 optimal weight: 20.0000 chunk 1035 optimal weight: 8.9990 chunk 859 optimal weight: 8.9990 chunk 479 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 342 optimal weight: 1.9990 chunk 543 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS M 3 GLN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN O 29 HIS Q 55 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 HIS ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.7340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 160065 Z= 0.236 Angle : 0.641 14.826 238709 Z= 0.330 Chirality : 0.036 0.314 30410 Planarity : 0.005 0.099 13334 Dihedral : 15.902 179.859 61719 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.80 % Favored : 89.95 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 6286 helix: -0.13 (0.11), residues: 1975 sheet: -1.66 (0.16), residues: 962 loop : -2.07 (0.10), residues: 3349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1535 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1530 time to evaluate : 6.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 1533 average time/residue: 1.5189 time to fit residues: 4012.4577 Evaluate side-chains 1216 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1214 time to evaluate : 6.518 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1571 time to fit residues: 11.5655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 998 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 589 optimal weight: 4.9990 chunk 756 optimal weight: 40.0000 chunk 585 optimal weight: 50.0000 chunk 871 optimal weight: 7.9990 chunk 578 optimal weight: 8.9990 chunk 1031 optimal weight: 4.9990 chunk 645 optimal weight: 40.0000 chunk 628 optimal weight: 4.9990 chunk 476 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS M 3 GLN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 55 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 HIS ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 ASN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.7485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 160065 Z= 0.186 Angle : 0.602 13.681 238709 Z= 0.309 Chirality : 0.034 0.326 30410 Planarity : 0.005 0.097 13334 Dihedral : 15.761 179.195 61719 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.74 % Favored : 90.04 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.28 % 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: -1.95 (0.10), residues: 6286 helix: -0.04 (0.12), residues: 1976 sheet: -1.54 (0.16), residues: 968 loop : -2.03 (0.10), residues: 3342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1534 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1532 time to evaluate : 6.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 1533 average time/residue: 1.3829 time to fit residues: 3637.6423 Evaluate side-chains 1226 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1225 time to evaluate : 6.631 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0797 time to fit residues: 9.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 638 optimal weight: 40.0000 chunk 411 optimal weight: 30.0000 chunk 615 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 202 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 655 optimal weight: 40.0000 chunk 702 optimal weight: 30.0000 chunk 509 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 810 optimal weight: 50.0000 overall best weight: 15.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN H 2 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 99 ASN M 3 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS U 68 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 HIS ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 85 ASN ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.8898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.251 160065 Z= 0.457 Angle : 0.899 14.683 238709 Z= 0.453 Chirality : 0.046 0.405 30410 Planarity : 0.008 0.102 13334 Dihedral : 16.949 179.794 61719 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 51.10 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.87 % Favored : 87.80 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.41 % 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: -2.58 (0.10), residues: 6286 helix: -0.75 (0.11), residues: 1953 sheet: -1.95 (0.15), residues: 944 loop : -2.27 (0.10), residues: 3389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1459 time to evaluate : 6.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1461 average time/residue: 1.5069 time to fit residues: 3816.0604 Evaluate side-chains 1105 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1105 time to evaluate : 6.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 938 optimal weight: 30.0000 chunk 988 optimal weight: 5.9990 chunk 901 optimal weight: 10.0000 chunk 961 optimal weight: 30.0000 chunk 987 optimal weight: 7.9990 chunk 578 optimal weight: 20.0000 chunk 418 optimal weight: 0.0970 chunk 754 optimal weight: 40.0000 chunk 294 optimal weight: 30.0000 chunk 868 optimal weight: 40.0000 chunk 908 optimal weight: 20.0000 overall best weight: 8.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 30 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 11 GLN T 59 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 GLN ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** s 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 51 ASN ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.168 160065 Z= 0.272 Angle : 0.704 13.541 238709 Z= 0.361 Chirality : 0.039 0.306 30410 Planarity : 0.006 0.116 13334 Dihedral : 16.624 179.681 61719 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 34.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.72 % Favored : 89.06 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.33 % 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: -2.33 (0.10), residues: 6286 helix: -0.48 (0.11), residues: 1951 sheet: -1.67 (0.16), residues: 950 loop : -2.20 (0.10), residues: 3385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1465 time to evaluate : 6.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 1466 average time/residue: 1.3813 time to fit residues: 3483.8631 Evaluate side-chains 1176 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1175 time to evaluate : 6.576 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0692 time to fit residues: 9.3559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 957 optimal weight: 0.0970 chunk 631 optimal weight: 0.5980 chunk 1016 optimal weight: 50.0000 chunk 620 optimal weight: 30.0000 chunk 482 optimal weight: 20.0000 chunk 706 optimal weight: 40.0000 chunk 1065 optimal weight: 6.9990 chunk 981 optimal weight: 3.9990 chunk 848 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 chunk 655 optimal weight: 30.0000 overall best weight: 6.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 164 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN T 59 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN f 63 ASN h 37 ASN ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 HIS ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 426 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.8938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 160065 Z= 0.219 Angle : 0.652 13.261 238709 Z= 0.335 Chirality : 0.037 0.315 30410 Planarity : 0.006 0.109 13334 Dihedral : 16.337 179.632 61719 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 30.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.83 % Favored : 88.93 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.28 % 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: -2.17 (0.10), residues: 6286 helix: -0.28 (0.11), residues: 1952 sheet: -1.59 (0.16), residues: 951 loop : -2.15 (0.10), residues: 3383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1471 time to evaluate : 6.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1473 average time/residue: 1.3880 time to fit residues: 3545.8752 Evaluate side-chains 1183 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1183 time to evaluate : 6.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 520 optimal weight: 7.9990 chunk 674 optimal weight: 30.0000 chunk 904 optimal weight: 20.0000 chunk 260 optimal weight: 30.0000 chunk 782 optimal weight: 40.0000 chunk 125 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 850 optimal weight: 0.0980 chunk 355 optimal weight: 6.9990 chunk 873 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 overall best weight: 8.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN M 3 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 18 HIS b 14 HIS ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN d 39 GLN d 151 GLN e 77 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.043440 restraints weight = 1107617.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045267 restraints weight = 392624.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.046292 restraints weight = 200819.197| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.9232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.132 160065 Z= 0.254 Angle : 0.677 13.302 238709 Z= 0.347 Chirality : 0.038 0.318 30410 Planarity : 0.006 0.094 13334 Dihedral : 16.435 179.953 61719 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 34.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.85 % Favored : 88.94 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.10), residues: 6286 helix: -0.32 (0.11), residues: 1943 sheet: -1.48 (0.16), residues: 964 loop : -2.15 (0.10), residues: 3379 =============================================================================== Job complete usr+sys time: 52238.49 seconds wall clock time: 897 minutes 46.33 seconds (53866.33 seconds total)