Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 23 02:40:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/07_2023/6gxp_0083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/07_2023/6gxp_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_0083/07_2023/6gxp_0083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/07_2023/6gxp_0083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/07_2023/6gxp_0083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gxp_0083/07_2023/6gxp_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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: {'p5*END': 1, 'rna2p_pur': 207, 'rna2p_pyr': 91, 'rna3p_pur': 1465, 'rna3p_pyr': 1133} Link IDs: {'rna2p': 298, 'rna3p': 2597} Chain breaks: 2 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} 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: {'p5*END': 1, 'rna2p_pur': 90, 'rna2p_pyr': 44, 'rna3p_pur': 784, 'rna3p_pyr': 621} Link IDs: {'rna2p': 134, 'rna3p': 1404} 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: 50.12, per 1000 atoms: 0.34 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: 60.53 Conformation dependent library (CDL) restraints added in 6.0 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: 60.57 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: 257.01 Time building geometry restraints manager: 65.91 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 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 19.520 Check model and map are aligned: 1.600 Set scattering table: 0.980 Process input model: 531.210 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 562.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 5.45 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 : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2 residues processed: 2634 average time/residue: 1.4930 time to fit residues: 6520.3472 Evaluate side-chains 1541 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1539 time to evaluate : 6.385 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.9862 time to fit residues: 10.7951 ------------------------------------------------------------------------------- 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: 7.9990 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: 5.9788 ------------------------------------------------------------------------------- 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 K 5 GLN 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 160065 Z= 0.231 Angle : 0.640 13.443 238709 Z= 0.331 Chirality : 0.035 0.300 30410 Planarity : 0.006 0.116 13334 Dihedral : 14.602 179.586 61719 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.18 % Favored : 91.50 % Rotamer Outliers : 0.23 % 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: -2.85 (0.09), residues: 6286 helix: -0.95 (0.11), residues: 1950 sheet: -2.03 (0.15), residues: 983 loop : -2.47 (0.09), residues: 3353 *********************** 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 1910 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1898 time to evaluate : 6.527 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 outliers start: 12 outliers final: 1 residues processed: 1905 average time/residue: 1.4561 time to fit residues: 4642.5307 Evaluate side-chains 1391 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1390 time to evaluate : 6.377 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2096 time to fit residues: 9.0903 ------------------------------------------------------------------------------- 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: 8.9990 chunk 301 optimal weight: 20.0000 chunk 808 optimal weight: 9.9990 chunk 661 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 973 optimal weight: 8.9990 chunk 1051 optimal weight: 10.0000 chunk 866 optimal weight: 7.9990 chunk 965 optimal weight: 50.0000 chunk 331 optimal weight: 8.9990 chunk 780 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 62 GLN ** 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** M 3 GLN N 62 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS 1 18 HIS 3 42 HIS ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN c 189 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 h 15 ASN ** h 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN i 3 ASN j 70 HIS k 21 HIS ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 HIS w 85 ASN ** w 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 426 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** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.164 160065 Z= 0.307 Angle : 0.742 20.030 238709 Z= 0.379 Chirality : 0.039 0.355 30410 Planarity : 0.007 0.102 13334 Dihedral : 15.365 179.986 61719 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.51 % Favored : 90.25 % Rotamer Outliers : 0.46 % 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: -2.35 (0.10), residues: 6286 helix: -0.45 (0.11), residues: 1953 sheet: -1.93 (0.15), residues: 990 loop : -2.15 (0.10), residues: 3343 *********************** 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 1737 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1713 time to evaluate : 6.241 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 outliers start: 24 outliers final: 4 residues processed: 1728 average time/residue: 1.4266 time to fit residues: 4165.0858 Evaluate side-chains 1303 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1299 time to evaluate : 6.358 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.0817 time to fit residues: 15.2815 ------------------------------------------------------------------------------- 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: 5.9990 chunk 731 optimal weight: 40.0000 chunk 505 optimal weight: 8.9990 chunk 107 optimal weight: 50.0000 chunk 464 optimal weight: 30.0000 chunk 653 optimal weight: 30.0000 chunk 976 optimal weight: 10.0000 chunk 1034 optimal weight: 20.0000 chunk 510 optimal weight: 8.9990 chunk 925 optimal weight: 0.9990 chunk 278 optimal weight: 30.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 116 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** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 164 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS G 142 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN L 38 GLN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 11 GLN ** P 55 HIS ** 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 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN ** Y 25 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 18 HIS 2 26 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN d 119 HIS ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 GLN f 3 HIS ** f 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** i 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 HIS ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 510 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 160065 Z= 0.226 Angle : 0.623 13.093 238709 Z= 0.321 Chirality : 0.035 0.290 30410 Planarity : 0.005 0.101 13334 Dihedral : 15.334 178.375 61719 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.80 % Favored : 90.95 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -2.02 (0.10), residues: 6286 helix: -0.04 (0.11), residues: 1963 sheet: -1.66 (0.15), residues: 989 loop : -2.08 (0.10), residues: 3334 *********************** 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 1660 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1653 time to evaluate : 6.506 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 outliers start: 7 outliers final: 1 residues processed: 1657 average time/residue: 1.5507 time to fit residues: 4380.5056 Evaluate side-chains 1280 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1279 time to evaluate : 6.134 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.1928 time to fit residues: 8.8979 ------------------------------------------------------------------------------- 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: 50.0000 chunk 587 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 770 optimal weight: 50.0000 chunk 426 optimal weight: 40.0000 chunk 882 optimal weight: 6.9990 chunk 714 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 528 optimal weight: 1.9990 chunk 928 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- 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 142 ASN ** 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** 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 H 66 ASN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 99 ASN ** 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** O 29 HIS ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 HIS X 22 ASN Y 58 ASN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN c 189 HIS ** d 119 HIS ** 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN ** 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** o 49 HIS ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** 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 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.120 160065 Z= 0.347 Angle : 0.765 14.015 238709 Z= 0.390 Chirality : 0.041 0.303 30410 Planarity : 0.007 0.157 13334 Dihedral : 16.099 179.978 61719 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 38.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.50 % Favored : 89.25 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.29 % 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: -2.30 (0.10), residues: 6286 helix: -0.40 (0.11), residues: 1970 sheet: -1.83 (0.15), residues: 1008 loop : -2.16 (0.10), residues: 3308 *********************** 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 1546 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1539 time to evaluate : 6.537 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 outliers start: 7 outliers final: 1 residues processed: 1543 average time/residue: 1.3952 time to fit residues: 3651.1779 Evaluate side-chains 1193 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1192 time to evaluate : 6.421 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.1851 time to fit residues: 9.2446 ------------------------------------------------------------------------------- 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: 0.0030 chunk 931 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 607 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 1035 optimal weight: 20.0000 chunk 859 optimal weight: 7.9990 chunk 479 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 342 optimal weight: 30.0000 chunk 543 optimal weight: 6.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN C 162 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** 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** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN 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 9 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 HIS b 121 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN d 119 HIS ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN ** j 56 HIS ** 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 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS 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 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.7128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 160065 Z= 0.196 Angle : 0.620 14.566 238709 Z= 0.319 Chirality : 0.035 0.327 30410 Planarity : 0.005 0.099 13334 Dihedral : 15.840 179.898 61719 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.43 % Favored : 90.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.10), residues: 6286 helix: -0.19 (0.11), residues: 1971 sheet: -1.62 (0.15), residues: 995 loop : -2.05 (0.10), residues: 3320 *********************** 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 1542 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1542 time to evaluate : 6.565 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 outliers start: 0 outliers final: 0 residues processed: 1542 average time/residue: 1.4150 time to fit residues: 3707.9199 Evaluate side-chains 1210 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1210 time to evaluate : 6.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9770 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 30.0000 chunk 589 optimal weight: 20.0000 chunk 756 optimal weight: 40.0000 chunk 585 optimal weight: 4.9990 chunk 871 optimal weight: 10.0000 chunk 578 optimal weight: 8.9990 chunk 1031 optimal weight: 50.0000 chunk 645 optimal weight: 40.0000 chunk 628 optimal weight: 20.0000 chunk 476 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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 116 GLN ** C 142 ASN ** 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** ** 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** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** 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 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** M 3 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** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** S 7 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 49 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 ASN d 139 ASN d 151 GLN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 11 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 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 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** o 79 GLN r 53 GLN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 0.8427 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 160065 Z= 0.259 Angle : 0.668 15.405 238709 Z= 0.343 Chirality : 0.037 0.318 30410 Planarity : 0.006 0.245 13334 Dihedral : 16.023 179.943 61719 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 32.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.66 % Favored : 89.17 % 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: -2.08 (0.10), residues: 6286 helix: -0.18 (0.11), residues: 1970 sheet: -1.59 (0.16), residues: 980 loop : -2.10 (0.10), residues: 3336 *********************** 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 1480 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1477 time to evaluate : 5.891 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: 2 residues processed: 1479 average time/residue: 1.4835 time to fit residues: 3780.6949 Evaluate side-chains 1183 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1181 time to evaluate : 5.817 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1094 time to fit residues: 10.4076 ------------------------------------------------------------------------------- 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: 8.9990 chunk 310 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 655 optimal weight: 30.0000 chunk 702 optimal weight: 30.0000 chunk 509 optimal weight: 0.0980 chunk 96 optimal weight: 20.0000 chunk 810 optimal weight: 10.0000 overall best weight: 9.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** 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** 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** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS M 3 GLN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN Q 55 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 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 25 GLN Y 58 ASN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 147 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 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 GLN ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 GLN q 46 HIS q 49 ASN 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** ** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 160065 Z= 0.293 Angle : 0.714 14.597 238709 Z= 0.366 Chirality : 0.039 0.389 30410 Planarity : 0.006 0.111 13334 Dihedral : 16.415 179.988 61719 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 35.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.58 % Favored : 89.20 % 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: -2.28 (0.10), residues: 6286 helix: -0.44 (0.11), residues: 1944 sheet: -1.83 (0.16), residues: 966 loop : -2.10 (0.10), residues: 3376 *********************** 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 1451 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1448 time to evaluate : 6.406 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: 1 residues processed: 1449 average time/residue: 1.4525 time to fit residues: 3622.2919 Evaluate side-chains 1145 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1144 time to evaluate : 6.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2070 time to fit residues: 9.1735 ------------------------------------------------------------------------------- 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: 20.0000 chunk 988 optimal weight: 8.9990 chunk 901 optimal weight: 8.9990 chunk 961 optimal weight: 7.9990 chunk 987 optimal weight: 20.0000 chunk 578 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 chunk 754 optimal weight: 40.0000 chunk 294 optimal weight: 30.0000 chunk 868 optimal weight: 9.9990 chunk 908 optimal weight: 0.9980 overall best weight: 7.3988 ------------------------------------------------------------------------------- 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** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 88 ASN M 3 GLN N 11 ASN N 23 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** 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 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 HIS ** o 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** t 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.8642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.112 160065 Z= 0.237 Angle : 0.662 14.065 238709 Z= 0.339 Chirality : 0.037 0.315 30410 Planarity : 0.006 0.093 13334 Dihedral : 16.303 179.806 61719 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 32.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.40 % Favored : 89.42 % Rotamer Outliers : 0.02 % 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: -2.14 (0.10), residues: 6286 helix: -0.26 (0.11), residues: 1950 sheet: -1.74 (0.16), residues: 977 loop : -2.07 (0.10), residues: 3359 *********************** 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 1456 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1455 time to evaluate : 6.474 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 outliers start: 1 outliers final: 1 residues processed: 1455 average time/residue: 1.3550 time to fit residues: 3374.1312 Evaluate side-chains 1142 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1141 time to evaluate : 5.711 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9314 time to fit residues: 8.1443 ------------------------------------------------------------------------------- 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: 2.9990 chunk 631 optimal weight: 0.9990 chunk 1016 optimal weight: 8.9990 chunk 620 optimal weight: 10.0000 chunk 482 optimal weight: 7.9990 chunk 706 optimal weight: 40.0000 chunk 1065 optimal weight: 0.4980 chunk 981 optimal weight: 0.1980 chunk 848 optimal weight: 7.9990 chunk 88 optimal weight: 50.0000 chunk 655 optimal weight: 30.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 242 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 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 K 88 ASN M 3 GLN N 11 ASN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN R 6 GLN R 11 GLN R 12 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** 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 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 HIS t 74 HIS w 426 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.8469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.091 160065 Z= 0.156 Angle : 0.609 13.213 238709 Z= 0.311 Chirality : 0.034 0.311 30410 Planarity : 0.005 0.106 13334 Dihedral : 15.877 178.838 61719 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.37 % Favored : 90.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 6286 helix: -0.09 (0.12), residues: 1950 sheet: -1.49 (0.16), residues: 959 loop : -2.01 (0.10), residues: 3377 ********************** 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 1487 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1487 time to evaluate : 6.496 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 outliers start: 0 outliers final: 0 residues processed: 1487 average time/residue: 1.3767 time to fit residues: 3508.5539 Evaluate side-chains 1193 residues out of total 5230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1193 time to evaluate : 6.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9231 ------------------------------------------------------------------------------- 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: 0.0970 chunk 674 optimal weight: 30.0000 chunk 904 optimal weight: 50.0000 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: 40.0000 chunk 355 optimal weight: 0.4980 chunk 873 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 overall best weight: 10.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 ASN ** 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 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 30 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS 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** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 88 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 11 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 197 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** 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 9 HIS ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.059030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043433 restraints weight = 1120212.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045270 restraints weight = 395163.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.046285 restraints weight = 201417.228| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.9028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.152 160065 Z= 0.296 Angle : 0.704 12.603 238709 Z= 0.360 Chirality : 0.038 0.317 30410 Planarity : 0.006 0.108 13334 Dihedral : 16.305 179.673 61719 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 36.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.14 % Favored : 88.74 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.29 % 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: -2.14 (0.10), residues: 6286 helix: -0.26 (0.12), residues: 1942 sheet: -1.69 (0.16), residues: 971 loop : -2.08 (0.10), residues: 3373 =============================================================================== Job complete usr+sys time: 50806.89 seconds wall clock time: 884 minutes 25.08 seconds (53065.08 seconds total)