Starting phenix.real_space_refine (version: dev) on Sun May 22 22:43:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gwt_0076/05_2022/6gwt_0076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gwt_0076/05_2022/6gwt_0076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gwt_0076/05_2022/6gwt_0076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gwt_0076/05_2022/6gwt_0076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gwt_0076/05_2022/6gwt_0076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gwt_0076/05_2022/6gwt_0076_updated.pdb" } resolution = 3.8 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "v GLU 123": "OE1" <-> "OE2" Residue "v ARG 174": "NH1" <-> "NH2" Residue "v PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 245": "NH1" <-> "NH2" Residue "w PHE 77": "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 TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 12": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 151484 Number of models: 1 Model: "" Number of chains: 59 Chain: "A" Number of atoms: 62177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2896, 62177 Classifications: {'RNA': 2896} Modifications used: {'rna2p_pyr': 93, 'rna3p_pyr': 1131, 'p5*END': 1, 'rna3p_pur': 1466, 'rna2p_pur': 206} Link IDs: {'rna3p': 2596, 'rna2p': 299} Chain breaks: 2 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 53, 'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 62, 'rna2p_pyr': 2} Link IDs: {'rna3p': 114, 'rna2p': 5} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "7" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 151 Classifications: {'RNA': 7} Modifications used: {'rna3p_pyr': 2, 'rna2p_pur': 2, 'rna3p_pur': 3} Link IDs: {'rna3p': 5, 'rna2p': 1} Chain: "a" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pyr': 44, 'rna3p_pyr': 621, 'p5*END': 1, 'rna3p_pur': 783, 'rna2p_pur': 91} Link IDs: {'rna3p': 1403, 'rna2p': 135} 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: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "v" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1932 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain: "w" Number of atoms: 4027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4027 Classifications: {'peptide': 525} Incomplete info: {'backbone_only': 30} Link IDs: {'PTRANS': 20, 'TRANS': 504} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "x" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 32, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 6, '5*END': 1} Link IDs: {'rna3p': 65, 'rna2p': 11} 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: 60.33, per 1000 atoms: 0.40 Number of scatterers: 151484 At special positions: 0 Unit cell: (269.494, 274.799, 241.908, 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 178 16.00 P 4641 15.00 O 41565 8.00 N 28187 7.00 C 76913 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: 53.11 Conformation dependent library (CDL) restraints added in 6.2 seconds 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12206 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: 198 helices and 71 sheets defined 37.9% alpha, 16.3% beta 1451 base pairs and 2587 stacking pairs defined. Time for finding SS restraints: 62.65 Creating SS restraints... Processing helix chain 'C' and resid 11 through 16 removed outlier: 4.609A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.197A 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: 3.940A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.650A 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: 4.030A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.672A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.238A 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: 3.560A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.464A 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: 4.298A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.786A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.142A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.830A 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: 3.685A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.518A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.692A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.940A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.583A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.699A 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: 3.791A pdb=" N ASP F 5 " --> pdb=" O ALA F 1 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.754A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 92 through 110 removed outlier: 4.077A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.342A 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: 4.355A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.134A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.439A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 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: 4.317A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.700A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 6.007A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.512A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.903A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.153A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.676A 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: 4.956A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.235A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 4.882A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.673A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.531A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.321A 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: 4.481A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.135A 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: 4.069A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.522A 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 'K' and resid 104 through 109 removed outlier: 4.859A pdb=" N SER K 109 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.805A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.772A 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: 3.695A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.164A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.790A 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: 6.518A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.506A 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: 6.453A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.712A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.684A 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: 4.039A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.911A 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: 3.937A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG N 71 " --> pdb=" O PHE N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.647A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.502A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.550A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.895A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.567A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.524A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.546A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.626A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.023A 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: 3.916A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.536A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 71 removed outlier: 4.297A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.585A 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: 3.548A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.939A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.832A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.382A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.760A 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: 3.913A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.508A 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: 4.089A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.171A 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: 3.824A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 4.251A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.309A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 4.750A 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: 4.524A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 5.110A 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: 4.086A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.956A 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: 3.540A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 20 removed outlier: 4.854A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.072A 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: 3.604A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 4.975A 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: 3.768A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 45 removed outlier: 3.894A 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: 4.616A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.162A 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: 3.648A pdb=" N ASP 5 7 " --> pdb=" O LEU 5 3 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.604A pdb=" N ALA 5 48 " --> pdb=" O ALA 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 68 removed outlier: 4.093A pdb=" N GLY 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) removed outlier: 3.740A 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: 4.456A pdb=" N ALA 5 75 " --> pdb=" O CYS 5 71 " (cutoff:3.500A) removed outlier: 4.974A 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: 3.919A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.566A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 3.713A 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: 4.499A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 123 removed outlier: 3.882A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.127A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.822A pdb=" N VAL b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY b 223 " --> pdb=" O THR b 219 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.774A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 47 removed outlier: 5.335A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.707A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.716A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.850A 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: 3.651A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.820A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.660A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.708A 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: 4.402A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 6.387A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.284A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.064A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.244A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 147 removed outlier: 5.498A pdb=" N ASN e 147 " --> pdb=" O LEU e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 removed outlier: 4.235A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.205A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.581A 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: 4.095A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.512A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET g 30 " --> pdb=" O VAL g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.870A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.831A pdb=" N PHE g 61 " --> pdb=" O GLU g 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU g 65 " --> pdb=" O PHE g 61 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.684A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.862A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 147 removed outlier: 3.814A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.752A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 38 removed outlier: 3.757A 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: 5.573A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 5.851A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 101 removed outlier: 4.816A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 5.279A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.804A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.275A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.456A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 72 removed outlier: 3.585A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.614A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 removed outlier: 3.663A pdb=" N LEU l 6 " --> pdb=" O THR l 2 " (cutoff:3.500A) Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.926A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 3.658A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 4.017A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.111A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.516A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA m 60 " --> pdb=" O ARG m 56 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 removed outlier: 3.777A 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: 3.788A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.120A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 6.072A 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 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 46 removed outlier: 4.537A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N HIS o 45 " --> pdb=" O HIS o 41 " (cutoff:3.500A) removed outlier: 5.749A 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: 3.742A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.796A pdb=" N ASN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 4.801A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.171A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.962A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) removed outlier: 3.977A 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: 3.734A 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: 4.544A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.751A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 4.556A 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: 4.078A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 6.397A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 4.146A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 34 removed outlier: 5.272A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 61 removed outlier: 3.637A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 104 through 110 removed outlier: 3.510A pdb=" N GLU v 108 " --> pdb=" O ASP v 104 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG v 109 " --> pdb=" O PRO v 105 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN v 110 " --> pdb=" O ASP v 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 104 through 110' Processing helix chain 'v' and resid 121 through 143 removed outlier: 3.884A pdb=" N LEU v 126 " --> pdb=" O ASP v 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA v 141 " --> pdb=" O ARG v 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG v 142 " --> pdb=" O TYR v 138 " (cutoff:3.500A) Processing helix chain 'v' and resid 170 through 176 removed outlier: 3.969A pdb=" N ARG v 174 " --> pdb=" O GLY v 170 " (cutoff:3.500A) Processing helix chain 'v' and resid 218 through 223 removed outlier: 5.425A pdb=" N ARG v 223 " --> pdb=" O PRO v 219 " (cutoff:3.500A) Processing helix chain 'v' and resid 234 through 240 removed outlier: 3.808A pdb=" N ASN v 238 " --> pdb=" O ALA v 234 " (cutoff:3.500A) Processing helix chain 'v' and resid 262 through 299 removed outlier: 3.814A pdb=" N LYS v 269 " --> pdb=" O LYS v 265 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR v 293 " --> pdb=" O ALA v 289 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN v 296 " --> pdb=" O SER v 292 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY v 299 " --> pdb=" O ARG v 295 " (cutoff:3.500A) Processing helix chain 'v' and resid 328 through 335 removed outlier: 6.284A pdb=" N VAL v 332 " --> pdb=" O ARG v 328 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET v 333 " --> pdb=" O LEU v 329 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU v 334 " --> pdb=" O ASP v 330 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY v 335 " --> pdb=" O GLU v 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 328 through 335' Processing helix chain 'v' and resid 337 through 351 Proline residue: v 343 - end of helix removed outlier: 3.800A pdb=" N ALA v 350 " --> pdb=" O GLN v 346 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP v 351 " --> pdb=" O GLU v 347 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 14 removed outlier: 3.745A pdb=" N LYS w 12 " --> pdb=" O GLN w 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG w 13 " --> pdb=" O GLU w 9 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG w 14 " --> pdb=" O VAL w 10 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 46 removed outlier: 3.694A pdb=" N LEU w 35 " --> pdb=" O GLU w 31 " (cutoff:3.500A) Processing helix chain 'w' and resid 58 through 63 Processing helix chain 'w' and resid 96 through 107 removed outlier: 3.858A pdb=" N TYR w 100 " --> pdb=" O SER w 96 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG w 101 " --> pdb=" O GLU w 97 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR w 104 " --> pdb=" O TYR w 100 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA w 105 " --> pdb=" O ARG w 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL w 106 " --> pdb=" O THR w 102 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP w 107 " --> pdb=" O LEU w 103 " (cutoff:3.500A) Processing helix chain 'w' and resid 120 through 134 removed outlier: 4.206A pdb=" N LEU w 132 " --> pdb=" O GLU w 128 " (cutoff:3.500A) removed outlier: 4.363A 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: 4.306A pdb=" N PHE w 246 " --> pdb=" O ASP w 242 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU w 247 " --> pdb=" O LYS w 243 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA w 248 " --> pdb=" O GLU w 244 " (cutoff:3.500A) Processing helix chain 'w' and resid 262 through 275 removed outlier: 5.345A pdb=" N ASP w 266 " --> pdb=" O ASN w 262 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS w 267 " --> pdb=" O PHE w 263 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET w 268 " --> pdb=" O GLY w 264 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU w 269 " --> pdb=" O VAL w 265 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP w 270 " --> pdb=" O ASP w 266 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY w 271 " --> pdb=" O HIS w 267 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 421 removed outlier: 3.514A pdb=" N LEU w 416 " --> pdb=" O LEU w 412 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL w 417 " --> pdb=" O LEU w 413 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU w 421 " --> pdb=" O VAL w 417 " (cutoff:3.500A) Processing helix chain 'w' and resid 445 through 454 removed outlier: 4.352A pdb=" N LEU w 453 " --> pdb=" O VAL w 449 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS w 454 " --> pdb=" O VAL w 450 " (cutoff:3.500A) Processing helix chain 'w' and resid 479 through 490 removed outlier: 6.875A pdb=" N GLU w 483 " --> pdb=" O ALA w 479 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU w 484 " --> pdb=" O LYS w 480 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE w 485 " --> pdb=" O LYS w 481 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN w 489 " --> pdb=" O PHE w 485 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU w 490 " --> pdb=" O LYS w 486 " (cutoff:3.500A) Processing helix chain 'w' and resid 507 through 518 removed outlier: 3.666A pdb=" N LEU w 511 " --> pdb=" O SER w 507 " (cutoff:3.500A) removed outlier: 3.633A 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: 6.849A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.870A 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: 3.536A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 175 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.722A 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: 5.550A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.770A 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: 4.350A 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: 4.602A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.781A 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: 6.659A pdb=" N GLN D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE D 48 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS D 38 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG D 46 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.503A 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: 5.658A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 187 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 149 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 4.093A 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: 3.511A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP F 152 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (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 93 through 97 removed outlier: 3.708A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.609A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 2 through 5 removed outlier: 5.193A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.748A 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: 7.079A 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: 3.791A 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: 3.612A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.937A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 88 through 91 Processing sheet with id= 19, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.960A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET M 105 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE M 31 " --> pdb=" O MET M 105 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 30 through 36 removed outlier: 6.947A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS M 34 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 6.379A 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: 4.667A 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: 3.528A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.925A 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: 6.453A 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: 7.967A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.949A 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: 4.196A pdb=" N LYS R 24 " --> pdb=" O TRP R 92 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N TRP R 92 " --> pdb=" O LYS R 24 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.567A 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: 5.091A 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: 3.586A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.542A 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: 5.773A 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: 3.652A pdb=" N ARG V 9 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.929A 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: 6.785A 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: 7.114A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 4.420A 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 18 removed outlier: 4.171A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) 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: 4.365A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS Z 2 " --> pdb=" O ASP Z 39 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '1' and resid 7 through 11 Processing sheet with id= 40, first strand: chain '1' and resid 33 through 36 removed outlier: 6.455A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '3' and resid 21 through 24 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 43, first strand: chain 'b' and resid 29 through 33 removed outlier: 7.545A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN b 41 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.702A pdb=" N LEU b 160 " --> pdb=" O PRO b 181 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 53 through 58 Processing sheet with id= 46, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.864A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.982A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TRP d 169 " --> pdb=" O LYS d 182 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'e' and resid 16 through 23 removed outlier: 3.912A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.064A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL e 84 " --> pdb=" O MET e 95 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'f' and resid 43 through 46 removed outlier: 6.012A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 72 through 76 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.843A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.607A pdb=" N ILE h 100 " --> pdb=" O VAL h 128 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.613A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU i 62 " --> pdb=" O LYS i 26 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 42 through 52 removed outlier: 5.148A pdb=" N LEU j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 57, first strand: chain 'l' and resid 34 through 40 removed outlier: 4.573A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 80 through 84 removed outlier: 4.993A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG l 93 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.815A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 6 through 10 removed outlier: 3.878A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 18 through 29 removed outlier: 5.795A pdb=" N LYS q 18 " --> pdb=" O ASP q 47 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP q 47 " --> pdb=" O LYS q 18 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 29 through 33 removed outlier: 4.242A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR s 32 " --> pdb=" O ALA s 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS s 51 " --> pdb=" O THR s 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 145 through 149 removed outlier: 3.832A pdb=" N ARG v 145 " --> pdb=" O CYS v 167 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS v 167 " --> pdb=" O ARG v 145 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE v 163 " --> pdb=" O MET v 149 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS v 160 " --> pdb=" O ALA v 117 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA v 200 " --> pdb=" O GLY v 118 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG v 308 " --> pdb=" O GLY v 181 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG v 183 " --> pdb=" O ARG v 308 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL v 187 " --> pdb=" O PHE v 312 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR v 309 " --> pdb=" O THR v 318 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR v 318 " --> pdb=" O THR v 309 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 224 through 227 Processing sheet with id= 65, first strand: chain 'v' and resid 150 through 153 removed outlier: 3.551A pdb=" N GLU v 161 " --> pdb=" O SER v 152 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'w' and resid 16 through 20 removed outlier: 3.612A pdb=" N ALA w 17 " --> pdb=" O CYS w 108 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU w 110 " --> pdb=" O ALA w 17 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'w' and resid 71 through 75 removed outlier: 5.850A pdb=" N THR w 71 " --> pdb=" O THR w 89 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER w 73 " --> pdb=" O LEU w 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU w 87 " --> pdb=" O SER w 73 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET w 75 " --> pdb=" O ASN w 85 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN w 85 " --> pdb=" O MET w 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'w' and resid 180 through 185 removed outlier: 6.460A pdb=" N LYS w 180 " --> pdb=" O TYR w 193 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU w 189 " --> pdb=" O HIS w 184 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'w' and resid 281 through 284 removed outlier: 3.690A pdb=" N ARG w 282 " --> pdb=" O VAL w 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG w 287 " --> pdb=" O THR w 284 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'w' and resid 328 through 334 removed outlier: 4.496A pdb=" N MET w 329 " --> pdb=" O ILE w 342 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE w 342 " --> pdb=" O MET w 329 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'w' and resid 425 through 429 removed outlier: 3.632A pdb=" N GLN w 426 " --> pdb=" O GLY w 439 " (cutoff:3.500A) 1862 hydrogen bonds defined for protein. 5514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3678 hydrogen bonds 5834 hydrogen bond angles 0 basepair planarities 1451 basepair parallelities 2587 stacking parallelities Total time for adding SS restraints: 281.31 Time building geometry restraints manager: 59.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 15704 1.32 - 1.47: 82567 1.47 - 1.61: 65509 1.61 - 1.76: 56 1.76 - 1.91: 320 Bond restraints: 164156 Sorted by residual: bond pdb=" C LEU w 35 " pdb=" N PHE w 36 " ideal model delta sigma weight residual 1.334 1.910 -0.575 1.43e-02 4.89e+03 1.62e+03 bond pdb=" C PRO z 14 " pdb=" N HIS z 15 " ideal model delta sigma weight residual 1.327 1.735 -0.408 1.54e-02 4.22e+03 7.01e+02 bond pdb=" CA THR v 240 " pdb=" CB THR v 240 " ideal model delta sigma weight residual 1.528 1.801 -0.272 1.59e-02 3.96e+03 2.94e+02 bond pdb=" O3' U 7 20 " pdb=" P A 7 21 " ideal model delta sigma weight residual 1.607 1.373 0.234 1.50e-02 4.44e+03 2.43e+02 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 7.07e+01 ... (remaining 164151 not shown) Histogram of bond angle deviations from ideal: 56.33 - 80.17: 2 80.17 - 104.02: 15089 104.02 - 127.86: 220956 127.86 - 151.71: 8582 151.71 - 175.55: 2 Bond angle restraints: 244631 Sorted by residual: angle pdb=" CA LEU w 35 " pdb=" C LEU w 35 " pdb=" N PHE w 36 " ideal model delta sigma weight residual 117.82 56.33 61.49 1.42e+00 4.96e-01 1.88e+03 angle pdb=" N THR v 240 " pdb=" CA THR v 240 " pdb=" C THR v 240 " ideal model delta sigma weight residual 111.36 156.07 -44.71 1.09e+00 8.42e-01 1.68e+03 angle pdb=" O LEU w 35 " pdb=" C LEU w 35 " pdb=" N PHE w 36 " ideal model delta sigma weight residual 122.33 175.55 -53.22 1.34e+00 5.57e-01 1.58e+03 angle pdb=" C LEU w 35 " pdb=" N PHE w 36 " pdb=" CA PHE w 36 " ideal model delta sigma weight residual 120.58 56.91 63.67 1.71e+00 3.42e-01 1.39e+03 angle pdb=" CA PRO z 13 " pdb=" C PRO z 13 " pdb=" N PRO z 14 " ideal model delta sigma weight residual 117.93 99.72 18.21 1.20e+00 6.94e-01 2.30e+02 ... (remaining 244626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 85471 35.98 - 71.96: 2440 71.96 - 107.94: 199 107.94 - 143.92: 29 143.92 - 179.90: 40 Dihedral angle restraints: 88179 sinusoidal: 69224 harmonic: 18955 Sorted by residual: 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 -118.10 -61.90 0 5.00e+00 4.00e-02 1.53e+02 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 -120.32 -59.68 0 5.00e+00 4.00e-02 1.42e+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 -121.32 -58.68 0 5.00e+00 4.00e-02 1.38e+02 ... (remaining 88176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 31090 0.327 - 0.653: 15 0.653 - 0.980: 2 0.980 - 1.307: 0 1.307 - 1.634: 1 Chirality restraints: 31108 Sorted by residual: chirality pdb=" CA THR v 240 " pdb=" N THR v 240 " pdb=" C THR v 240 " pdb=" CB THR v 240 " both_signs ideal model delta sigma weight residual False 2.53 0.89 1.63 2.00e-01 2.50e+01 6.67e+01 chirality pdb=" CB THR v 240 " pdb=" CA THR v 240 " pdb=" OG1 THR v 240 " pdb=" CG2 THR v 240 " both_signs ideal model delta sigma weight residual False 2.55 3.26 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA THR v 239 " pdb=" N THR v 239 " pdb=" C THR v 239 " pdb=" CB THR v 239 " both_signs ideal model delta sigma weight residual False 2.53 1.83 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 31105 not shown) Planarity restraints: 13809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER w 57 " 0.038 2.00e-02 2.50e+03 8.08e-02 6.53e+01 pdb=" C SER w 57 " -0.140 2.00e-02 2.50e+03 pdb=" O SER w 57 " 0.055 2.00e-02 2.50e+03 pdb=" N ASP w 58 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN v 238 " -0.037 2.00e-02 2.50e+03 6.97e-02 4.86e+01 pdb=" C ASN v 238 " 0.121 2.00e-02 2.50e+03 pdb=" O ASN v 238 " -0.043 2.00e-02 2.50e+03 pdb=" N THR v 239 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO z 13 " -0.027 2.00e-02 2.50e+03 6.75e-02 4.56e+01 pdb=" C PRO z 13 " 0.116 2.00e-02 2.50e+03 pdb=" O PRO z 13 " -0.049 2.00e-02 2.50e+03 pdb=" N PRO z 14 " -0.041 2.00e-02 2.50e+03 ... (remaining 13806 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 13 2.00 - 2.72: 13111 2.72 - 3.45: 190303 3.45 - 4.17: 479358 4.17 - 4.90: 651108 Nonbonded interactions: 1333893 Sorted by model distance: nonbonded pdb=" O HIS v 236 " pdb=" CG2 THR v 240 " model vdw 1.272 3.460 nonbonded pdb=" CZ PHE w 36 " pdb=" CD1 LEU w 269 " model vdw 1.302 3.760 nonbonded pdb=" N LEU w 35 " pdb=" N PHE w 36 " model vdw 1.302 2.560 nonbonded pdb=" NZ LYS v 265 " pdb=" OP2 C x 75 " model vdw 1.341 2.520 nonbonded pdb=" O VAL v 237 " pdb=" OG1 THR v 240 " model vdw 1.603 2.440 ... (remaining 1333888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4641 5.49 5 S 178 5.16 5 C 76913 2.51 5 N 28187 2.21 5 O 41565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.090 Extract box with map and model: 19.700 Check model and map are aligned: 1.610 Convert atoms to be neutral: 0.940 Process input model: 563.830 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 594.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.004 0.575 164156 Z= 0.215 Angle : 0.840 63.666 244631 Z= 0.460 Chirality : 0.040 1.634 31108 Planarity : 0.006 0.128 13809 Dihedral : 13.813 179.904 75973 Min Nonbonded Distance : 1.272 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.20 % Favored : 91.33 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -4.05 (0.08), residues: 6564 helix: -2.76 (0.08), residues: 1952 sheet: -2.23 (0.14), residues: 1066 loop : -2.83 (0.08), residues: 3546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3380 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 3370 time to evaluate : 6.670 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 outliers start: 10 outliers final: 0 residues processed: 3373 average time/residue: 1.6461 time to fit residues: 9425.7668 Evaluate side-chains 2158 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2158 time to evaluate : 6.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 932 optimal weight: 30.0000 chunk 836 optimal weight: 40.0000 chunk 464 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 564 optimal weight: 9.9990 chunk 447 optimal weight: 20.0000 chunk 865 optimal weight: 20.0000 chunk 334 optimal weight: 0.9980 chunk 526 optimal weight: 20.0000 chunk 644 optimal weight: 20.0000 chunk 1002 optimal weight: 20.0000 overall best weight: 14.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN C 89 ASN C 225 ASN C 238 ASN D 49 GLN D 150 GLN E 156 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN M 3 GLN N 9 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 107 ASN Q 36 GLN R 18 GLN R 43 ASN R 87 GLN S 7 HIS S 9 HIS S 40 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS X 15 ASN Y 27 ASN Y 58 ASN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN 3 27 ASN 4 35 GLN 5 57 ASN 5 88 HIS ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 ASN c 18 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 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** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 11 HIS f 55 HIS h 3 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN m 13 HIS ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 ASN o 49 HIS p 26 ASN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN r 51 GLN ** s 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS v 156 HIS ** v 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 279 HIS ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 296 ASN w 160 ASN ** w 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.163 164156 Z= 0.549 Angle : 0.967 20.402 244631 Z= 0.490 Chirality : 0.048 0.487 31108 Planarity : 0.009 0.138 13809 Dihedral : 15.147 178.705 63037 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 32.84 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.63 % Favored : 89.90 % Rotamer Outliers : 10.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -2.81 (0.09), residues: 6564 helix: -0.96 (0.10), residues: 2039 sheet: -1.77 (0.15), residues: 1105 loop : -2.51 (0.09), residues: 3420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2899 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 549 poor density : 2350 time to evaluate : 6.256 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 outliers start: 549 outliers final: 336 residues processed: 2606 average time/residue: 1.4213 time to fit residues: 6386.5178 Evaluate side-chains 2316 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1980 time to evaluate : 6.224 Switching outliers to nearest non-outliers outliers start: 336 outliers final: 0 residues processed: 336 average time/residue: 1.2531 time to fit residues: 806.7331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 557 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 834 optimal weight: 20.0000 chunk 682 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 1004 optimal weight: 20.0000 chunk 1084 optimal weight: 4.9990 chunk 894 optimal weight: 7.9990 chunk 995 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 805 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN D 126 ASN D 167 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN G 114 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 54 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN S 57 ASN T 48 GLN U 68 ASN V 75 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN X 15 ASN Y 20 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN d 73 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 52 ASN h 75 GLN j 58 ASN k 28 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS r 53 GLN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 258 GLN v 266 ASN ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 333 GLN w 370 HIS ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 445 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 164156 Z= 0.262 Angle : 0.666 19.550 244631 Z= 0.343 Chirality : 0.037 0.288 31108 Planarity : 0.006 0.120 13809 Dihedral : 14.783 178.148 63037 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.82 % Favored : 90.80 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 6564 helix: -0.38 (0.11), residues: 2050 sheet: -1.62 (0.15), residues: 1115 loop : -2.25 (0.10), residues: 3399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2428 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 2211 time to evaluate : 6.853 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 outliers start: 217 outliers final: 112 residues processed: 2285 average time/residue: 1.4133 time to fit residues: 5581.8196 Evaluate side-chains 2073 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1961 time to evaluate : 8.840 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 1.2907 time to fit residues: 280.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 992 optimal weight: 7.9990 chunk 755 optimal weight: 20.0000 chunk 521 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 479 optimal weight: 10.0000 chunk 674 optimal weight: 10.0000 chunk 1007 optimal weight: 10.0000 chunk 1067 optimal weight: 20.0000 chunk 526 optimal weight: 10.0000 chunk 955 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS K 29 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 51 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 HIS b 169 HIS b 202 ASN c 122 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 51 ASN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 156 HIS v 193 GLN ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 160 ASN z 15 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 164156 Z= 0.354 Angle : 0.715 20.895 244631 Z= 0.369 Chirality : 0.039 0.310 31108 Planarity : 0.006 0.094 13809 Dihedral : 14.960 178.613 63037 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.12 % Favored : 89.52 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.23 (0.10), residues: 6564 helix: -0.28 (0.11), residues: 2052 sheet: -1.63 (0.15), residues: 1094 loop : -2.23 (0.10), residues: 3418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2398 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 2088 time to evaluate : 6.419 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 outliers start: 310 outliers final: 212 residues processed: 2200 average time/residue: 1.3984 time to fit residues: 5326.2446 Evaluate side-chains 2115 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1903 time to evaluate : 6.833 Switching outliers to nearest non-outliers outliers start: 212 outliers final: 0 residues processed: 212 average time/residue: 1.1601 time to fit residues: 472.7102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 888 optimal weight: 6.9990 chunk 605 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 794 optimal weight: 30.0000 chunk 440 optimal weight: 20.0000 chunk 910 optimal weight: 9.9990 chunk 737 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 544 optimal weight: 6.9990 chunk 957 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 31 GLN V 78 GLN X 5 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 156 HIS v 263 GLN ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 164156 Z= 0.329 Angle : 0.703 20.714 244631 Z= 0.362 Chirality : 0.039 0.343 31108 Planarity : 0.006 0.089 13809 Dihedral : 15.044 179.907 63037 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 25.71 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.15 % Favored : 89.46 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 6564 helix: -0.25 (0.11), residues: 2050 sheet: -1.70 (0.14), residues: 1160 loop : -2.22 (0.10), residues: 3354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2263 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 2047 time to evaluate : 6.789 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 outliers start: 216 outliers final: 117 residues processed: 2133 average time/residue: 1.3924 time to fit residues: 5137.1769 Evaluate side-chains 2027 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1910 time to evaluate : 6.715 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 0 residues processed: 117 average time/residue: 1.1800 time to fit residues: 263.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 359 optimal weight: 2.9990 chunk 961 optimal weight: 7.9990 chunk 210 optimal weight: 50.0000 chunk 626 optimal weight: 30.0000 chunk 263 optimal weight: 10.0000 chunk 1068 optimal weight: 20.0000 chunk 886 optimal weight: 20.0000 chunk 494 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 353 optimal weight: 4.9990 chunk 560 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 ASN D 173 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 38 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 31 GLN X 5 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 HIS ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN d 130 ASN d 163 GLN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN k 14 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN r 53 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 193 GLN v 235 GLN v 266 ASN ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 323 ASN ** w 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 164156 Z= 0.263 Angle : 0.672 19.378 244631 Z= 0.345 Chirality : 0.037 0.346 31108 Planarity : 0.006 0.116 13809 Dihedral : 15.005 179.292 63037 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.18 % Favored : 89.44 % Rotamer Outliers : 4.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6564 helix: -0.18 (0.11), residues: 2055 sheet: -1.64 (0.15), residues: 1150 loop : -2.20 (0.10), residues: 3359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2283 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 2050 time to evaluate : 6.628 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 outliers start: 233 outliers final: 152 residues processed: 2127 average time/residue: 1.3823 time to fit residues: 5110.3128 Evaluate side-chains 2073 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1921 time to evaluate : 6.754 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 152 outliers final: 1 residues processed: 152 average time/residue: 1.1644 time to fit residues: 337.7672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 1029 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 608 optimal weight: 20.0000 chunk 780 optimal weight: 20.0000 chunk 604 optimal weight: 8.9990 chunk 899 optimal weight: 0.0970 chunk 596 optimal weight: 8.9990 chunk 1064 optimal weight: 0.1980 chunk 665 optimal weight: 20.0000 chunk 648 optimal weight: 20.0000 chunk 491 optimal weight: 5.9990 overall best weight: 4.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS N 9 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS c 122 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN j 58 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 79 ASN r 53 GLN ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 ASN v 110 ASN v 193 GLN v 263 GLN ** v 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 164156 Z= 0.228 Angle : 0.661 19.093 244631 Z= 0.338 Chirality : 0.036 0.321 31108 Planarity : 0.006 0.092 13809 Dihedral : 14.934 178.765 63037 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.93 % Favored : 89.70 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -2.09 (0.10), residues: 6564 helix: -0.15 (0.11), residues: 2047 sheet: -1.55 (0.15), residues: 1150 loop : -2.14 (0.10), residues: 3367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2177 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 2040 time to evaluate : 6.929 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 outliers start: 137 outliers final: 77 residues processed: 2080 average time/residue: 1.4513 time to fit residues: 5274.0155 Evaluate side-chains 1993 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1916 time to evaluate : 7.042 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 1.2245 time to fit residues: 186.9475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 658 optimal weight: 30.0000 chunk 424 optimal weight: 50.0000 chunk 635 optimal weight: 40.0000 chunk 320 optimal weight: 0.0980 chunk 209 optimal weight: 40.0000 chunk 206 optimal weight: 10.0000 chunk 676 optimal weight: 20.0000 chunk 724 optimal weight: 10.0000 chunk 526 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 836 optimal weight: 20.0000 overall best weight: 9.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS L 38 GLN N 9 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 HIS ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 193 GLN ** v 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 323 ASN ** w 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.164 164156 Z= 0.361 Angle : 0.744 17.029 244631 Z= 0.382 Chirality : 0.040 0.447 31108 Planarity : 0.006 0.110 13809 Dihedral : 15.224 179.357 63037 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.00 % Favored : 88.65 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -2.26 (0.10), residues: 6564 helix: -0.35 (0.11), residues: 2069 sheet: -1.62 (0.15), residues: 1154 loop : -2.23 (0.10), residues: 3341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2142 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1943 time to evaluate : 6.776 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 outliers start: 199 outliers final: 133 residues processed: 2003 average time/residue: 1.4458 time to fit residues: 5058.3824 Evaluate side-chains 2006 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1873 time to evaluate : 7.747 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 0 residues processed: 133 average time/residue: 1.1371 time to fit residues: 291.7971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 967 optimal weight: 0.8980 chunk 1019 optimal weight: 10.0000 chunk 930 optimal weight: 30.0000 chunk 991 optimal weight: 9.9990 chunk 596 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 778 optimal weight: 10.0000 chunk 304 optimal weight: 0.8980 chunk 896 optimal weight: 0.7980 chunk 937 optimal weight: 7.9990 chunk 988 optimal weight: 0.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN H 18 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 99 ASN e 134 ASN ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 193 GLN v 263 GLN ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 323 ASN ** w 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.142 164156 Z= 0.180 Angle : 0.668 15.999 244631 Z= 0.339 Chirality : 0.035 0.393 31108 Planarity : 0.006 0.180 13809 Dihedral : 14.902 177.064 63037 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.38 % Favored : 90.30 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.30 % 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: 6564 helix: -0.21 (0.11), residues: 2038 sheet: -1.44 (0.15), residues: 1082 loop : -2.12 (0.10), residues: 3444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2140 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 2071 time to evaluate : 6.599 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 outliers start: 69 outliers final: 40 residues processed: 2086 average time/residue: 1.3757 time to fit residues: 4984.3500 Evaluate side-chains 1974 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1934 time to evaluate : 6.610 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 1.2418 time to fit residues: 97.9006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 651 optimal weight: 20.0000 chunk 1048 optimal weight: 50.0000 chunk 639 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 728 optimal weight: 10.0000 chunk 1099 optimal weight: 20.0000 chunk 1012 optimal weight: 8.9990 chunk 875 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 676 optimal weight: 20.0000 chunk 537 optimal weight: 7.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS M 3 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 ASN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 110 ASN v 193 GLN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.263 164156 Z= 0.343 Angle : 0.747 19.936 244631 Z= 0.384 Chirality : 0.039 0.396 31108 Planarity : 0.007 0.168 13809 Dihedral : 15.085 179.367 63037 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.94 % Favored : 88.68 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -2.21 (0.10), residues: 6564 helix: -0.34 (0.11), residues: 2050 sheet: -1.54 (0.15), residues: 1134 loop : -2.18 (0.10), residues: 3380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13128 Ramachandran restraints generated. 6564 Oldfield, 0 Emsley, 6564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2013 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1931 time to evaluate : 6.839 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 outliers start: 82 outliers final: 62 residues processed: 1943 average time/residue: 1.4014 time to fit residues: 4731.8332 Evaluate side-chains 1950 residues out of total 5456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1888 time to evaluate : 6.869 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 1.1041 time to fit residues: 138.7910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1104 random chunks: chunk 695 optimal weight: 10.0000 chunk 932 optimal weight: 20.0000 chunk 268 optimal weight: 10.0000 chunk 807 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 877 optimal weight: 20.0000 chunk 367 optimal weight: 7.9990 chunk 900 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- 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** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 42 HIS ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 193 GLN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.049161 restraints weight = 729488.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.050633 restraints weight = 227368.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051511 restraints weight = 112580.243| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.149 164156 Z= 0.372 Angle : 0.781 19.487 244631 Z= 0.400 Chirality : 0.041 0.373 31108 Planarity : 0.007 0.153 13809 Dihedral : 15.348 179.098 63037 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.82 % Favored : 87.77 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.10), residues: 6564 helix: -0.48 (0.11), residues: 2059 sheet: -1.64 (0.15), residues: 1121 loop : -2.24 (0.10), residues: 3384 =============================================================================== Job complete usr+sys time: 68891.50 seconds wall clock time: 1174 minutes 2.93 seconds (70442.93 seconds total)