Starting phenix.real_space_refine (version: dev) on Tue Apr 26 23:04:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1g_24800/04_2022/7s1g_24800_trim_updated.pdb" } resolution = 2.48 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= -0.004 sd= 0.721 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 "2 GLU 15": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E GLU 206": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "K ASP 229": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L ASP 181": "OD1" <-> "OD2" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ASP 191": "OD1" <-> "OD2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "O ASP 39": "OD1" <-> "OD2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 86": "OD1" <-> "OD2" Residue "Q ASP 58": "OD1" <-> "OD2" Residue "R TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 49": "OD1" <-> "OD2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 129": "OE1" <-> "OE2" Residue "T GLU 136": "OE1" <-> "OE2" Residue "U GLU 111": "OE1" <-> "OE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 84": "OE1" <-> "OE2" Residue "X GLU 44": "OE1" <-> "OE2" Residue "X GLU 112": "OE1" <-> "OE2" Residue "Y GLU 111": "OE1" <-> "OE2" Residue "Z GLU 16": "OE1" <-> "OE2" Residue "Z ASP 95": "OD1" <-> "OD2" Residue "a GLU 52": "OE1" <-> "OE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "b GLU 25": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 101": "OE1" <-> "OE2" Residue "d GLU 11": "OE1" <-> "OE2" Residue "d TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "g GLU 12": "OE1" <-> "OE2" Residue "g GLU 24": "OE1" <-> "OE2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "n ASP 126": "OD1" <-> "OD2" Residue "o ASP 5": "OD1" <-> "OD2" Residue "o ASP 9": "OD1" <-> "OD2" Residue "o GLU 43": "OE1" <-> "OE2" Residue "o GLU 52": "OE1" <-> "OE2" Residue "o GLU 60": "OE1" <-> "OE2" Residue "o ASP 90": "OD1" <-> "OD2" Residue "p TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p ASP 107": "OD1" <-> "OD2" Residue "q ASP 14": "OD1" <-> "OD2" Residue "q GLU 81": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "t GLU 76": "OE1" <-> "OE2" Residue "u GLU 50": "OE1" <-> "OE2" Residue "u ASP 82": "OD1" <-> "OD2" Residue "v ASP 18": "OD1" <-> "OD2" Residue "w GLU 14": "OE1" <-> "OE2" Residue "x GLU 48": "OE1" <-> "OE2" Residue "x ASP 55": "OD1" <-> "OD2" Residue "x GLU 77": "OE1" <-> "OE2" Residue "y ASP 15": "OD1" <-> "OD2" Residue "y GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 240537 Number of models: 1 Model: "" Number of chains: 66 Chain: "1" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1303 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "2" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "3" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1219 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 3, 'rna3p_pur': 2, 'rna2p_pyr': 1, '3*END': 1} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 2444 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 32, 'rna2p_pur': 7, 'rna3p_pur': 33, 'rna2p_pyr': 4} Link IDs: {'rna3p': 65, 'rna2p': 10} Chain: "C" Number of atoms: 49665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 49665 Classifications: {'RNA': 1540} Modifications used: {'rna3p_pyr': 565, 'rna2p_pur': 119, 'rna3p_pur': 756, 'rna2p_pyr': 100, '3*END': 1} Link IDs: {'rna3p': 1321, 'rna2p': 218} Chain: "D" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3438 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3321 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "F" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3352 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "G" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2254 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1625 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "I" Number of atoms: 93268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93268 Classifications: {'RNA': 2898} Modifications used: {'rna3p': 17, 'rna2p': 7, '3*END': 1, 'rna3p_pur': 1385, 'rna3p_pyr': 1061, 'rna2p_pur': 279, 'rna2p_pyr': 149} Link IDs: {'rna3p': 2463, 'rna2p': 434} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "J" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3809 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 8, 'rna3p_pur': 56, 'rna2p_pyr': 6} Link IDs: {'rna3p': 103, 'rna2p': 14} Chain: "K" Number of atoms: 4263 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 4238 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Conformer: "B" Number of residues, atoms: 271, 4238 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} bond proxies already assigned to first conformer: 4251 Chain: "L" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3184 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3172 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2855 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "O" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2696 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "P" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2259 Classifications: {'peptide': 149} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "Q" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 963 Classifications: {'peptide': 60} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "R" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2292 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1951 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2219 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1961 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1817 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "X" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1880 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Y" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1968 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Z" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1657 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "a" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1780 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "b" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1546 Classifications: {'peptide': 93} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1611 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "d" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1534 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "e" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1168 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "f" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1278 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "g" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1033 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "h" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 938 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "i" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 904 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "j" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 851 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 795 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "l" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1077 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "m" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 645 Classifications: {'peptide': 38} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "n" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2419 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "o" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2011 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "p" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2093 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "q" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1615 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "r" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1765 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "s" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Classifications: {'peptide': 5} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 4} Chain: "t" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1972 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "u" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1845 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "v" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1600 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "w" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1441 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "x" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1315 Classifications: {'peptide': 82} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "y" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1341 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "z" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 934 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Unusual residues: {' MG': 83} Classifications: {'undetermined': 83} Link IDs: {None: 82} Chain: "I" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 134 Unusual residues: {'ZLD': 1, ' MG': 110} Classifications: {'undetermined': 111} Link IDs: {None: 110} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 111 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "k" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A1UBN SG CYS Q 16 145.347 122.530 15.360 1.00119.46 S ATOM A1UC9 SG CYS Q 18 143.468 123.522 12.177 1.00120.58 S ATOM A1UK8 SG CYS Q 37 143.987 126.081 14.908 1.00118.33 S ATOM A1ULG SG CYS Q 40 141.614 123.252 15.489 1.00118.64 S ATOM A2K1L SG CYS m 11 83.630 173.765 92.053 1.00 86.47 S ATOM A2K2Y SG CYS m 14 86.327 175.620 93.837 1.00 84.81 S ATOM A2K99 SG CYS m 27 83.096 174.960 95.674 1.00 84.66 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG K 203 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG K 203 " occ=0.50 residue: pdb="MG MG C3065 " occ=0.50 residue: pdb="MG MG C3066 " occ=0.50 Time building chain proxies: 77.88, per 1000 atoms: 0.32 Number of scatterers: 240537 At special positions: 0 Unit cell: (264.875, 262.438, 232.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 145 16.00 P 4638 15.00 Mg 196 11.99 F 1 9.00 O 40141 8.00 N 26825 7.00 C 72190 6.00 H 96399 1.00 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=0, symmetry=0 Time building additional restraints: 148.17 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN Q 101 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 37 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 18 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 40 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 16 " pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" ND1 HIS m 33 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 14 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 11 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 27 " Number of angles added : 9 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10404 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: 173 helices and 71 sheets defined 38.9% alpha, 18.4% beta 1428 base pairs and 2586 stacking pairs defined. Time for finding SS restraints: 105.61 Creating SS restraints... Processing helix chain '1' and resid 12 through 26 removed outlier: 3.741A pdb=" N GLU 1 24 " --> pdb=" O GLU 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 76 removed outlier: 4.364A pdb=" N PHE 1 74 " --> pdb=" O LYS 1 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA 1 75 " --> pdb=" O LEU 1 71 " (cutoff:3.500A) Proline residue: 1 76 - end of helix No H-bonds generated for 'chain '1' and resid 70 through 76' Processing helix chain '1' and resid 64 through 69 removed outlier: 3.610A pdb=" N VAL 1 67 " --> pdb=" O ASP 1 64 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY 1 68 " --> pdb=" O GLU 1 65 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 41 removed outlier: 3.537A pdb=" N ILE 2 12 " --> pdb=" O LYS 2 8 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 65 removed outlier: 3.762A pdb=" N LYS 2 49 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '2' and resid 68 through 87 removed outlier: 5.111A pdb=" N LEU 2 86 " --> pdb=" O GLN 2 82 " (cutoff:3.500A) Processing helix chain '3' and resid 11 through 27 removed outlier: 3.795A pdb=" N LYS 3 25 " --> pdb=" O ARG 3 21 " (cutoff:3.500A) Processing helix chain '3' and resid 28 through 37 removed outlier: 4.497A pdb=" N PHE 3 37 " --> pdb=" O ARG 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 69 removed outlier: 3.581A pdb=" N ARG 3 67 " --> pdb=" O GLU 3 63 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG 3 69 " --> pdb=" O ALA 3 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.649A pdb=" N ILE D 31 " --> pdb=" O MET D 27 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 27 through 32' Processing helix chain 'D' and resid 43 through 64 Proline residue: D 48 - end of helix Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.878A pdb=" N LYS D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 124 removed outlier: 4.233A pdb=" N GLN D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 124 " --> pdb=" O GLN D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 4.494A pdb=" N ARG D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU D 141 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 removed outlier: 3.618A pdb=" N HIS D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 206 through 226 removed outlier: 4.004A pdb=" N LEU D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 removed outlier: 4.176A pdb=" N TRP D 104 " --> pdb=" O GLY D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 104' Processing helix chain 'E' and resid 6 through 15 removed outlier: 3.653A pdb=" N ILE E 10 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 11 " --> pdb=" O PRO E 7 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLY E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 48 removed outlier: 3.596A pdb=" N LYS E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 78 removed outlier: 3.521A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 108 through 113 removed outlier: 4.134A pdb=" N ASP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 113' Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 129 through 145 removed outlier: 3.555A pdb=" N LEU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.463A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 68 through 83 removed outlier: 5.278A pdb=" N LYS F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 removed outlier: 3.514A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 106 removed outlier: 3.632A pdb=" N GLY F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 121 removed outlier: 4.046A pdb=" N LYS F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 166 removed outlier: 6.894A pdb=" N LYS F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 3.893A pdb=" N SER F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 206 removed outlier: 4.244A pdb=" N ILE F 200 " --> pdb=" O ASN F 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS F 206 " --> pdb=" O GLU F 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 71 removed outlier: 4.603A pdb=" N ASN G 70 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N MET G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 119 removed outlier: 6.905A pdb=" N ALA G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 removed outlier: 4.461A pdb=" N ARG G 138 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA G 139 " --> pdb=" O ASN G 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE G 141 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN G 148 " --> pdb=" O LEU G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.811A pdb=" N GLY G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.986A pdb=" N GLU H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN H 17 " --> pdb=" O ASP H 13 " (cutoff:3.500A) Proline residue: H 19 - end of helix Processing helix chain 'H' and resid 20 through 33 removed outlier: 3.636A pdb=" N ARG H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 81 removed outlier: 3.812A pdb=" N THR H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 16 removed outlier: 7.730A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.750A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.849A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.999A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 260 through 268 removed outlier: 4.049A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.632A pdb=" N VAL L 60 " --> pdb=" O LYS L 56 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 61' Processing helix chain 'L' and resid 62 through 72 removed outlier: 3.694A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 103 removed outlier: 4.228A pdb=" N ALA L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 98 through 103' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 39 through 44 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.671A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.927A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.573A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.554A pdb=" N LEU M 180 " --> pdb=" O ASP M 176 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.699A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 21 removed outlier: 4.895A pdb=" N VAL N 13 " --> pdb=" O LYS N 9 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS N 14 " --> pdb=" O ASP N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 47 removed outlier: 3.950A pdb=" N LYS N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 62 removed outlier: 4.549A pdb=" N GLY N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 removed outlier: 3.573A pdb=" N TRP N 97 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL N 108 " --> pdb=" O ILE N 104 " (cutoff:3.500A) Proline residue: N 109 - end of helix Processing helix chain 'N' and resid 162 through 174 removed outlier: 3.789A pdb=" N PHE N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 139 removed outlier: 3.979A pdb=" N ILE N 137 " --> pdb=" O GLU N 134 " (cutoff:3.500A) Proline residue: N 139 - end of helix Processing helix chain 'O' and resid 2 through 8 Proline residue: O 8 - end of helix Processing helix chain 'O' and resid 62 through 81 removed outlier: 3.722A pdb=" N THR O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 153 removed outlier: 3.564A pdb=" N ILE O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.124A pdb=" N GLY P 34 " --> pdb=" O LEU P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 51 removed outlier: 3.882A pdb=" N ARG P 50 " --> pdb=" O PHE P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 76 removed outlier: 3.837A pdb=" N LEU P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU P 76 " --> pdb=" O ILE P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 107 removed outlier: 5.339A pdb=" N ALA P 106 " --> pdb=" O ALA P 102 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY P 107 " --> pdb=" O VAL P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 46 Processing helix chain 'Q' and resid 55 through 65 Processing helix chain 'R' and resid 24 through 38 removed outlier: 3.695A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 97 through 110 removed outlier: 4.377A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 123 removed outlier: 3.821A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 119 Processing helix chain 'T' and resid 37 through 42 removed outlier: 3.625A pdb=" N ARG T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER T 42 " --> pdb=" O GLN T 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 37 through 42' Processing helix chain 'T' and resid 56 through 62 Proline residue: T 62 - end of helix Processing helix chain 'T' and resid 68 through 75 removed outlier: 3.937A pdb=" N ALA T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.833A pdb=" N LYS T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 99 Processing helix chain 'T' and resid 128 through 139 Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.779A pdb=" N LYS U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 125 removed outlier: 3.922A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Proline residue: U 125 - end of helix Processing helix chain 'V' and resid 13 through 32 Processing helix chain 'V' and resid 37 through 57 removed outlier: 4.201A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 4.476A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 Processing helix chain 'V' and resid 72 through 88 removed outlier: 4.708A pdb=" N GLY V 84 " --> pdb=" O PHE V 80 " (cutoff:3.500A) Proline residue: V 85 - end of helix Processing helix chain 'W' and resid 2 through 22 removed outlier: 3.540A pdb=" N THR W 12 " --> pdb=" O ILE W 8 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG W 15 " --> pdb=" O ALA W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 63 removed outlier: 4.573A pdb=" N GLN W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU W 62 " --> pdb=" O ILE W 58 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 86 Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'X' and resid 2 through 13 removed outlier: 4.223A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 104 removed outlier: 4.529A pdb=" N ARG X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU X 102 " --> pdb=" O TYR X 98 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG X 103 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR X 104 " --> pdb=" O LEU X 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 97 through 104' Processing helix chain 'Y' and resid 6 through 22 removed outlier: 3.522A pdb=" N GLN Y 20 " --> pdb=" O LYS Y 16 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 removed outlier: 3.935A pdb=" N ARG Y 30 " --> pdb=" O GLY Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 37 removed outlier: 3.974A pdb=" N GLN Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 73 removed outlier: 3.982A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 87 Processing helix chain 'Y' and resid 91 through 102 Processing helix chain 'Y' and resid 103 through 118 Processing helix chain 'a' and resid 13 through 25 removed outlier: 3.503A pdb=" N LEU a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 removed outlier: 3.511A pdb=" N TYR a 38 " --> pdb=" O ASP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 61 removed outlier: 3.824A pdb=" N VAL a 45 " --> pdb=" O LYS a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 70 removed outlier: 3.531A pdb=" N LEU a 69 " --> pdb=" O ASP a 65 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS a 70 " --> pdb=" O ILE a 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 65 through 70' Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.594A pdb=" N LEU b 7 " --> pdb=" O ARG b 3 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL b 10 " --> pdb=" O ARG b 6 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 26 Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'c' and resid 66 through 71 removed outlier: 3.863A pdb=" N VAL c 70 " --> pdb=" O GLN c 66 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA c 71 " --> pdb=" O VAL c 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 66 through 71' Processing helix chain 'd' and resid 13 through 24 removed outlier: 3.554A pdb=" N ASN d 24 " --> pdb=" O LEU d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 3.604A pdb=" N ALA d 52 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS d 53 " --> pdb=" O ASN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 59 removed outlier: 4.171A pdb=" N SER d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 63 Processing helix chain 'f' and resid 64 through 75 Processing helix chain 'g' and resid 2 through 10 removed outlier: 3.539A pdb=" N GLU g 8 " --> pdb=" O LYS g 4 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER g 10 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 removed outlier: 3.803A pdb=" N ASN g 15 " --> pdb=" O VAL g 11 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 62 removed outlier: 4.764A pdb=" N LEU g 43 " --> pdb=" O GLN g 39 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY g 62 " --> pdb=" O ASN g 58 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 28 Processing helix chain 'h' and resid 41 through 52 removed outlier: 3.507A pdb=" N VAL h 51 " --> pdb=" O MET h 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 21 removed outlier: 4.504A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP i 20 " --> pdb=" O ARG i 16 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA i 21 " --> pdb=" O ARG i 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 16 Processing helix chain 'k' and resid 17 through 25 removed outlier: 4.055A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS k 25 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 38 Processing helix chain 'l' and resid 7 through 14 removed outlier: 4.004A pdb=" N ARG l 13 " --> pdb=" O GLY l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 37 removed outlier: 4.424A pdb=" N LYS l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA l 37 " --> pdb=" O LEU l 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 32 through 37' Processing helix chain 'l' and resid 38 through 46 Proline residue: l 46 - end of helix Processing helix chain 'l' and resid 51 through 63 removed outlier: 4.412A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) Proline residue: l 63 - end of helix Processing helix chain 'l' and resid 26 through 31 removed outlier: 4.886A pdb=" N LEU l 29 " --> pdb=" O HIS l 26 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG l 30 " --> pdb=" O ALA l 27 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS l 31 " --> pdb=" O ASN l 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 26 through 31' Processing helix chain 'n' and resid 20 through 31 removed outlier: 3.580A pdb=" N ASN n 28 " --> pdb=" O ALA n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 35 through 55 Processing helix chain 'n' and resid 57 through 70 removed outlier: 3.569A pdb=" N VAL n 69 " --> pdb=" O ALA n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 112 removed outlier: 3.733A pdb=" N ASN n 97 " --> pdb=" O PRO n 93 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS n 110 " --> pdb=" O GLU n 106 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG n 111 " --> pdb=" O ALA n 107 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLY n 112 " --> pdb=" O ALA n 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 130 Processing helix chain 'n' and resid 132 through 149 Processing helix chain 'o' and resid 5 through 21 Processing helix chain 'o' and resid 30 through 44 Processing helix chain 'o' and resid 112 through 120 Processing helix chain 'p' and resid 34 through 39 Processing helix chain 'p' and resid 44 through 53 removed outlier: 4.703A pdb=" N VAL p 48 " --> pdb=" O ALA p 44 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG p 49 " --> pdb=" O ARG p 45 " (cutoff:3.500A) Proline residue: p 51 - end of helix Processing helix chain 'p' and resid 71 through 89 removed outlier: 3.548A pdb=" N MET p 88 " --> pdb=" O THR p 84 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU p 89 " --> pdb=" O ARG p 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 91 through 102 removed outlier: 3.836A pdb=" N ARG p 95 " --> pdb=" O ASP p 91 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU p 97 " --> pdb=" O SER p 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 33 removed outlier: 3.965A pdb=" N ILE q 18 " --> pdb=" O ASP q 14 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN q 20 " --> pdb=" O ARG q 16 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 91 removed outlier: 3.834A pdb=" N MET q 88 " --> pdb=" O VAL q 84 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG q 89 " --> pdb=" O ASP q 85 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP q 91 " --> pdb=" O LEU q 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 removed outlier: 4.277A pdb=" N GLY r 51 " --> pdb=" O ALA r 47 " (cutoff:3.500A) Processing helix chain 'r' and resid 54 through 60 removed outlier: 3.919A pdb=" N SER r 58 " --> pdb=" O GLY r 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR r 59 " --> pdb=" O SER r 55 " (cutoff:3.500A) Proline residue: r 60 - end of helix No H-bonds generated for 'chain 'r' and resid 54 through 60' Processing helix chain 'r' and resid 61 through 75 Processing helix chain 'r' and resid 90 through 104 removed outlier: 5.030A pdb=" N GLU r 94 " --> pdb=" O GLY r 90 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER r 95 " --> pdb=" O PRO r 91 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE r 97 " --> pdb=" O ARG r 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN r 101 " --> pdb=" O ILE r 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY r 104 " --> pdb=" O LEU r 100 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 11 Proline residue: t 11 - end of helix Processing helix chain 't' and resid 113 through 118 removed outlier: 3.787A pdb=" N TYR t 117 " --> pdb=" O ALA t 113 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 22 removed outlier: 3.905A pdb=" N THR u 20 " --> pdb=" O VAL u 16 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER u 21 " --> pdb=" O ILE u 17 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE u 22 " --> pdb=" O ALA u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 38 Processing helix chain 'u' and resid 49 through 64 removed outlier: 3.740A pdb=" N ASP u 54 " --> pdb=" O GLU u 50 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR u 55 " --> pdb=" O GLY u 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU u 56 " --> pdb=" O GLN u 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS u 62 " --> pdb=" O ASP u 58 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE u 63 " --> pdb=" O GLU u 59 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL u 64 " --> pdb=" O VAL u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 84 removed outlier: 3.513A pdb=" N GLY u 84 " --> pdb=" O LEU u 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 85 through 94 Processing helix chain 'u' and resid 106 through 111 Processing helix chain 'v' and resid 3 through 20 Processing helix chain 'v' and resid 22 through 34 removed outlier: 4.590A pdb=" N GLU v 26 " --> pdb=" O ALA v 22 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE v 31 " --> pdb=" O LEU v 27 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER v 32 " --> pdb=" O LYS v 28 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 48 removed outlier: 3.979A pdb=" N VAL v 45 " --> pdb=" O ARG v 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS v 47 " --> pdb=" O ASN v 43 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU v 48 " --> pdb=" O ALA v 44 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 91 Processing helix chain 'w' and resid 4 through 16 Processing helix chain 'w' and resid 24 through 44 removed outlier: 4.363A pdb=" N GLY w 41 " --> pdb=" O ASN w 37 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS w 42 " --> pdb=" O HIS w 38 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 74 removed outlier: 3.765A pdb=" N GLY w 55 " --> pdb=" O HIS w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 86 Processing helix chain 'x' and resid 53 through 64 removed outlier: 3.626A pdb=" N ILE x 57 " --> pdb=" O ASP x 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 68 through 81 Processing helix chain 'z' and resid 25 through 34 removed outlier: 4.174A pdb=" N ASN z 31 " --> pdb=" O ALA z 27 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR z 32 " --> pdb=" O THR z 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR z 34 " --> pdb=" O LYS z 30 " (cutoff:3.500A) Processing helix chain 'z' and resid 41 through 46 Processing helix chain 'z' and resid 48 through 66 Processing sheet with id= 1, first strand: chain '1' and resid 30 through 34 removed outlier: 5.046A pdb=" N LEU 1 47 " --> pdb=" O VAL 1 62 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= 3, first strand: chain 'E' and resid 54 through 59 removed outlier: 3.563A pdb=" N ILE E 64 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 164 through 169 removed outlier: 5.849A pdb=" N ARG E 164 " --> pdb=" O GLY E 155 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 141 through 144 removed outlier: 4.081A pdb=" N ASP F 141 " --> pdb=" O PHE F 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'G' and resid 12 through 16 removed outlier: 6.855A pdb=" N LEU G 36 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE G 30 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 17 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 84 through 88 removed outlier: 3.909A pdb=" N ALA G 99 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN G 122 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'H' and resid 38 through 43 removed outlier: 3.547A pdb=" N ARG H 38 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR H 59 " --> pdb=" O TRP H 42 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS H 3 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'H' and resid 44 through 47 removed outlier: 6.817A pdb=" N HIS H 55 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'K' and resid 2 through 5 Processing sheet with id= 12, first strand: chain 'K' and resid 80 through 83 removed outlier: 6.616A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE K 74 " --> pdb=" O SER K 118 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER K 118 " --> pdb=" O ILE K 74 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.889A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'K' and resid 90 through 96 removed outlier: 5.533A pdb=" N ASN K 90 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'L' and resid 3 through 7 removed outlier: 7.057A pdb=" N ASP L 200 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR L 112 " --> pdb=" O ASP L 200 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L' and resid 10 through 16 removed outlier: 3.508A pdb=" N GLY L 10 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 79 through 84 removed outlier: 5.720A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN L 49 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN L 94 " --> pdb=" O VAL L 34 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 105 through 108 removed outlier: 6.416A pdb=" N LYS L 105 " --> pdb=" O VAL L 177 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 42 through 47 removed outlier: 7.553A pdb=" N GLY M 42 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP M 91 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 117 through 120 removed outlier: 3.547A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'N' and resid 65 through 70 removed outlier: 6.200A pdb=" N LEU N 66 " --> pdb=" O CYS N 87 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS N 87 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR N 68 " --> pdb=" O ILE N 85 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR N 83 " --> pdb=" O ALA N 70 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLY N 39 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY N 151 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 72 through 75 removed outlier: 5.419A pdb=" N SER N 73 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG N 80 " --> pdb=" O SER N 73 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA N 75 " --> pdb=" O LYS N 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'O' and resid 16 through 19 Processing sheet with id= 24, first strand: chain 'O' and resid 41 through 45 Processing sheet with id= 25, first strand: chain 'O' and resid 82 through 89 removed outlier: 5.795A pdb=" N THR O 129 " --> pdb=" O LEU O 89 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 94 through 98 removed outlier: 3.578A pdb=" N VAL O 113 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 77 through 82 removed outlier: 4.334A pdb=" N SER P 82 " --> pdb=" O VAL P 147 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU P 114 " --> pdb=" O GLN P 133 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Q' and resid 20 through 25 removed outlier: 4.668A pdb=" N ASN Q 20 " --> pdb=" O CYS Q 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS Q 16 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 52 through 57 removed outlier: 4.777A pdb=" N ASP R 19 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 74 through 78 removed outlier: 7.427A pdb=" N GLY R 83 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 18 through 21 removed outlier: 4.394A pdb=" N THR S 6 " --> pdb=" O CYS S 21 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 38 through 41 Processing sheet with id= 33, first strand: chain 'U' and resid 37 through 40 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.567A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU U 33 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS U 100 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 30 through 36 removed outlier: 7.653A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS U 127 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'V' and resid 33 through 36 removed outlier: 5.262A pdb=" N MET V 110 " --> pdb=" O CYS V 100 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 49 through 52 removed outlier: 3.630A pdb=" N VAL W 28 " --> pdb=" O ASP W 93 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'X' and resid 38 through 45 removed outlier: 6.641A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 49 through 52 removed outlier: 3.780A pdb=" N ALA X 49 " --> pdb=" O THR X 60 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Z' and resid 11 through 15 Processing sheet with id= 41, first strand: chain 'Z' and resid 18 through 23 removed outlier: 4.106A pdb=" N GLN Z 18 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP Z 95 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS Z 60 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU Z 31 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Z' and resid 57 through 60 Processing sheet with id= 43, first strand: chain 'Z' and resid 65 through 68 removed outlier: 3.701A pdb=" N ALA Z 65 " --> pdb=" O ASP Z 95 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Z' and resid 71 through 78 removed outlier: 4.176A pdb=" N TYR Z 83 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'a' and resid 2 through 8 Processing sheet with id= 46, first strand: chain 'b' and resid 28 through 33 removed outlier: 6.227A pdb=" N ASN b 28 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS b 66 " --> pdb=" O ARG b 77 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP b 79 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS b 64 " --> pdb=" O ASP b 79 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS b 81 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL b 62 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA b 83 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR b 60 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL b 85 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL b 58 " --> pdb=" O VAL b 85 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 40 through 45 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'c' and resid 83 through 86 Processing sheet with id= 49, first strand: chain 'd' and resid 69 through 72 removed outlier: 6.629A pdb=" N ALA d 39 " --> pdb=" O ARG d 9 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE d 89 " --> pdb=" O PRO d 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP d 76 " --> pdb=" O ASP d 90 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 29 through 32 removed outlier: 4.502A pdb=" N GLU e 29 " --> pdb=" O VAL e 67 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE e 82 " --> pdb=" O GLY e 48 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 51 through 54 removed outlier: 4.227A pdb=" N THR e 58 " --> pdb=" O GLY e 54 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 12 through 19 removed outlier: 3.853A pdb=" N THR f 25 " --> pdb=" O ASN f 17 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN f 23 " --> pdb=" O SER f 19 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 35 through 41 removed outlier: 3.702A pdb=" N ARG f 45 " --> pdb=" O VAL f 40 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 33 through 39 removed outlier: 4.405A pdb=" N HIS h 34 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE h 7 " --> pdb=" O VAL h 36 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS h 6 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET h 54 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 29 through 32 removed outlier: 4.741A pdb=" N GLU i 36 " --> pdb=" O ASP i 31 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 8 through 13 removed outlier: 6.057A pdb=" N HIS j 19 " --> pdb=" O SER j 13 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 22 through 25 removed outlier: 5.737A pdb=" N PHE l 22 " --> pdb=" O VAL l 50 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'm' and resid 1 through 5 removed outlier: 3.674A pdb=" N LYS m 2 " --> pdb=" O LYS m 34 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY m 38 " --> pdb=" O ARG m 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS m 33 " --> pdb=" O CYS m 27 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N CYS m 27 " --> pdb=" O HIS m 33 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE m 23 " --> pdb=" O GLN m 37 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'n' and resid 72 through 79 removed outlier: 7.030A pdb=" N THR n 72 " --> pdb=" O VAL n 91 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'o' and resid 23 through 29 removed outlier: 6.278A pdb=" N ALA o 23 " --> pdb=" O LEU o 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP o 48 " --> pdb=" O THR o 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'o' and resid 74 through 77 removed outlier: 3.868A pdb=" N SER o 74 " --> pdb=" O ALA o 130 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 103 through 106 removed outlier: 6.748A pdb=" N VAL o 103 " --> pdb=" O ILE o 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.620A pdb=" N PHE p 20 " --> pdb=" O TYR p 64 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 5 through 13 removed outlier: 3.561A pdb=" N ILE q 6 " --> pdb=" O ILE q 76 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU q 71 " --> pdb=" O LEU q 42 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 44 through 50 Processing sheet with id= 66, first strand: chain 'r' and resid 42 through 45 Processing sheet with id= 67, first strand: chain 't' and resid 29 through 33 removed outlier: 5.126A pdb=" N LEU t 81 " --> pdb=" O VAL t 98 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS t 96 " --> pdb=" O ARG t 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 't' and resid 35 through 41 removed outlier: 5.120A pdb=" N LYS t 51 " --> pdb=" O ILE t 67 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 4 through 10 removed outlier: 5.519A pdb=" N PHE x 16 " --> pdb=" O HIS x 9 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY x 37 " --> pdb=" O VAL x 19 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY x 49 " --> pdb=" O ASN x 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'y' and resid 7 through 11 removed outlier: 7.210A pdb=" N GLU y 60 " --> pdb=" O VAL y 76 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'y' and resid 19 through 30 No H-bonds generated for sheet with id= 71 1810 hydrogen bonds defined for protein. 5352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3506 hydrogen bonds 5496 hydrogen bond angles 0 basepair planarities 1428 basepair parallelities 2586 stacking parallelities Total time for adding SS restraints: 287.31 Time building geometry restraints manager: 156.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 96368 1.03 - 1.23: 995 1.23 - 1.42: 79323 1.42 - 1.62: 75894 1.62 - 1.81: 259 Bond restraints: 252839 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.805 1.412 0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.805 1.413 0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.638 1.366 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.638 1.369 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.150 1.349 -0.199 2.00e-02 2.50e+03 9.93e+01 ... (remaining 252834 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.85: 28457 106.85 - 113.90: 267499 113.90 - 120.94: 99599 120.94 - 127.98: 50932 127.98 - 135.02: 7673 Bond angle restraints: 454160 Sorted by residual: angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 103.27 126.16 -22.89 3.00e+00 1.11e-01 5.82e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C4 2MA I2503 " ideal model delta sigma weight residual 103.49 126.19 -22.70 3.00e+00 1.11e-01 5.72e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 106.81 126.39 -19.58 3.00e+00 1.11e-01 4.26e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 144.94 126.40 18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" C1' 2MG I1835 " pdb=" N9 2MG I1835 " pdb=" C4 2MG I1835 " ideal model delta sigma weight residual 109.53 126.51 -16.98 3.00e+00 1.11e-01 3.20e+01 ... (remaining 454155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 96694 35.81 - 71.62: 2865 71.62 - 107.43: 250 107.43 - 143.25: 29 143.25 - 179.06: 40 Dihedral angle restraints: 99878 sinusoidal: 81827 harmonic: 18051 Sorted by residual: dihedral pdb=" C4' G I1025 " pdb=" C3' G I1025 " pdb=" C2' G I1025 " pdb=" C1' G I1025 " ideal model delta sinusoidal sigma weight residual -35.00 33.58 -68.58 1 8.00e+00 1.56e-02 9.52e+01 dihedral pdb=" C5' G I1025 " pdb=" C4' G I1025 " pdb=" C3' G I1025 " pdb=" O3' G I1025 " ideal model delta sinusoidal sigma weight residual 147.00 82.83 64.17 1 8.00e+00 1.56e-02 8.46e+01 dihedral pdb=" O4' U A 32 " pdb=" C1' U A 32 " pdb=" N1 U A 32 " pdb=" C2 U A 32 " ideal model delta sinusoidal sigma weight residual 200.00 31.48 168.52 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 99875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 28935 0.063 - 0.127: 910 0.127 - 0.190: 30 0.190 - 0.253: 7 0.253 - 0.317: 2 Chirality restraints: 29884 Sorted by residual: chirality pdb=" C3' G I1025 " pdb=" C4' G I1025 " pdb=" O3' G I1025 " pdb=" C2' G I1025 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" P A I2418 " pdb=" OP1 A I2418 " pdb=" OP2 A I2418 " pdb=" O5' A I2418 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" P G A 1 " pdb=" OP1 G A 1 " pdb=" OP2 G A 1 " pdb=" O5' G A 1 " both_signs ideal model delta sigma weight residual True 2.41 2.66 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 29881 not shown) Planarity restraints: 21545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.041 2.00e-02 2.50e+03 5.93e-01 7.92e+03 pdb=" C4' OMG I2251 " 0.447 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.683 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.600 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.203 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.926 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.917 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.057 2.00e-02 2.50e+03 5.89e-01 7.79e+03 pdb=" C4' OMC I2498 " 0.434 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.613 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.600 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.622 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.183 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.962 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.229 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.890 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " 0.032 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 2MG I2445 " 0.449 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " 0.703 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " -0.577 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " -0.217 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " 0.900 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " 0.213 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " -0.912 2.00e-02 2.50e+03 ... (remaining 21542 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 605 1.82 - 2.51: 141724 2.51 - 3.21: 647643 3.21 - 3.90: 994682 3.90 - 4.60: 1506110 Nonbonded interactions: 3290764 Sorted by model distance: nonbonded pdb=" HE2 HIS L 140 " pdb="MG MG L 301 " model vdw 1.121 1.700 nonbonded pdb=" HE1 HIS V 3 " pdb="MG MG V 201 " model vdw 1.165 1.700 nonbonded pdb=" H1 G C 21 " pdb="MG MG C3067 " model vdw 1.300 1.700 nonbonded pdb="HD21 ASN T 99 " pdb="MG MG I3015 " model vdw 1.306 1.700 nonbonded pdb=" O3' A A 76 " pdb=" C PHE s 5 " model vdw 1.320 3.100 ... (remaining 3290759 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4638 5.49 5 Mg 196 5.21 5 S 145 5.16 5 C 72190 2.51 5 N 26825 2.21 5 O 40141 1.98 5 F 1 1.80 5 H 96399 0.53 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.900 Extract box with map and model: 39.490 Check model and map are aligned: 2.350 Convert atoms to be neutral: 1.330 Process input model: 865.250 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.480 Set refine NCS operators: 0.010 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 931.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 0.393 156440 Z= 0.230 Angle : 0.384 22.887 234176 Z= 0.196 Chirality : 0.027 0.317 29884 Planarity : 0.015 0.593 12430 Dihedral : 14.277 179.058 73041 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 5557 helix: 1.99 (0.13), residues: 1783 sheet: 0.58 (0.16), residues: 1109 loop : 0.49 (0.13), residues: 2665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1375 time to evaluate : 7.851 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 outliers start: 37 outliers final: 26 residues processed: 1395 average time/residue: 3.4201 time to fit residues: 6819.0038 Evaluate side-chains 1244 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1218 time to evaluate : 7.799 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 9 average time/residue: 1.8581 time to fit residues: 37.4953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 848 optimal weight: 6.9990 chunk 761 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 513 optimal weight: 0.6980 chunk 406 optimal weight: 6.9990 chunk 787 optimal weight: 4.9990 chunk 304 optimal weight: 20.0000 chunk 478 optimal weight: 20.0000 chunk 586 optimal weight: 5.9990 chunk 912 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 41 GLN H 81 ASN L 49 GLN O 22 GLN O 48 ASN O 143 GLN Q 30 HIS Q 61 ASN T 93 ASN X 66 ASN Z 43 ASN a 31 GLN a 61 ASN d 12 GLN g 20 ASN g 25 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN r 40 ASN ** r 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 8 ASN v 62 ASN ** x 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 156440 Z= 0.356 Angle : 0.603 15.812 234176 Z= 0.319 Chirality : 0.040 0.284 29884 Planarity : 0.006 0.148 12430 Dihedral : 13.198 179.858 61878 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.98 (0.11), residues: 5557 helix: 1.57 (0.12), residues: 1842 sheet: 0.33 (0.15), residues: 1114 loop : 0.25 (0.12), residues: 2601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1252 time to evaluate : 8.104 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 outliers start: 187 outliers final: 114 residues processed: 1356 average time/residue: 3.4121 time to fit residues: 6619.4319 Evaluate side-chains 1352 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1238 time to evaluate : 7.848 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 70 residues processed: 48 average time/residue: 1.9854 time to fit residues: 172.6531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 507 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 759 optimal weight: 6.9990 chunk 621 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 914 optimal weight: 0.0970 chunk 987 optimal weight: 5.9990 chunk 814 optimal weight: 3.9990 chunk 906 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 733 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 41 GLN H 81 ASN L 49 GLN O 22 GLN O 48 ASN O 143 GLN P 20 ASN Q 30 HIS ** W 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN Y 20 GLN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN g 20 ASN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN v 66 GLN ** x 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 156440 Z= 0.176 Angle : 0.529 13.362 234176 Z= 0.289 Chirality : 0.034 0.245 29884 Planarity : 0.005 0.128 12430 Dihedral : 13.434 179.723 61878 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.97 (0.11), residues: 5557 helix: 1.55 (0.12), residues: 1864 sheet: 0.31 (0.15), residues: 1096 loop : 0.25 (0.12), residues: 2597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1289 time to evaluate : 8.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 94 residues processed: 1376 average time/residue: 3.3879 time to fit residues: 6696.1571 Evaluate side-chains 1333 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1239 time to evaluate : 7.864 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 66 residues processed: 32 average time/residue: 1.7593 time to fit residues: 110.6428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 903 optimal weight: 6.9990 chunk 687 optimal weight: 0.0670 chunk 474 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 436 optimal weight: 5.9990 chunk 613 optimal weight: 5.9990 chunk 917 optimal weight: 10.0000 chunk 971 optimal weight: 10.0000 chunk 479 optimal weight: 50.0000 chunk 869 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 HIS E 19 ASN E 123 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN L 49 GLN O 22 GLN O 48 ASN O 143 GLN P 20 ASN P 43 ASN Q 30 HIS T 93 ASN ** W 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN f 34 HIS k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 148 ASN ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN w 37 ASN x 63 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 156440 Z= 0.219 Angle : 0.533 13.476 234176 Z= 0.292 Chirality : 0.035 0.262 29884 Planarity : 0.005 0.134 12430 Dihedral : 13.498 179.932 61878 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.94 (0.11), residues: 5557 helix: 1.63 (0.12), residues: 1863 sheet: 0.21 (0.16), residues: 1082 loop : 0.19 (0.12), residues: 2612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1301 time to evaluate : 7.869 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 outliers start: 161 outliers final: 107 residues processed: 1388 average time/residue: 3.4912 time to fit residues: 6943.9676 Evaluate side-chains 1361 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1254 time to evaluate : 7.862 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 70 residues processed: 38 average time/residue: 1.9805 time to fit residues: 139.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 809 optimal weight: 7.9990 chunk 551 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 723 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 chunk 828 optimal weight: 10.0000 chunk 671 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 871 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 GLN E 19 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN O 22 GLN O 45 HIS O 48 ASN O 143 GLN P 43 ASN Q 30 HIS T 93 ASN X 66 ASN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN ** r 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 156440 Z= 0.396 Angle : 0.617 14.411 234176 Z= 0.332 Chirality : 0.041 0.321 29884 Planarity : 0.006 0.145 12430 Dihedral : 13.756 179.055 61878 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer Outliers : 4.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.66 (0.11), residues: 5557 helix: 1.42 (0.12), residues: 1863 sheet: 0.10 (0.15), residues: 1107 loop : -0.03 (0.12), residues: 2587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1264 time to evaluate : 7.870 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 outliers start: 204 outliers final: 127 residues processed: 1362 average time/residue: 3.5312 time to fit residues: 6854.8001 Evaluate side-chains 1362 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1235 time to evaluate : 7.825 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 78 residues processed: 52 average time/residue: 2.0025 time to fit residues: 188.3822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 326 optimal weight: 3.9990 chunk 874 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 570 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 chunk 972 optimal weight: 0.9980 chunk 807 optimal weight: 3.9990 chunk 450 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 510 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 GLN 2 55 GLN E 19 ASN E 41 GLN E 100 GLN E 102 ASN G 97 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN L 49 GLN O 22 GLN O 48 ASN O 143 GLN P 43 ASN Q 20 ASN T 93 ASN X 66 ASN Z 6 GLN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN g 25 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 148 ASN o 18 GLN ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN t 5 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 156440 Z= 0.188 Angle : 0.560 13.553 234176 Z= 0.306 Chirality : 0.035 0.251 29884 Planarity : 0.005 0.131 12430 Dihedral : 13.794 178.902 61878 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.74 (0.11), residues: 5557 helix: 1.52 (0.12), residues: 1867 sheet: 0.09 (0.16), residues: 1102 loop : 0.02 (0.12), residues: 2588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1428 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1279 time to evaluate : 8.023 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 outliers start: 149 outliers final: 101 residues processed: 1375 average time/residue: 3.5495 time to fit residues: 6933.3234 Evaluate side-chains 1328 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1227 time to evaluate : 7.835 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 77 residues processed: 26 average time/residue: 2.2429 time to fit residues: 103.9993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 937 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 554 optimal weight: 7.9990 chunk 710 optimal weight: 6.9990 chunk 550 optimal weight: 6.9990 chunk 818 optimal weight: 9.9990 chunk 542 optimal weight: 7.9990 chunk 968 optimal weight: 2.9990 chunk 606 optimal weight: 4.9990 chunk 590 optimal weight: 0.5980 chunk 447 optimal weight: 0.6980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 41 GLN E 100 GLN E 102 ASN ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN L 49 GLN O 22 GLN O 48 ASN O 143 GLN P 43 ASN Q 30 HIS T 93 ASN ** W 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN g 25 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN t 5 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 156440 Z= 0.236 Angle : 0.549 13.530 234176 Z= 0.300 Chirality : 0.035 0.271 29884 Planarity : 0.005 0.134 12430 Dihedral : 13.769 178.978 61878 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.78 (0.11), residues: 5557 helix: 1.58 (0.12), residues: 1869 sheet: 0.09 (0.15), residues: 1108 loop : 0.02 (0.12), residues: 2580 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1238 time to evaluate : 8.866 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 outliers start: 132 outliers final: 100 residues processed: 1323 average time/residue: 3.4890 time to fit residues: 6591.8273 Evaluate side-chains 1310 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1210 time to evaluate : 7.756 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 79 residues processed: 24 average time/residue: 1.9246 time to fit residues: 88.7859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 599 optimal weight: 6.9990 chunk 386 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 615 optimal weight: 5.9990 chunk 659 optimal weight: 9.9990 chunk 478 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 761 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 GLN 2 55 GLN E 19 ASN E 41 GLN ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS L 49 GLN O 22 GLN O 48 ASN O 143 GLN P 43 ASN Q 20 ASN T 93 ASN X 66 ASN Z 6 GLN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 GLN g 25 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 148 ASN q 99 GLN t 5 ASN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 156440 Z= 0.427 Angle : 0.622 14.465 234176 Z= 0.334 Chirality : 0.041 0.322 29884 Planarity : 0.006 0.145 12430 Dihedral : 13.876 179.035 61878 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.11), residues: 5557 helix: 1.42 (0.12), residues: 1863 sheet: 0.01 (0.16), residues: 1091 loop : -0.16 (0.12), residues: 2603 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1224 time to evaluate : 7.996 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 outliers start: 166 outliers final: 113 residues processed: 1321 average time/residue: 3.5707 time to fit residues: 6735.4410 Evaluate side-chains 1308 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1195 time to evaluate : 7.908 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 77 residues processed: 40 average time/residue: 2.0506 time to fit residues: 149.7530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 881 optimal weight: 4.9990 chunk 927 optimal weight: 2.9990 chunk 846 optimal weight: 0.9980 chunk 902 optimal weight: 0.0470 chunk 543 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 chunk 708 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 815 optimal weight: 5.9990 chunk 853 optimal weight: 7.9990 chunk 899 optimal weight: 9.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 GLN E 19 ASN E 41 GLN ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 GLN O 143 GLN P 20 ASN P 43 ASN Q 20 ASN T 93 ASN ** W 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN Z 6 GLN Z 43 ASN Z 86 GLN g 25 GLN g 31 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN t 5 ASN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 29 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 156440 Z= 0.209 Angle : 0.555 13.508 234176 Z= 0.304 Chirality : 0.035 0.257 29884 Planarity : 0.005 0.133 12430 Dihedral : 13.908 179.217 61878 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.68 (0.11), residues: 5557 helix: 1.54 (0.12), residues: 1868 sheet: 0.07 (0.16), residues: 1079 loop : -0.09 (0.12), residues: 2610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1218 time to evaluate : 7.802 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 outliers start: 116 outliers final: 91 residues processed: 1297 average time/residue: 3.5944 time to fit residues: 6721.7122 Evaluate side-chains 1307 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1216 time to evaluate : 7.890 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 73 residues processed: 23 average time/residue: 2.1044 time to fit residues: 91.7427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 592 optimal weight: 3.9990 chunk 954 optimal weight: 4.9990 chunk 582 optimal weight: 6.9990 chunk 452 optimal weight: 5.9990 chunk 663 optimal weight: 9.9990 chunk 1001 optimal weight: 5.9990 chunk 921 optimal weight: 8.9990 chunk 797 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 615 optimal weight: 3.9990 chunk 488 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 55 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 GLN O 143 GLN P 43 ASN Q 20 ASN T 93 ASN ** W 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN Z 86 GLN g 31 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN t 5 ASN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 79 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 156440 Z= 0.336 Angle : 0.588 14.020 234176 Z= 0.319 Chirality : 0.039 0.293 29884 Planarity : 0.006 0.141 12430 Dihedral : 13.918 179.733 61878 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.58 (0.11), residues: 5557 helix: 1.52 (0.12), residues: 1851 sheet: -0.02 (0.16), residues: 1089 loop : -0.18 (0.12), residues: 2617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11114 Ramachandran restraints generated. 5557 Oldfield, 0 Emsley, 5557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1222 time to evaluate : 7.939 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 outliers start: 105 outliers final: 87 residues processed: 1294 average time/residue: 3.6193 time to fit residues: 6693.3384 Evaluate side-chains 1295 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1208 time to evaluate : 7.802 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 70 residues processed: 19 average time/residue: 2.1444 time to fit residues: 77.1890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 633 optimal weight: 0.3980 chunk 849 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 735 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 798 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 819 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 41 GLN ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN O 22 GLN O 143 GLN P 43 ASN Q 20 ASN T 93 ASN ** W 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 ASN Z 6 GLN Z 43 ASN Z 86 GLN g 25 GLN g 31 GLN k 29 GLN ** n 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN t 5 ASN ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 29 ASN x 79 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.081874 restraints weight = 520655.915| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 0.83 r_work: 0.3011 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.2992 rms_B_bonded: 0.93 restraints_weight: 0.1250 r_work: 0.2982 rms_B_bonded: 1.06 restraints_weight: 0.0625 r_work: 0.2971 rms_B_bonded: 1.22 restraints_weight: 0.0312 r_work: 0.2959 rms_B_bonded: 1.42 restraints_weight: 0.0156 r_work: 0.2946 rms_B_bonded: 1.65 restraints_weight: 0.0078 r_work: 0.2932 rms_B_bonded: 1.92 restraints_weight: 0.0039 r_work: 0.2916 rms_B_bonded: 2.23 restraints_weight: 0.0020 r_work: 0.2899 rms_B_bonded: 2.59 restraints_weight: 0.0010 r_work: 0.2879 rms_B_bonded: 3.02 restraints_weight: 0.0005 r_work: 0.2857 rms_B_bonded: 3.51 restraints_weight: 0.0002 r_work: 0.2833 rms_B_bonded: 4.10 restraints_weight: 0.0001 r_work: 0.2806 rms_B_bonded: 4.79 restraints_weight: 0.0001 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 156440 Z= 0.180 Angle : 0.560 13.573 234176 Z= 0.307 Chirality : 0.034 0.260 29884 Planarity : 0.005 0.132 12430 Dihedral : 13.938 179.782 61878 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.45 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.64 (0.11), residues: 5557 helix: 1.58 (0.12), residues: 1857 sheet: -0.00 (0.16), residues: 1082 loop : -0.13 (0.12), residues: 2618 =============================================================================== Job complete usr+sys time: 107087.91 seconds wall clock time: 1823 minutes 14.55 seconds (109394.55 seconds total)