Starting phenix.real_space_refine (version: dev) on Sat Feb 25 13:27:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkn_11255/02_2023/6zkn_11255_updated.pdb" } resolution = 2.9 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= 0.003 sd= 0.033 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 Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "9 TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65955 Number of models: 1 Model: "" Number of chains: 67 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3427 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2498 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 291} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4425 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 25, 'TRANS': 532} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'3PE': 1, '970': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, '970': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'3PE': 1, '970': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 196 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 104.392 52.956 242.617 1.00 22.42 S ATOM 2695 SG CYS 1 362 107.007 53.061 237.204 1.00 36.86 S ATOM 2676 SG CYS 1 359 111.524 53.252 243.319 1.00 39.65 S ATOM 3039 SG CYS 1 405 108.235 47.332 241.788 1.00 34.13 S ATOM 4116 SG CYS 2 103 102.004 48.070 261.437 1.00 53.10 S ATOM 4150 SG CYS 2 108 99.966 45.525 263.471 1.00 58.73 S ATOM 4430 SG CYS 2 144 103.883 44.500 257.917 1.00 58.70 S ATOM 4453 SG CYS 2 148 102.065 41.617 259.411 1.00 61.28 S ATOM 5793 SG CYS 3 114 106.294 71.022 227.627 1.00 29.23 S ATOM 5732 SG CYS 3 105 101.025 74.340 229.419 1.00 33.01 S ATOM 5753 SG CYS 3 108 107.092 76.106 231.290 1.00 18.64 S ATOM 6125 SG CYS 3 156 113.724 63.818 232.545 1.00 24.60 S ATOM 6102 SG CYS 3 153 111.564 66.864 238.046 1.00 25.29 S ATOM 6149 SG CYS 3 159 117.673 67.818 236.370 1.00 59.31 S ATOM 6479 SG CYS 3 203 113.594 70.027 232.517 1.00 25.81 S ATOM 5238 SG CYS 3 41 113.116 57.281 230.671 1.00 19.75 S ATOM 5324 SG CYS 3 52 109.355 58.261 229.916 1.00 28.94 S ATOM 5349 SG CYS 3 55 109.937 53.125 226.569 1.00 47.72 S ATOM 5450 SG CYS 3 69 113.492 53.255 228.044 1.00 27.98 S ATOM 15650 SG CYS 6 55 84.795 99.624 206.246 1.00 47.19 S ATOM 16148 SG CYS 6 119 91.047 95.813 204.615 1.00 47.26 S ATOM 16378 SG CYS 6 149 87.827 93.696 209.467 1.00 29.95 S ATOM 15644 SG CYS 6 54 84.369 93.305 203.622 1.00 79.01 S ATOM 17570 SG CYS 9 116 91.732 94.651 216.003 1.00 41.30 S ATOM 17617 SG CYS 9 122 92.436 90.316 220.794 1.00 24.20 S ATOM 17344 SG CYS 9 87 96.431 90.050 215.547 1.00 18.82 S ATOM 17646 SG CYS 9 126 94.583 87.074 228.194 1.00 12.05 S ATOM 17317 SG CYS 9 83 98.155 88.900 223.133 1.00 26.16 S ATOM 17275 SG CYS 9 77 100.179 90.608 228.965 1.00 19.03 S ATOM 17294 SG CYS 9 80 99.841 84.079 227.136 1.00 23.28 S ATOM 39992 SG CYS b 59 96.320 83.136 243.709 1.00 35.50 S ATOM 40170 SG CYS b 84 99.274 83.333 241.152 1.00 26.54 S ATOM 40192 SG CYS b 87 97.568 85.987 242.060 1.00 31.87 S Time building chain proxies: 28.02, per 1000 atoms: 0.42 Number of scatterers: 65955 At special positions: 0 Unit cell: (177.187, 196.285, 293.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 461 16.00 P 37 15.00 O 11817 8.00 N 10951 7.00 C 42659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.12 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 502 " pdb="FE4 SF4 6 502 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 502 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 502 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 502 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 327 helices and 30 sheets defined 50.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.649A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 50 Processing helix chain '1' and resid 52 through 63 removed outlier: 3.693A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.780A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 237 removed outlier: 4.400A pdb=" N SER 1 231 " --> pdb=" O THR 1 227 " (cutoff:3.500A) Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 239 through 243 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.437A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 4.001A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 436 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.792A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.536A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.887A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.801A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 32 Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 202 Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 272 removed outlier: 5.125A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 309 removed outlier: 3.688A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 3.809A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.846A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 4.206A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.059A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 104 Proline residue: 4 101 - end of helix removed outlier: 3.962A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.585A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.020A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.942A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.647A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.662A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.709A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 3.777A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.973A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 138 removed outlier: 3.910A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 26 through 44 Processing helix chain '6' and resid 54 through 63 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 118 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.776A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.840A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 31 Proline residue: H 12 - end of helix removed outlier: 3.514A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.558A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.816A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 220 through 242 removed outlier: 3.880A pdb=" N MET H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.612A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 88 through 110 Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.061A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.647A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 82 removed outlier: 3.989A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.707A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.736A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.964A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.764A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.937A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.900A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 232 through 238 removed outlier: 4.097A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.600A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.748A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.461A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 389 No H-bonds generated for 'chain 'L' and resid 387 through 389' Processing helix chain 'L' and resid 392 through 399 Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.732A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.818A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 542 Proline residue: L 530 - end of helix removed outlier: 4.830A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.156A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.589A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.630A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.674A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.319A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 145 through 155 Processing helix chain 'M' and resid 157 through 170 Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.938A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.934A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.807A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 266 removed outlier: 3.562A pdb=" N MET M 263 " --> pdb=" O TYR M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 278 removed outlier: 3.634A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.496A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.483A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.686A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 3.992A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 144 removed outlier: 3.973A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 168 Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 233 removed outlier: 4.020A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 3.536A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 271 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 298 removed outlier: 3.538A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.926A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.775A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.550A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.560A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 removed outlier: 3.543A pdb=" N LEU X 21 " --> pdb=" O TYR X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 74 removed outlier: 4.093A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU Y 57 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU Y 58 " --> pdb=" O CYS Y 55 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA Y 66 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU Y 67 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Y 68 " --> pdb=" O CYS Y 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG Y 71 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN Y 72 " --> pdb=" O PHE Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.623A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 3.938A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.835A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.693A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 43 No H-bonds generated for 'chain 'b' and resid 40 through 43' Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.289A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.572A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 29 through 39 removed outlier: 3.863A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.086A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 321 removed outlier: 4.887A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 46 removed outlier: 4.815A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS e 38 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG e 39 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR e 40 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL e 41 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU e 42 " --> pdb=" O ARG e 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS e 45 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.033A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.892A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.210A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.530A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'i' and resid 3 through 17 Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.803A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 35 through 44 removed outlier: 4.478A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 141 removed outlier: 3.935A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 160 Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 5.250A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 238 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 272 removed outlier: 5.190A pdb=" N TYR k 272 " --> pdb=" O GLU k 268 " (cutoff:3.500A) Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 3.901A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 98 No H-bonds generated for 'chain 'l' and resid 95 through 98' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 33 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 36 through 46 removed outlier: 3.973A pdb=" N LYS m 39 " --> pdb=" O PRO m 36 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG m 46 " --> pdb=" O MET m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 45 through 51 removed outlier: 4.665A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 2 through 7 removed outlier: 3.991A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 17 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 95 removed outlier: 3.884A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 20 through 22 No H-bonds generated for 'chain 'p' and resid 20 through 22' Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.896A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 75 removed outlier: 4.049A pdb=" N ASN p 74 " --> pdb=" O ALA p 70 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL p 75 " --> pdb=" O ARG p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 116 removed outlier: 3.510A pdb=" N GLY p 93 " --> pdb=" O GLY p 89 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE p 94 " --> pdb=" O ALA p 90 " (cutoff:3.500A) Proline residue: p 96 - end of helix Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 141 removed outlier: 6.521A pdb=" N PHE q 139 " --> pdb=" O SER q 135 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE q 140 " --> pdb=" O THR q 136 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 48 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 92 through 96 removed outlier: 4.211A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 4.127A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU t 142 " --> pdb=" O GLN t 138 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 70 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.147A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 15 through 34 removed outlier: 3.516A pdb=" N GLY y 23 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 29 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.814A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 137 through 142 removed outlier: 6.635A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 315 through 319 removed outlier: 6.860A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.258A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.739A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 46 through 48 removed outlier: 5.990A pdb=" N VAL 6 75 " --> pdb=" O PRO 6 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '6' and resid 85 through 89 removed outlier: 6.599A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 65 through 67 Processing sheet with id= S, first strand: chain '9' and resid 92 through 98 removed outlier: 5.836A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= U, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= V, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.551A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= X, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Y, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.416A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.796A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.378A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.307A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP k 173 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR k 223 " --> pdb=" O ASP k 173 " (cutoff:3.500A) 2685 hydrogen bonds defined for protein. 7572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.18 Time building geometry restraints manager: 24.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.43: 27791 1.43 - 1.66: 38980 1.66 - 1.90: 751 1.90 - 2.13: 0 2.13 - 2.37: 80 Bond restraints: 67602 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.601 0.232 3.80e-02 6.93e+02 3.74e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.330 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" OA3 CDL h 201 " pdb=" PA1 CDL h 201 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.73e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.66e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.337 0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 67597 not shown) Histogram of bond angle deviations from ideal: 61.91 - 77.00: 73 77.00 - 92.10: 9 92.10 - 107.19: 3229 107.19 - 122.28: 77704 122.28 - 137.37: 10431 Bond angle restraints: 91446 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 72.55 48.05 3.00e+00 1.11e-01 2.57e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.67 38.63 3.00e+00 1.11e-01 1.66e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.26 14.07 1.14e+00 7.69e-01 1.52e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.05 14.28 1.20e+00 6.94e-01 1.42e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.93 -23.19 1.95e+00 2.62e-01 1.41e+02 ... (remaining 91441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 40107 34.68 - 69.37: 509 69.37 - 104.05: 42 104.05 - 138.74: 4 138.74 - 173.42: 3 Dihedral angle restraints: 40665 sinusoidal: 17344 harmonic: 23321 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual 180.00 -127.99 -52.01 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual 180.00 -134.38 -45.62 0 5.00e+00 4.00e-02 8.32e+01 dihedral pdb=" CA THR 3 366 " pdb=" C THR 3 366 " pdb=" N THR 3 367 " pdb=" CA THR 3 367 " ideal model delta harmonic sigma weight residual 180.00 144.93 35.07 0 5.00e+00 4.00e-02 4.92e+01 ... (remaining 40662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 9884 4.238 - 8.476: 5 8.476 - 12.715: 0 12.715 - 16.953: 0 16.953 - 21.191: 24 Chirality restraints: 9913 Sorted by residual: chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " pdb=" S4 SF4 3 802 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 9 403 " pdb=" S1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.60 -21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9910 not shown) Planarity restraints: 11432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 970 M 601 " -0.128 2.00e-02 2.50e+03 1.24e-01 3.87e+02 pdb=" C06 970 M 601 " 0.017 2.00e-02 2.50e+03 pdb=" C07 970 M 601 " 0.024 2.00e-02 2.50e+03 pdb=" C09 970 M 601 " 0.085 2.00e-02 2.50e+03 pdb=" C10 970 M 601 " 0.087 2.00e-02 2.50e+03 pdb=" C11 970 M 601 " 0.043 2.00e-02 2.50e+03 pdb=" C12 970 M 601 " 0.067 2.00e-02 2.50e+03 pdb=" C24 970 M 601 " -0.274 2.00e-02 2.50e+03 pdb=" O08 970 M 601 " -0.098 2.00e-02 2.50e+03 pdb=" O13 970 M 601 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 970 M 601 " -0.058 2.00e-02 2.50e+03 7.55e-02 1.42e+02 pdb=" C18 970 M 601 " -0.038 2.00e-02 2.50e+03 pdb=" C19 970 M 601 " -0.010 2.00e-02 2.50e+03 pdb=" C20 970 M 601 " -0.041 2.00e-02 2.50e+03 pdb=" C21 970 M 601 " -0.090 2.00e-02 2.50e+03 pdb=" C22 970 M 601 " -0.070 2.00e-02 2.50e+03 pdb=" C23 970 M 601 " 0.157 2.00e-02 2.50e+03 pdb=" O16 970 M 601 " 0.012 2.00e-02 2.50e+03 pdb=" O26 970 M 601 " 0.032 2.00e-02 2.50e+03 pdb=" O28 970 M 601 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 970 H 501 " 0.029 2.00e-02 2.50e+03 5.14e-02 6.62e+01 pdb=" C06 970 H 501 " 0.008 2.00e-02 2.50e+03 pdb=" C07 970 H 501 " 0.001 2.00e-02 2.50e+03 pdb=" C09 970 H 501 " 0.040 2.00e-02 2.50e+03 pdb=" C10 970 H 501 " 0.059 2.00e-02 2.50e+03 pdb=" C11 970 H 501 " 0.029 2.00e-02 2.50e+03 pdb=" C12 970 H 501 " 0.016 2.00e-02 2.50e+03 pdb=" C24 970 H 501 " -0.100 2.00e-02 2.50e+03 pdb=" O08 970 H 501 " -0.096 2.00e-02 2.50e+03 pdb=" O13 970 H 501 " 0.014 2.00e-02 2.50e+03 ... (remaining 11429 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 18485 2.81 - 3.39: 71352 3.39 - 3.98: 137802 3.98 - 4.56: 192070 4.56 - 5.14: 277405 Nonbonded interactions: 697114 Sorted by model distance: nonbonded pdb=" OD1 ASP g 116 " pdb=" OG SER g 119 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR d 22 " pdb=" OG SER d 88 " model vdw 2.247 2.440 nonbonded pdb=" O LEU A 71 " pdb=" OH TYR J 147 " model vdw 2.257 2.440 nonbonded pdb=" O LEU M 14 " pdb=" OG SER M 18 " model vdw 2.261 2.440 nonbonded pdb=" O ALA L 245 " pdb=" OG SER L 249 " model vdw 2.262 2.440 ... (remaining 697109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'X' and resid 5 through 86) selection = chain 'j' } 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 37 5.49 5 S 461 5.16 5 C 42659 2.51 5 N 10951 2.21 5 O 11817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.880 Check model and map are aligned: 0.730 Process input model: 151.700 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.450 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.008 0.232 67602 Z= 0.509 Angle : 1.035 48.049 91446 Z= 0.549 Chirality : 1.037 21.191 9913 Planarity : 0.008 0.124 11432 Dihedral : 11.597 173.421 25601 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.08), residues: 7884 helix: -1.82 (0.06), residues: 4084 sheet: -1.56 (0.23), residues: 404 loop : -1.67 (0.10), residues: 3396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1974 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1967 time to evaluate : 5.914 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 outliers start: 7 outliers final: 2 residues processed: 1971 average time/residue: 1.5997 time to fit residues: 4052.8183 Evaluate side-chains 1277 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1275 time to evaluate : 5.887 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.3354 time to fit residues: 9.6211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 656 optimal weight: 6.9990 chunk 589 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 chunk 609 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 370 optimal weight: 20.0000 chunk 453 optimal weight: 5.9990 chunk 706 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 1 224 ASN 1 250 ASN 1 356 HIS 1 373 ASN 2 74 GLN 2 155 GLN 3 179 ASN 3 237 ASN 3 444 GLN 3 535 GLN 3 581 GLN 3 682 GLN 4 59 HIS 4 79 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 4 409 HIS 5 69 ASN 5 144 ASN 5 211 GLN 9 65 HIS A 2 ASN A 108 GLN H 5 ASN J 46 ASN K 52 HIS L 2 ASN L 23 ASN L 136 ASN L 210 ASN L 248 HIS L 269 ASN L 270 ASN L 332 HIS L 348 HIS L 351 ASN L 434 GLN ** L 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 471 ASN M 44 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN M 144 ASN M 169 ASN M 304 GLN M 338 HIS M 422 HIS N 120 GLN N 134 GLN N 172 GLN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 GLN Y 63 ASN Z 54 GLN Z 55 HIS Z 90 GLN Z 103 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN b 32 GLN c 29 HIS c 44 ASN c 46 GLN d 37 HIS d 87 HIS e 72 GLN e 79 ASN e 85 GLN ** f 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 85 ASN g 44 ASN h 8 GLN ** i 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 72 ASN i 91 HIS j 74 GLN ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 188 ASN k 190 HIS l 97 HIS m 51 ASN p 49 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN s 43 GLN s 91 HIS t 25 HIS ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 28 ASN v 56 GLN v 99 ASN v 126 GLN v 132 GLN w 27 GLN y 30 ASN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.267 67602 Z= 0.512 Angle : 1.606 51.047 91446 Z= 1.033 Chirality : 0.318 6.695 9913 Planarity : 0.006 0.095 11432 Dihedral : 10.927 167.778 9724 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.09 (0.09), residues: 7884 helix: -0.25 (0.08), residues: 4133 sheet: -1.27 (0.23), residues: 391 loop : -1.13 (0.10), residues: 3360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1302 time to evaluate : 6.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 72 residues processed: 1408 average time/residue: 1.5587 time to fit residues: 2853.7189 Evaluate side-chains 1274 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1202 time to evaluate : 5.896 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 42 residues processed: 33 average time/residue: 0.7223 time to fit residues: 46.8469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 392 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 588 optimal weight: 9.9990 chunk 481 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 707 optimal weight: 30.0000 chunk 764 optimal weight: 30.0000 chunk 630 optimal weight: 40.0000 chunk 701 optimal weight: 20.0000 chunk 241 optimal weight: 0.9990 chunk 567 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 3 444 GLN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 313 GLN 5 211 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN L 248 HIS ** L 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN N 120 GLN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN W 143 ASN Y 15 GLN Y 63 ASN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN d 288 HIS ** f 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 85 ASN g 44 ASN h 72 GLN ** i 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 ASN l 96 HIS ** p 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 116 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN s 91 HIS u 16 GLN u 21 GLN v 66 HIS v 99 ASN v 132 GLN v 137 ASN x 5 GLN y 30 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 67602 Z= 0.520 Angle : 1.593 51.185 91446 Z= 1.028 Chirality : 0.316 6.490 9913 Planarity : 0.005 0.070 11432 Dihedral : 10.458 167.554 9724 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 3.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.32 (0.09), residues: 7884 helix: 0.41 (0.08), residues: 4147 sheet: -1.04 (0.24), residues: 388 loop : -0.79 (0.11), residues: 3349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1261 time to evaluate : 5.860 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 outliers start: 262 outliers final: 101 residues processed: 1395 average time/residue: 1.5144 time to fit residues: 2775.6710 Evaluate side-chains 1270 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1169 time to evaluate : 5.907 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 67 residues processed: 38 average time/residue: 0.7335 time to fit residues: 54.3863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 699 optimal weight: 2.9990 chunk 532 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 475 optimal weight: 20.0000 chunk 710 optimal weight: 5.9990 chunk 752 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 673 optimal weight: 20.0000 chunk 202 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 3 444 GLN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 41 GLN 5 211 GLN L 199 GLN L 442 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN M 338 HIS N 120 GLN Y 15 GLN Y 63 ASN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 GLN b 32 GLN c 44 ASN f 49 GLN f 85 ASN g 44 ASN i 69 ASN k 141 GLN k 180 GLN ** p 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN s 91 HIS u 16 GLN v 99 ASN v 132 GLN ** x 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 67602 Z= 0.496 Angle : 1.578 50.771 91446 Z= 1.022 Chirality : 0.314 6.437 9913 Planarity : 0.004 0.068 11432 Dihedral : 10.071 167.927 9724 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.12 (0.09), residues: 7884 helix: 0.80 (0.08), residues: 4128 sheet: -0.87 (0.24), residues: 387 loop : -0.62 (0.11), residues: 3369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1240 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 102 residues processed: 1373 average time/residue: 1.5294 time to fit residues: 2760.1244 Evaluate side-chains 1268 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1166 time to evaluate : 5.910 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 73 residues processed: 32 average time/residue: 0.6901 time to fit residues: 44.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 626 optimal weight: 5.9990 chunk 426 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 559 optimal weight: 20.0000 chunk 310 optimal weight: 30.0000 chunk 641 optimal weight: 8.9990 chunk 519 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 384 optimal weight: 3.9990 chunk 674 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 2 155 GLN ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN 5 211 GLN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN L 136 ASN L 442 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 120 GLN Y 15 GLN Y 63 ASN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN c 44 ASN f 85 ASN g 44 ASN k 180 GLN l 26 HIS ** p 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 125 GLN s 91 HIS t 168 HIS u 16 GLN v 72 ASN v 99 ASN v 132 GLN x 34 GLN y 30 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 67602 Z= 0.534 Angle : 1.595 50.839 91446 Z= 1.028 Chirality : 0.316 6.494 9913 Planarity : 0.005 0.085 11432 Dihedral : 10.132 167.233 9724 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.24 (0.09), residues: 7884 helix: 0.87 (0.08), residues: 4132 sheet: -0.80 (0.25), residues: 391 loop : -0.53 (0.11), residues: 3361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1198 time to evaluate : 6.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 114 residues processed: 1343 average time/residue: 1.5347 time to fit residues: 2701.1223 Evaluate side-chains 1261 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1147 time to evaluate : 5.875 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 78 residues processed: 40 average time/residue: 0.6872 time to fit residues: 54.1031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 253 optimal weight: 9.9990 chunk 677 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 441 optimal weight: 7.9990 chunk 185 optimal weight: 0.0070 chunk 752 optimal weight: 20.0000 chunk 624 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 249 optimal weight: 30.0000 chunk 395 optimal weight: 10.0000 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 155 GLN 3 437 HIS 3 444 GLN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN L 442 ASN L 524 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 120 GLN Y 15 GLN Y 63 ASN Y 72 GLN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN f 72 GLN g 44 ASN h 107 GLN ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 69 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN s 43 GLN s 91 HIS v 97 ASN v 99 ASN v 132 GLN x 5 GLN x 34 GLN y 30 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.241 67602 Z= 0.533 Angle : 1.595 50.783 91446 Z= 1.028 Chirality : 0.316 6.465 9913 Planarity : 0.005 0.076 11432 Dihedral : 10.118 167.340 9724 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.32 (0.09), residues: 7884 helix: 0.92 (0.08), residues: 4130 sheet: -0.70 (0.25), residues: 382 loop : -0.47 (0.11), residues: 3372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1189 time to evaluate : 5.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 245 outliers final: 126 residues processed: 1334 average time/residue: 1.5589 time to fit residues: 2733.3751 Evaluate side-chains 1264 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1138 time to evaluate : 5.871 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 91 residues processed: 40 average time/residue: 0.8173 time to fit residues: 59.3953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 725 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 428 optimal weight: 40.0000 chunk 549 optimal weight: 9.9990 chunk 425 optimal weight: 20.0000 chunk 633 optimal weight: 0.9980 chunk 420 optimal weight: 3.9990 chunk 749 optimal weight: 30.0000 chunk 469 optimal weight: 20.0000 chunk 457 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 1 250 ASN ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 155 GLN 3 444 GLN 4 50 ASN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN L 175 ASN L 442 ASN L 524 ASN M 26 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 49 ASN N 120 GLN Y 63 ASN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 321 HIS f 72 GLN f 85 ASN g 44 ASN h 50 ASN h 107 GLN j 74 GLN k 180 GLN n 47 ASN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 125 GLN s 43 GLN s 91 HIS v 97 ASN v 99 ASN v 132 GLN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN y 13 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 67602 Z= 0.513 Angle : 1.588 50.886 91446 Z= 1.025 Chirality : 0.315 6.508 9913 Planarity : 0.005 0.067 11432 Dihedral : 9.988 167.416 9724 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.42 (0.10), residues: 7884 helix: 1.00 (0.08), residues: 4141 sheet: -0.65 (0.25), residues: 386 loop : -0.43 (0.11), residues: 3357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1177 time to evaluate : 6.618 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 outliers start: 218 outliers final: 123 residues processed: 1325 average time/residue: 1.5291 time to fit residues: 2672.8882 Evaluate side-chains 1248 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1125 time to evaluate : 5.947 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 98 residues processed: 28 average time/residue: 0.7994 time to fit residues: 43.7656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 463 optimal weight: 7.9990 chunk 299 optimal weight: 20.0000 chunk 447 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 476 optimal weight: 10.0000 chunk 510 optimal weight: 7.9990 chunk 370 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 589 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 1 250 ASN ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 155 GLN 3 119 GLN 3 444 GLN 3 461 ASN 4 50 ASN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN L 524 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 120 GLN ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN f 72 GLN f 85 ASN g 44 ASN h 50 ASN h 107 GLN j 47 GLN ** k 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 47 ASN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN s 91 HIS v 97 ASN v 99 ASN v 132 GLN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN y 30 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.242 67602 Z= 0.511 Angle : 1.589 50.829 91446 Z= 1.026 Chirality : 0.315 6.542 9913 Planarity : 0.005 0.056 11432 Dihedral : 9.923 167.293 9724 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.47 (0.10), residues: 7884 helix: 1.03 (0.08), residues: 4137 sheet: -0.61 (0.25), residues: 386 loop : -0.39 (0.11), residues: 3361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1146 time to evaluate : 5.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 121 residues processed: 1287 average time/residue: 1.5342 time to fit residues: 2610.1982 Evaluate side-chains 1239 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1118 time to evaluate : 5.923 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 99 residues processed: 26 average time/residue: 0.6838 time to fit residues: 38.1497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 682 optimal weight: 0.7980 chunk 718 optimal weight: 40.0000 chunk 655 optimal weight: 6.9990 chunk 698 optimal weight: 1.9990 chunk 420 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 chunk 548 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 631 optimal weight: 8.9990 chunk 660 optimal weight: 20.0000 chunk 696 optimal weight: 0.0870 overall best weight: 3.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 1 250 ASN 2 155 GLN 3 444 GLN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 HIS L 136 ASN L 442 ASN L 524 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 120 GLN N 134 GLN ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 72 GLN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN f 72 GLN f 85 ASN g 44 ASN h 50 ASN h 107 GLN j 47 GLN ** k 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 47 ASN s 43 GLN s 91 HIS v 97 ASN v 99 ASN v 132 GLN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN y 30 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 67602 Z= 0.503 Angle : 1.588 50.740 91446 Z= 1.025 Chirality : 0.315 6.487 9913 Planarity : 0.004 0.056 11432 Dihedral : 9.812 167.211 9724 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.51 (0.10), residues: 7884 helix: 1.07 (0.08), residues: 4142 sheet: -0.56 (0.25), residues: 394 loop : -0.38 (0.11), residues: 3348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1171 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 110 residues processed: 1295 average time/residue: 1.5470 time to fit residues: 2653.3090 Evaluate side-chains 1234 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1124 time to evaluate : 5.948 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 101 residues processed: 13 average time/residue: 0.5906 time to fit residues: 22.0209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 458 optimal weight: 4.9990 chunk 738 optimal weight: 5.9990 chunk 451 optimal weight: 20.0000 chunk 350 optimal weight: 0.8980 chunk 513 optimal weight: 8.9990 chunk 775 optimal weight: 10.0000 chunk 713 optimal weight: 9.9990 chunk 617 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 476 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 ASN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 155 GLN 3 444 GLN 4 50 ASN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN L 524 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS N 120 GLN ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 GLN Y 63 ASN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN f 72 GLN f 85 ASN g 44 ASN h 107 GLN ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 ASN ** k 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 47 ASN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 91 HIS t 140 GLN v 97 ASN v 99 ASN v 132 GLN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN y 30 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.241 67602 Z= 0.527 Angle : 1.600 50.817 91446 Z= 1.029 Chirality : 0.316 6.554 9913 Planarity : 0.005 0.054 11432 Dihedral : 9.894 167.158 9724 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.46 (0.10), residues: 7884 helix: 1.01 (0.08), residues: 4140 sheet: -0.60 (0.25), residues: 398 loop : -0.36 (0.11), residues: 3346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15768 Ramachandran restraints generated. 7884 Oldfield, 0 Emsley, 7884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1127 time to evaluate : 6.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 113 residues processed: 1249 average time/residue: 1.5482 time to fit residues: 2562.0364 Evaluate side-chains 1226 residues out of total 7003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1113 time to evaluate : 5.909 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 98 residues processed: 19 average time/residue: 0.6934 time to fit residues: 31.5411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 778 random chunks: chunk 490 optimal weight: 3.9990 chunk 657 optimal weight: 0.0770 chunk 189 optimal weight: 10.0000 chunk 569 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 618 optimal weight: 30.0000 chunk 258 optimal weight: 2.9990 chunk 634 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 1 250 ASN 2 37 ASN 2 155 GLN 3 444 GLN 4 50 ASN 4 59 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** 9 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN L 524 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN M 338 HIS N 120 GLN ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 72 GLN Z 90 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN e 30 GLN f 72 GLN f 85 ASN g 44 ASN h 107 GLN ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 47 ASN s 91 HIS v 97 ASN v 99 ASN v 126 GLN v 132 GLN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN y 30 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094336 restraints weight = 93440.125| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.47 r_work: 0.3010 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 67602 Z= 0.494 Angle : 1.587 50.779 91446 Z= 1.025 Chirality : 0.314 6.484 9913 Planarity : 0.004 0.057 11432 Dihedral : 9.663 167.554 9724 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.60 (0.10), residues: 7884 helix: 1.12 (0.08), residues: 4138 sheet: -0.52 (0.25), residues: 396 loop : -0.31 (0.11), residues: 3350 =============================================================================== Job complete usr+sys time: 35271.07 seconds wall clock time: 608 minutes 35.94 seconds (36515.94 seconds total)