Starting phenix.real_space_refine (version: dev) on Sun Feb 26 18:11:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkk_11252/02_2023/6zkk_11252_updated.pdb" } resolution = 3.7 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= 0.040 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 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 642": "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 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 "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "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 "L TYR 485": "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 "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" 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 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 86": "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 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 "d ARG 325": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" 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 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 149": "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" 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: 67950 Number of models: 1 Model: "" Number of chains: 68 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: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3457 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} 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: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} 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: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} 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: "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: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2748 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} 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: "4" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'3PE': 1, '970': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 321 Unusual residues: {'3PE': 2, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "M" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 252 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 141 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "V" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 158 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 43 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: {'rna2p': 1} Chain: "o" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 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: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 105.437 53.502 238.591 1.00 14.41 S ATOM 4116 SG CYS 2 103 102.910 47.758 257.433 1.00 61.52 S ATOM 4150 SG CYS 2 108 100.542 45.539 259.351 1.00 43.23 S ATOM 4430 SG CYS 2 144 104.723 44.525 254.017 1.00122.43 S ATOM 4453 SG CYS 2 148 102.993 41.433 255.077 1.00 88.55 S ATOM 5793 SG CYS 3 114 107.002 72.144 224.573 1.00 68.31 S ATOM 5732 SG CYS 3 105 101.463 75.204 226.570 1.00 44.25 S ATOM 5753 SG CYS 3 108 107.420 77.389 228.188 1.00 96.31 S ATOM 6125 SG CYS 3 156 114.395 64.847 229.277 1.00 44.07 S ATOM 6102 SG CYS 3 153 111.840 67.864 234.455 1.00 42.12 S ATOM 6149 SG CYS 3 159 118.091 69.030 233.084 1.00 47.52 S ATOM 6479 SG CYS 3 203 114.035 71.227 229.145 1.00 58.04 S ATOM 5238 SG CYS 3 41 113.782 58.561 227.124 1.00 73.76 S ATOM 5324 SG CYS 3 52 110.103 59.304 226.200 1.00 17.15 S ATOM 5349 SG CYS 3 55 110.779 54.584 222.604 1.00 17.11 S ATOM 5450 SG CYS 3 69 114.462 54.568 224.212 1.00116.51 S ATOM 15674 SG CYS 6 54 84.239 94.750 201.242 1.00 67.22 S ATOM 17600 SG CYS 9 116 91.573 96.059 213.709 1.00 29.51 S ATOM 17647 SG CYS 9 122 92.309 91.632 218.433 1.00 12.41 S ATOM 17374 SG CYS 9 87 96.329 91.685 213.243 1.00 27.77 S ATOM 17676 SG CYS 9 126 94.591 88.039 225.587 1.00 89.37 S ATOM 17347 SG CYS 9 83 98.227 90.015 220.656 1.00 37.46 S ATOM 17305 SG CYS 9 77 100.016 91.960 226.362 1.00 55.71 S ATOM 17324 SG CYS 9 80 99.878 85.295 225.135 1.00130.64 S ATOM 41371 SG CYS b 59 96.442 83.420 241.055 1.00 74.31 S ATOM 41549 SG CYS b 84 99.441 83.630 238.745 1.00 14.75 S ATOM 41571 SG CYS b 87 97.689 86.353 239.488 1.00 20.08 S Time building chain proxies: 28.83, per 1000 atoms: 0.42 Number of scatterers: 67950 At special positions: 0 Unit cell: (178.248, 194.163, 290.714, 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 468 16.00 P 44 15.00 O 12184 8.00 N 11233 7.00 C 43991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.04 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 58 " - pdb=" SG CYS s 89 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.05 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: 21.27 Conformation dependent library (CDL) restraints added in 7.3 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="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " 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="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " 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 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " Number of angles added : 3 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 329 helices and 30 sheets defined 49.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 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 36 No H-bonds generated for 'chain '1' and resid 33 through 36' Processing helix chain '1' and resid 45 through 49 Processing helix chain '1' and resid 52 through 63 removed outlier: 3.855A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 82 removed outlier: 3.602A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 107 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 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: 4.364A 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: 4.506A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 removed outlier: 3.791A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 4.161A 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 35 Processing helix chain '2' and resid 43 through 58 removed outlier: 4.625A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 4.136A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.931A 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: 4.144A 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 166 through 176 Processing helix chain '3' and resid 26 through 31 Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 159 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 265 through 269 Processing helix chain '3' and resid 296 through 307 removed outlier: 3.894A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) 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 372 Processing helix chain '3' and resid 389 through 400 Processing helix chain '3' and resid 426 through 432 removed outlier: 4.355A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 4.143A 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 477 Processing helix chain '3' and resid 497 through 503 removed outlier: 4.609A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA 3 502 " --> pdb=" O SER 3 498 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 672 removed outlier: 4.086A pdb=" N TYR 3 672 " --> pdb=" O LYS 3 669 " (cutoff:3.500A) Processing helix chain '3' and resid 678 through 680 No H-bonds generated for 'chain '3' and resid 678 through 680' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 4.345A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 5.052A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 102 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 111 through 125 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 165 through 184 removed outlier: 4.100A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.784A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.817A 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: 4.312A 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 343 through 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.510A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.569A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.485A 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: 3.987A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.959A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 137 removed outlier: 3.892A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (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 25 through 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' 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 177 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 85 No H-bonds generated for 'chain '9' and resid 82 through 85' Processing helix chain '9' and resid 122 through 125 No H-bonds generated for 'chain '9' and resid 122 through 125' Processing helix chain '9' and resid 144 through 147 Processing helix chain '9' and resid 151 through 172 removed outlier: 5.511A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.182A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 4.170A pdb=" N LEU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.450A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.079A 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 10 removed outlier: 3.543A pdb=" N LEU H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 32 removed outlier: 4.550A pdb=" N VAL H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN H 32 " --> pdb=" O LEU H 28 " (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 56 removed outlier: 3.573A pdb=" N LEU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.199A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 146 removed outlier: 3.873A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.589A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.848A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 213 removed outlier: 3.825A pdb=" N VAL H 213 " --> pdb=" O GLY H 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 210 through 213' Processing helix chain 'H' and resid 221 through 242 removed outlier: 4.009A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 273 Processing helix chain 'H' and resid 286 through 289 No H-bonds generated for 'chain 'H' and resid 286 through 289' Processing helix chain 'H' and resid 293 through 311 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: 3.525A pdb=" N CYS J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU J 45 " --> pdb=" O CYS J 41 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 73 removed outlier: 4.254A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 108 removed outlier: 3.945A pdb=" N THR J 92 " --> pdb=" O VAL J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.872A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 148 removed outlier: 3.909A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.784A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 51 removed outlier: 3.610A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 84 removed outlier: 4.459A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 5.536A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET K 80 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR K 84 " --> pdb=" O VAL K 81 " (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 'L' and resid 4 through 23 removed outlier: 3.671A 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: 4.171A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.895A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 110 Proline residue: L 91 - end of helix removed outlier: 4.190A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS L 109 " --> pdb=" O MET L 105 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER L 110 " --> pdb=" O TRP L 106 " (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: 3.813A 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 231 through 238 removed outlier: 4.282A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.481A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.845A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.568A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.997A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.982A 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 392 through 400 Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.568A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 4.050A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.654A 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 532 removed outlier: 4.116A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix No H-bonds generated for 'chain 'L' and resid 526 through 532' Processing helix chain 'L' and resid 537 through 546 removed outlier: 3.521A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.199A 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 25 through 42 removed outlier: 4.156A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.527A 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 110 removed outlier: 3.763A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.929A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.674A 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 140 through 170 removed outlier: 3.872A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 5.101A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 220 Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.767A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.587A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.431A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.571A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.630A 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 393 through 413 removed outlier: 4.476A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 446 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 40 Processing helix chain 'N' and resid 43 through 45 No H-bonds generated for 'chain 'N' and resid 43 through 45' 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: 3.738A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.507A 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 169 removed outlier: 4.110A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 4.058A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 221 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.146A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.923A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 4.135A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.864A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 8 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 15 through 44 removed outlier: 3.764A pdb=" N LYS W 19 " --> pdb=" O GLY W 15 " (cutoff:3.500A) removed outlier: 4.741A 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: 3.572A 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 'X' and resid 8 through 20 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 29 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 74 Processing helix chain 'Y' and resid 78 through 90 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 57 removed outlier: 4.300A pdb=" N LYS Z 57 " --> pdb=" O ARG Z 53 " (cutoff:3.500A) 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 115 removed outlier: 4.571A 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 172 removed outlier: 3.739A pdb=" N ALA Z 172 " --> pdb=" O ALA Z 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.594A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.717A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 29 through 39 removed outlier: 3.762A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 62 removed outlier: 5.037A 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 124 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 194 through 197 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 263 through 270 removed outlier: 3.647A pdb=" N LEU d 269 " --> pdb=" O TRP d 265 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE d 270 " --> pdb=" O ILE d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 310 through 318 removed outlier: 5.303A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 44 removed outlier: 5.030A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS e 38 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG e 39 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR e 40 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL e 41 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU e 42 " --> pdb=" O ARG e 39 " (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: 4.741A 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: 4.221A 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 67 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 103 Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 54 through 56 No H-bonds generated for 'chain 'h' and resid 54 through 56' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.995A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) 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: 4.037A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.740A 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 73 through 83 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 14 through 16 No H-bonds generated for 'chain 'k' and resid 14 through 16' Processing helix chain 'k' and resid 38 through 46 Processing helix chain 'k' and resid 56 through 62 removed outlier: 4.578A pdb=" N ALA k 59 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP k 60 " --> pdb=" O HIS k 57 " (cutoff:3.500A) 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 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 3.976A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) 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 211 through 214 No H-bonds generated for 'chain 'k' and resid 211 through 214' Processing helix chain 'k' and resid 231 through 240 removed outlier: 4.011A pdb=" N TYR k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 271 through 273 No H-bonds generated for 'chain 'k' and resid 271 through 273' Processing helix chain 'k' and resid 286 through 296 Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' 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 42 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.349A 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 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 36 through 46 removed outlier: 3.985A pdb=" N LYS m 39 " --> pdb=" O PRO m 36 " (cutoff:3.500A) removed outlier: 3.506A 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 37 Processing helix chain 'n' and resid 48 through 52 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 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 4.122A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 27 through 47 removed outlier: 3.919A pdb=" N ALA p 31 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN p 32 " --> pdb=" O THR p 28 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 71 Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 93 removed outlier: 3.944A pdb=" N LEU p 91 " --> pdb=" O LEU p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 95 through 117 removed outlier: 3.799A pdb=" N GLU p 117 " --> pdb=" O LYS p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix removed outlier: 3.556A pdb=" N GLU q 92 " --> pdb=" O GLU q 88 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR q 95 " --> pdb=" O GLU q 91 " (cutoff:3.500A) 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 136 Processing helix chain 'r' and resid 5 through 25 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 88 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 50 removed outlier: 4.255A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 92 through 95 removed outlier: 4.137A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 92 through 95' 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 139 removed outlier: 4.283A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (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 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 63 Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 83 through 101 removed outlier: 3.914A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA w 89 " --> pdb=" O GLN w 86 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 44 Processing helix chain 'y' and resid 16 through 33 removed outlier: 3.620A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 27 removed outlier: 3.746A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 4.761A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing helix chain 'z' and resid 66 through 68 No H-bonds generated for 'chain 'z' and resid 66 through 68' Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.860A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 5.934A 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: 6.675A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (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 56 through 58 Processing sheet with id= F, first strand: chain '3' and resid 146 through 148 Processing sheet with id= G, first strand: chain '3' and resid 173 through 175 Processing sheet with id= H, first strand: chain '3' and resid 223 through 228 Processing sheet with id= I, first strand: chain '3' and resid 283 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.682A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 490 through 493 removed outlier: 8.629A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '3' and resid 572 through 574 Processing sheet with id= M, first strand: chain '4' and resid 47 through 51 removed outlier: 3.658A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 361 through 368 Processing sheet with id= O, first strand: chain '5' and resid 74 through 80 removed outlier: 6.751A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 173 through 177 Processing sheet with id= Q, first strand: chain '6' and resid 85 through 89 removed outlier: 6.806A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.594A 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: 5.519A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.291A 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 115 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: 6.566A 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 103 through 106 removed outlier: 6.453A pdb=" N ALA c 35 " --> pdb=" O ASP c 104 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU c 106 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE c 37 " --> pdb=" O GLU c 106 " (cutoff:3.500A) 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: 6.476A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 7.059A 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: 6.872A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.640A 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: 6.413A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'k' and resid 25 through 27 removed outlier: 6.474A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 2686 hydrogen bonds defined for protein. 7554 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: 21.32 Time building geometry restraints manager: 23.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 28855 1.43 - 1.66: 39945 1.66 - 1.90: 761 1.90 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69641 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.604 0.229 3.80e-02 6.93e+02 3.64e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.338 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.341 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.00e-02 1.00e+04 2.98e+01 bond pdb=" OB3 CDL h 201 " pdb=" PB2 CDL h 201 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.00e-02 1.00e+04 2.94e+01 ... (remaining 69636 not shown) Histogram of bond angle deviations from ideal: 62.23 - 77.26: 74 77.26 - 92.30: 8 92.30 - 107.33: 3519 107.33 - 122.36: 80905 122.36 - 137.40: 9652 Bond angle restraints: 94158 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 72.31 48.29 3.00e+00 1.11e-01 2.59e+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 71.29 38.01 3.00e+00 1.11e-01 1.61e+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 90.29 14.04 1.14e+00 7.69e-01 1.52e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 90.81 13.52 1.14e+00 7.69e-01 1.41e+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 90.21 14.12 1.20e+00 6.94e-01 1.39e+02 ... (remaining 94153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.35: 41249 33.35 - 66.69: 625 66.69 - 100.04: 37 100.04 - 133.39: 4 133.39 - 166.74: 2 Dihedral angle restraints: 41917 sinusoidal: 17942 harmonic: 23975 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual 180.00 -112.70 -67.30 0 5.00e+00 4.00e-02 1.81e+02 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 -126.37 -53.63 0 5.00e+00 4.00e-02 1.15e+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 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 41914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.244: 10164 4.244 - 8.488: 5 8.488 - 12.731: 0 12.731 - 16.975: 0 16.975 - 21.219: 24 Chirality restraints: 10193 Sorted by residual: chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.66 21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S3 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.58 -21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S4 SF4 9 402 " both_signs ideal model delta sigma weight residual False -10.55 10.57 -21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10190 not shown) Planarity restraints: 11751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 970 4 501 " 0.003 2.00e-02 2.50e+03 5.90e-02 8.72e+01 pdb=" C18 970 4 501 " 0.033 2.00e-02 2.50e+03 pdb=" C19 970 4 501 " 0.030 2.00e-02 2.50e+03 pdb=" C20 970 4 501 " -0.009 2.00e-02 2.50e+03 pdb=" C21 970 4 501 " -0.005 2.00e-02 2.50e+03 pdb=" C22 970 4 501 " 0.012 2.00e-02 2.50e+03 pdb=" C23 970 4 501 " 0.079 2.00e-02 2.50e+03 pdb=" O16 970 4 501 " -0.114 2.00e-02 2.50e+03 pdb=" O26 970 4 501 " -0.096 2.00e-02 2.50e+03 pdb=" O28 970 4 501 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NDP d 401 " -0.053 2.00e-02 2.50e+03 2.29e-02 1.44e+01 pdb=" C2A NDP d 401 " 0.007 2.00e-02 2.50e+03 pdb=" C4A NDP d 401 " 0.017 2.00e-02 2.50e+03 pdb=" C5A NDP d 401 " 0.015 2.00e-02 2.50e+03 pdb=" C6A NDP d 401 " -0.006 2.00e-02 2.50e+03 pdb=" C8A NDP d 401 " 0.014 2.00e-02 2.50e+03 pdb=" N1A NDP d 401 " -0.008 2.00e-02 2.50e+03 pdb=" N3A NDP d 401 " 0.022 2.00e-02 2.50e+03 pdb=" N6A NDP d 401 " -0.034 2.00e-02 2.50e+03 pdb=" N7A NDP d 401 " 0.018 2.00e-02 2.50e+03 pdb=" N9A NDP d 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.031 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR 6 125 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.008 2.00e-02 2.50e+03 ... (remaining 11748 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 17028 2.79 - 3.38: 72371 3.38 - 3.97: 136909 3.97 - 4.55: 190842 4.55 - 5.14: 285106 Nonbonded interactions: 702256 Sorted by model distance: nonbonded pdb=" O PHE A 56 " pdb=" OH TYR J 70 " model vdw 2.209 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.229 2.440 nonbonded pdb=" OG SER k 88 " pdb=" OD1 ASP k 90 " model vdw 2.268 2.440 nonbonded pdb=" OD2 ASP j 66 " pdb=" OH TYR j 79 " model vdw 2.269 2.440 ... (remaining 702251 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 44 5.49 5 S 468 5.16 5 C 43991 2.51 5 N 11233 2.21 5 O 12184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.050 Extract box with map and model: 6.760 Check model and map are aligned: 0.750 Process input model: 152.650 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.470 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.007 0.229 69641 Z= 0.442 Angle : 1.025 48.293 94158 Z= 0.542 Chirality : 1.023 21.219 10193 Planarity : 0.008 0.082 11751 Dihedral : 11.663 166.735 26437 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.15 % Favored : 94.84 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.56 (0.07), residues: 8122 helix: -2.31 (0.06), residues: 4171 sheet: -2.35 (0.23), residues: 379 loop : -2.29 (0.09), residues: 3572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2236 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2229 time to evaluate : 5.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 2234 average time/residue: 0.7250 time to fit residues: 2663.3800 Evaluate side-chains 1305 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1301 time to evaluate : 5.733 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4990 time to fit residues: 11.8653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 9.9990 chunk 607 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 410 optimal weight: 5.9990 chunk 324 optimal weight: 30.0000 chunk 628 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 382 optimal weight: 30.0000 chunk 467 optimal weight: 6.9990 chunk 728 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 373 ASN 2 42 HIS 2 99 HIS 3 293 HIS 3 535 GLN 3 640 ASN ** 3 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 5 GLN 4 50 ASN 4 55 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 5 95 ASN 5 211 GLN 6 82 GLN ** 6 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN H 287 HIS J 46 ASN K 52 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN L 230 HIS ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 471 ASN L 541 ASN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 HIS M 144 ASN M 169 ASN M 184 GLN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 338 HIS M 415 GLN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 197 ASN N 232 HIS ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 HIS d 87 HIS e 85 GLN f 36 HIS f 72 GLN g 98 GLN k 114 HIS k 180 GLN ** l 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 81 GLN o 46 ASN ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 126 HIS t 52 ASN t 61 GLN t 138 GLN ** t 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 GLN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.273 69641 Z= 0.573 Angle : 1.620 51.371 94158 Z= 1.033 Chirality : 0.309 6.525 10193 Planarity : 0.006 0.070 11751 Dihedral : 11.309 162.673 10174 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.95 % Favored : 95.04 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.09), residues: 8122 helix: -0.88 (0.07), residues: 4219 sheet: -2.16 (0.24), residues: 374 loop : -1.92 (0.10), residues: 3529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1447 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 214 outliers final: 130 residues processed: 1571 average time/residue: 0.6625 time to fit residues: 1777.9044 Evaluate side-chains 1384 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1254 time to evaluate : 5.831 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 0 residues processed: 130 average time/residue: 0.5426 time to fit residues: 138.4991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 20.0000 chunk 226 optimal weight: 7.9990 chunk 606 optimal weight: 9.9990 chunk 495 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 chunk 729 optimal weight: 30.0000 chunk 788 optimal weight: 5.9990 chunk 649 optimal weight: 5.9990 chunk 723 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 585 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS 3 401 HIS 4 50 ASN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 156 ASN ** 9 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN H 124 ASN K 7 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 354 GLN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN M 399 ASN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN X 74 GLN Y 162 HIS ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN f 85 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 59 HIS ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 HIS ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 69641 Z= 0.545 Angle : 1.593 50.905 94158 Z= 1.022 Chirality : 0.309 6.396 10193 Planarity : 0.005 0.069 11751 Dihedral : 10.735 161.961 10174 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.02 % Favored : 94.96 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.42 (0.09), residues: 8122 helix: -0.23 (0.08), residues: 4202 sheet: -1.98 (0.24), residues: 377 loop : -1.64 (0.10), residues: 3543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1366 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 74 residues processed: 1454 average time/residue: 0.7028 time to fit residues: 1765.4797 Evaluate side-chains 1290 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1216 time to evaluate : 6.120 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.5844 time to fit residues: 91.1363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 30.0000 chunk 548 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 348 optimal weight: 40.0000 chunk 489 optimal weight: 9.9990 chunk 732 optimal weight: 9.9990 chunk 775 optimal weight: 30.0000 chunk 382 optimal weight: 6.9990 chunk 693 optimal weight: 30.0000 chunk 208 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS 1 416 GLN ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 459 GLN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN 4 98 GLN 4 149 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 162 GLN ** 9 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN K 91 GLN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN Y 30 HIS ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 ASN f 72 GLN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 GLN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 HIS ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 126 HIS v 72 ASN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.241 69641 Z= 0.567 Angle : 1.604 50.929 94158 Z= 1.026 Chirality : 0.309 6.395 10193 Planarity : 0.005 0.072 11751 Dihedral : 10.634 161.909 10174 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.55 % Favored : 94.43 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.20 (0.09), residues: 8122 helix: -0.02 (0.08), residues: 4202 sheet: -1.82 (0.24), residues: 365 loop : -1.57 (0.10), residues: 3555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1300 time to evaluate : 5.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 109 residues processed: 1393 average time/residue: 0.6876 time to fit residues: 1659.5957 Evaluate side-chains 1312 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1203 time to evaluate : 5.824 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.5260 time to fit residues: 116.8198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 20.0000 chunk 440 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 577 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 661 optimal weight: 7.9990 chunk 535 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 395 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 308 GLN 3 548 HIS ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN 4 98 GLN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN K 91 GLN L 479 GLN L 541 ASN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 ASN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN Z 22 GLN ** d 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN g 98 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 GLN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 84 GLN ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 ASN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.243 69641 Z= 0.563 Angle : 1.602 50.764 94158 Z= 1.026 Chirality : 0.309 6.378 10193 Planarity : 0.005 0.068 11751 Dihedral : 10.577 162.244 10174 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.66 % Favored : 94.31 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.04 (0.09), residues: 8122 helix: 0.14 (0.08), residues: 4171 sheet: -1.94 (0.24), residues: 383 loop : -1.49 (0.10), residues: 3568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1279 time to evaluate : 5.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 77 residues processed: 1355 average time/residue: 0.6673 time to fit residues: 1554.8561 Evaluate side-chains 1261 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1184 time to evaluate : 5.808 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.5307 time to fit residues: 85.2156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 6.9990 chunk 698 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 775 optimal weight: 0.9990 chunk 644 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 407 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 157 ASN 3 311 GLN 4 50 ASN ** 9 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 484 HIS M 51 ASN M 81 GLN M 144 ASN M 415 GLN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN c 51 ASN f 72 GLN g 98 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 GLN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 126 HIS ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN v 72 ASN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.242 69641 Z= 0.532 Angle : 1.582 50.749 94158 Z= 1.017 Chirality : 0.309 6.379 10193 Planarity : 0.005 0.066 11751 Dihedral : 10.343 163.535 10174 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.83 (0.09), residues: 8122 helix: 0.30 (0.08), residues: 4186 sheet: -1.94 (0.24), residues: 387 loop : -1.37 (0.10), residues: 3549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1274 time to evaluate : 6.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 61 residues processed: 1323 average time/residue: 0.6732 time to fit residues: 1537.2197 Evaluate side-chains 1246 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1185 time to evaluate : 5.808 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5087 time to fit residues: 67.7460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 442 optimal weight: 6.9990 chunk 566 optimal weight: 4.9990 chunk 439 optimal weight: 30.0000 chunk 653 optimal weight: 30.0000 chunk 433 optimal weight: 1.9990 chunk 772 optimal weight: 0.6980 chunk 483 optimal weight: 0.4980 chunk 471 optimal weight: 0.0040 chunk 356 optimal weight: 8.9990 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN 9 65 HIS 9 156 ASN L 135 ASN M 51 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 ASN X 74 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN g 98 GLN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN v 72 ASN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 69641 Z= 0.514 Angle : 1.571 50.729 94158 Z= 1.013 Chirality : 0.308 6.371 10193 Planarity : 0.004 0.067 11751 Dihedral : 10.004 165.094 10174 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.76 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.09), residues: 8122 helix: 0.48 (0.08), residues: 4212 sheet: -1.78 (0.24), residues: 396 loop : -1.20 (0.11), residues: 3514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1268 time to evaluate : 5.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 31 residues processed: 1310 average time/residue: 0.6741 time to fit residues: 1519.1662 Evaluate side-chains 1212 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1181 time to evaluate : 5.828 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5483 time to fit residues: 39.8447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 20.0000 chunk 308 optimal weight: 6.9990 chunk 461 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 491 optimal weight: 9.9990 chunk 526 optimal weight: 9.9990 chunk 382 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 607 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 292 ASN M 144 ASN M 399 ASN M 415 GLN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN Z 90 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN g 50 GLN ** j 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 126 HIS ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN ** v 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 ASN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.245 69641 Z= 0.567 Angle : 1.612 50.978 94158 Z= 1.028 Chirality : 0.309 6.548 10193 Planarity : 0.005 0.068 11751 Dihedral : 10.235 163.012 10174 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.72 (0.09), residues: 8122 helix: 0.34 (0.08), residues: 4216 sheet: -1.90 (0.24), residues: 396 loop : -1.26 (0.11), residues: 3510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1227 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 49 residues processed: 1260 average time/residue: 0.6785 time to fit residues: 1478.2859 Evaluate side-chains 1218 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1169 time to evaluate : 5.883 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5389 time to fit residues: 58.1000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 9.9990 chunk 740 optimal weight: 6.9990 chunk 675 optimal weight: 7.9990 chunk 720 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 565 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 650 optimal weight: 7.9990 chunk 681 optimal weight: 9.9990 chunk 717 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 154 GLN ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 HIS ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN ** v 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 ASN ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 41 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 69641 Z= 0.549 Angle : 1.602 50.756 94158 Z= 1.024 Chirality : 0.309 6.409 10193 Planarity : 0.005 0.069 11751 Dihedral : 10.207 163.691 10174 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.69 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.71 (0.09), residues: 8122 helix: 0.34 (0.08), residues: 4201 sheet: -1.85 (0.24), residues: 408 loop : -1.24 (0.11), residues: 3513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1193 time to evaluate : 6.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 29 residues processed: 1217 average time/residue: 0.6792 time to fit residues: 1429.5216 Evaluate side-chains 1186 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1157 time to evaluate : 5.859 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5562 time to fit residues: 38.1872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 20.0000 chunk 761 optimal weight: 8.9990 chunk 464 optimal weight: 10.0000 chunk 361 optimal weight: 7.9990 chunk 529 optimal weight: 30.0000 chunk 798 optimal weight: 10.0000 chunk 735 optimal weight: 9.9990 chunk 636 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 491 optimal weight: 0.2980 chunk 390 optimal weight: 10.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN M 192 ASN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 GLN ** j 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 126 HIS ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN ** v 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 69641 Z= 0.545 Angle : 1.602 50.738 94158 Z= 1.025 Chirality : 0.309 6.409 10193 Planarity : 0.005 0.070 11751 Dihedral : 10.131 163.980 10174 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.79 % Favored : 94.19 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.09), residues: 8122 helix: 0.35 (0.08), residues: 4215 sheet: -1.81 (0.24), residues: 398 loop : -1.21 (0.11), residues: 3509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1181 time to evaluate : 6.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 1191 average time/residue: 0.6865 time to fit residues: 1414.7774 Evaluate side-chains 1166 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1147 time to evaluate : 5.859 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5233 time to fit residues: 27.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 6.9990 chunk 677 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 586 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 637 optimal weight: 0.9980 chunk 266 optimal weight: 9.9990 chunk 654 optimal weight: 30.0000 chunk 80 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 116 HIS ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN ** j 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 GLN ** t 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN ** v 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.159926 restraints weight = 105530.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161564 restraints weight = 85331.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162267 restraints weight = 59975.539| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 69641 Z= 0.525 Angle : 1.592 50.751 94158 Z= 1.020 Chirality : 0.308 6.389 10193 Planarity : 0.005 0.071 11751 Dihedral : 9.916 165.146 10174 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.78 % Favored : 95.20 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.49 (0.09), residues: 8122 helix: 0.47 (0.08), residues: 4210 sheet: -1.68 (0.24), residues: 398 loop : -1.08 (0.11), residues: 3514 =============================================================================== Job complete usr+sys time: 21540.78 seconds wall clock time: 376 minutes 39.14 seconds (22599.14 seconds total)