Starting phenix.real_space_refine (version: dev) on Sat Feb 25 11:46:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zks_11260/02_2023/6zks_11260_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.013 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 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "9 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "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 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 66294 Number of models: 1 Model: "" Number of chains: 67 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3381 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 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: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 336 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 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: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 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: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "N" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 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: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} 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: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 165 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "z" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 104.532 53.943 242.215 1.00 25.70 S ATOM 2676 SG CYS 1 359 111.551 54.513 242.832 1.00 47.00 S ATOM 3039 SG CYS 1 405 108.346 48.297 241.516 1.00 37.41 S ATOM 4116 SG CYS 2 103 102.501 49.538 261.373 1.00 52.00 S ATOM 4150 SG CYS 2 108 100.552 47.166 263.396 1.00 75.20 S ATOM 4430 SG CYS 2 144 104.182 46.015 257.688 1.00 76.68 S ATOM 4453 SG CYS 2 148 102.380 43.034 259.206 1.00 50.35 S ATOM 5793 SG CYS 3 114 106.651 71.997 227.277 1.00 32.51 S ATOM 5732 SG CYS 3 105 101.447 75.468 229.086 1.00 36.29 S ATOM 5753 SG CYS 3 108 107.541 77.209 230.896 1.00 21.92 S ATOM 6125 SG CYS 3 156 113.955 64.624 232.002 1.00 27.88 S ATOM 6102 SG CYS 3 153 111.856 67.904 237.449 1.00 28.57 S ATOM 6149 SG CYS 3 159 117.969 68.706 235.561 1.00 66.45 S ATOM 6479 SG CYS 3 203 113.832 70.888 231.846 1.00 80.31 S ATOM 5238 SG CYS 3 41 112.967 58.156 230.143 1.00 35.42 S ATOM 5324 SG CYS 3 52 109.290 59.162 229.457 1.00 32.22 S ATOM 5349 SG CYS 3 55 109.796 54.112 225.866 1.00 27.68 S ATOM 5450 SG CYS 3 69 113.465 54.394 227.222 1.00 31.26 S ATOM 16332 SG CYS 6 149 87.989 95.159 209.439 1.00 33.23 S ATOM 15598 SG CYS 6 54 84.474 94.868 203.560 1.00 82.29 S ATOM 17524 SG CYS 9 116 92.235 96.162 215.811 1.00 44.58 S ATOM 17571 SG CYS 9 122 92.935 91.781 220.597 1.00 27.48 S ATOM 17298 SG CYS 9 87 96.773 91.461 215.289 1.00 22.10 S ATOM 17600 SG CYS 9 126 95.141 88.592 227.896 1.00 15.33 S ATOM 17271 SG CYS 9 83 98.698 90.189 222.732 1.00 29.44 S ATOM 17229 SG CYS 9 77 100.917 91.892 228.495 1.00 22.31 S ATOM 17248 SG CYS 9 80 100.122 85.338 226.763 1.00 32.90 S ATOM 40512 SG CYS b 59 96.887 84.592 243.113 1.00 38.78 S ATOM 40690 SG CYS b 84 100.081 84.340 241.068 1.00 29.82 S ATOM 40712 SG CYS b 87 98.248 87.519 241.710 1.00 35.15 S Time building chain proxies: 28.07, per 1000 atoms: 0.42 Number of scatterers: 66294 At special positions: 0 Unit cell: (177.24, 197.285, 293.29, 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 464 16.00 P 34 15.00 O 11872 8.00 N 11018 7.00 C 42876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.99 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " 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 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 500 " - 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="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " 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="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb="FE2 SF4 9 402 " - pdb=" NE2 HIS 9 65 " pdb=" SF4 9 403 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 327 helices and 28 sheets defined 50.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 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 37 Processing helix chain '1' and resid 45 through 62 removed outlier: 3.692A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.736A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.700A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 157 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 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 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.374A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 4.224A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.880A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.437A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.994A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.929A 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 177 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 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 196 through 202 removed outlier: 3.740A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 265 through 275 removed outlier: 5.191A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 307 removed outlier: 4.013A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 432 removed outlier: 4.118A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.626A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 515 No H-bonds generated for 'chain '3' and resid 512 through 515' Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.602A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 90 No H-bonds generated for 'chain '4' and resid 87 through 90' Processing helix chain '4' and resid 96 through 104 Proline residue: 4 101 - end of helix removed outlier: 4.057A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 125 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.645A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.368A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 215 Processing helix chain '4' and resid 218 through 229 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: 4.600A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.774A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.072A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.202A 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: 3.878A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 4.103A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 137 removed outlier: 3.881A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.879A 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 26 through 44 removed outlier: 3.549A pdb=" N SER 6 44 " --> pdb=" O ALA 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 63 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 118 through 121 No H-bonds generated for 'chain '6' and resid 118 through 121' Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 42 removed outlier: 3.630A pdb=" N PHE 9 42 " --> pdb=" O LEU 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 144 through 147 Processing helix chain '9' and resid 151 through 172 removed outlier: 5.888A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.667A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.756A 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 32 Proline residue: H 12 - end of helix removed outlier: 3.617A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.689A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.768A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 removed outlier: 3.668A pdb=" N PHE J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.774A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 65 through 73 Processing helix chain 'J' and resid 86 through 89 No H-bonds generated for 'chain 'J' and resid 86 through 89' Processing helix chain 'J' and resid 91 through 106 Processing helix chain 'J' and resid 110 through 116 removed outlier: 3.798A pdb=" N GLU J 114 " --> pdb=" O ASP J 110 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.265A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 84 removed outlier: 3.785A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.891A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.761A 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: 4.055A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.751A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.931A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.805A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.936A 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: 4.022A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.790A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) removed outlier: 4.132A 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 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.826A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.380A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 389 No H-bonds generated for 'chain 'L' and resid 387 through 389' Processing helix chain 'L' and resid 392 through 399 Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.773A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.982A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.687A 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 509 removed outlier: 4.049A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 542 Proline residue: L 530 - end of helix removed outlier: 4.298A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix Processing helix chain 'L' and resid 550 through 553 No H-bonds generated for 'chain 'L' and resid 550 through 553' Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 565 through 577 Processing helix chain 'L' and resid 584 through 598 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.145A 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: 4.213A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.721A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.743A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.782A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.599A 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 155 removed outlier: 4.499A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 170 removed outlier: 3.657A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) 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: 5.033A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 250 removed outlier: 4.681A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 266 removed outlier: 5.633A pdb=" N TYR M 259 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix Processing helix chain 'M' and resid 268 through 278 removed outlier: 3.779A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.217A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.063A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.535A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.258A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.356A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.503A 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 167 Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.234A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 252 removed outlier: 3.913A pdb=" N LEU N 243 " --> pdb=" O ILE N 239 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU N 245 " --> pdb=" O THR N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 301 Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.611A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.892A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 98 Processing helix chain 'V' and resid 110 through 130 Processing helix chain 'W' and resid 17 through 45 removed outlier: 4.677A 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: 3.817A 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 21 removed outlier: 3.557A pdb=" N LEU X 21 " --> pdb=" O TYR X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 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 76 removed outlier: 4.547A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU Y 68 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.641A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 120 removed outlier: 3.781A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 removed outlier: 3.891A pdb=" N ALA Z 172 " --> pdb=" O ALA Z 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 45 No H-bonds generated for 'chain 'a' and resid 43 through 45' Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.694A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.719A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 removed outlier: 3.613A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 28 through 31 No H-bonds generated for 'chain 'c' and resid 28 through 31' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.415A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 29 through 41 removed outlier: 4.043A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 4.763A 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 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 318 removed outlier: 5.296A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 46 removed outlier: 4.021A pdb=" N TYR e 40 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL e 41 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU e 42 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU e 43 " --> 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: 4.443A 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: 4.087A 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 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.746A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'i' and resid 2 through 16 Processing helix chain 'i' and resid 20 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: 4.062A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.666A 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 82 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 44 removed outlier: 4.296A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 141 removed outlier: 3.761A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.460A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 4.086A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 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 272 through 274 No H-bonds generated for 'chain 'k' and resid 272 through 274' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 306 through 308 No H-bonds generated for 'chain 'k' and resid 306 through 308' Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' 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 48 through 54 removed outlier: 3.863A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.615A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 49 through 52 Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 2 through 7 removed outlier: 3.629A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 17 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.879A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 50 removed outlier: 4.041A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 83 through 92 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 removed outlier: 3.508A pdb=" N PHE q 35 " --> pdb=" O GLY q 31 " (cutoff:3.500A) Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 124 Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 96 Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 4.286A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.470A 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 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 70 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 3.859A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (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 46 Processing helix chain 'y' and resid 11 through 33 removed outlier: 3.644A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.413A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU y 32 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.724A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 4.096A 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 55 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.986A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 5.970A 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: 6.668A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.591A 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 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.587A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.213A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 removed outlier: 6.311A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.799A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 47 through 51 removed outlier: 6.605A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 6.049A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.672A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= V, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.274A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.915A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.606A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.382A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2691 hydrogen bonds defined for protein. 7539 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: 21.12 Time building geometry restraints manager: 24.96 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: 27968 1.43 - 1.66: 39130 1.66 - 1.90: 756 1.90 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 67934 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.600 0.233 3.80e-02 6.93e+02 3.76e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.336 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.00e-02 1.00e+04 3.30e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.337 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.16e+01 ... (remaining 67929 not shown) Histogram of bond angle deviations from ideal: 62.00 - 77.52: 72 77.52 - 93.03: 8 93.03 - 108.55: 4902 108.55 - 124.06: 84859 124.06 - 139.57: 2046 Bond angle restraints: 91887 Sorted by residual: angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 133.12 -25.38 1.95e+00 2.62e-01 1.69e+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 89.64 14.69 1.14e+00 7.69e-01 1.66e+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 89.75 14.58 1.20e+00 6.94e-01 1.48e+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 91.55 12.78 1.14e+00 7.69e-01 1.26e+02 angle pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " pdb="FE2 FES 3 803 " ideal model delta sigma weight residual 75.66 88.10 -12.44 1.14e+00 7.69e-01 1.19e+02 ... (remaining 91882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 40334 33.79 - 67.58: 531 67.58 - 101.36: 46 101.36 - 135.15: 4 135.15 - 168.94: 2 Dihedral angle restraints: 40917 sinusoidal: 17402 harmonic: 23515 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -132.21 -47.79 0 5.00e+00 4.00e-02 9.14e+01 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 -133.12 -46.88 0 5.00e+00 4.00e-02 8.79e+01 dihedral pdb=" CA LEU N 302 " pdb=" C LEU N 302 " pdb=" N THR N 303 " pdb=" CA THR N 303 " ideal model delta harmonic sigma weight residual 180.00 -135.46 -44.54 0 5.00e+00 4.00e-02 7.93e+01 ... (remaining 40914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.230: 9962 4.230 - 8.460: 4 8.460 - 12.690: 0 12.690 - 16.920: 0 16.920 - 21.150: 24 Chirality restraints: 9990 Sorted by residual: chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.15 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " 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="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 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9987 not shown) Planarity restraints: 11497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.023 2.00e-02 2.50e+03 3.18e-02 2.03e+01 pdb=" CG TYR 9 40 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.037 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR 6 125 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.028 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP 1 371 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.000 2.00e-02 2.50e+03 ... (remaining 11494 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 17370 2.80 - 3.39: 71197 3.39 - 3.97: 136073 3.97 - 4.56: 190821 4.56 - 5.14: 278742 Nonbonded interactions: 694203 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASP g 116 " pdb=" OG SER g 119 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR d 22 " pdb=" OG SER d 88 " model vdw 2.263 2.440 nonbonded pdb=" OG SER L 545 " pdb=" O SER M 274 " model vdw 2.270 2.440 nonbonded pdb=" OE2 GLU 4 224 " pdb=" OH TYR 9 40 " model vdw 2.270 2.440 ... (remaining 694198 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 34 5.49 5 S 464 5.16 5 C 42876 2.51 5 N 11018 2.21 5 O 11872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 7.150 Check model and map are aligned: 0.780 Process input model: 158.710 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.660 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 0.233 67934 Z= 0.464 Angle : 0.986 25.383 91887 Z= 0.530 Chirality : 1.032 21.150 9990 Planarity : 0.008 0.067 11497 Dihedral : 11.500 168.941 25726 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.08 % 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: -3.09 (0.08), residues: 7950 helix: -2.01 (0.06), residues: 4139 sheet: -1.71 (0.24), residues: 366 loop : -1.98 (0.09), residues: 3445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2052 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2045 time to evaluate : 6.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 2050 average time/residue: 0.7297 time to fit residues: 2422.0464 Evaluate side-chains 1340 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1336 time to evaluate : 6.160 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.7076 time to fit residues: 12.7698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 5.9990 chunk 595 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 401 optimal weight: 8.9990 chunk 318 optimal weight: 0.9980 chunk 616 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 374 optimal weight: 0.0170 chunk 458 optimal weight: 2.9990 chunk 713 optimal weight: 5.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 250 ASN 1 373 ASN 1 437 HIS 2 74 GLN 2 101 GLN ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 277 GLN 3 430 GLN 3 459 GLN 3 461 ASN 3 546 GLN 3 665 GLN 4 79 HIS ** 4 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 149 ASN 4 150 HIS 4 252 ASN 4 409 HIS 5 71 GLN 5 160 HIS 6 106 GLN 9 23 GLN A 26 GLN H 287 HIS H 292 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS L 175 ASN L 194 ASN ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN L 471 ASN L 546 GLN L 580 GLN M 44 GLN M 139 GLN M 279 GLN N 77 ASN N 222 ASN W 124 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 HIS Y 105 GLN Y 142 HIS Z 90 GLN Z 106 GLN Z 114 GLN ** Z 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 143 HIS b 36 ASN c 99 ASN c 121 ASN d 87 HIS d 115 GLN e 80 ASN f 49 GLN g 44 ASN g 125 HIS i 123 GLN k 107 GLN k 180 GLN k 204 ASN ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 ASN p 49 GLN q 60 GLN r 125 GLN ** s 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 72 HIS v 56 GLN v 66 HIS ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 10 HIS z 44 GLN z 68 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.286 67934 Z= 0.587 Angle : 1.585 50.994 91887 Z= 1.024 Chirality : 0.313 6.595 9990 Planarity : 0.005 0.054 11497 Dihedral : 10.616 166.780 9733 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -1.41 (0.09), residues: 7950 helix: -0.43 (0.07), residues: 4169 sheet: -1.27 (0.25), residues: 364 loop : -1.45 (0.10), residues: 3417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1528 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1405 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 87 residues processed: 1474 average time/residue: 0.6959 time to fit residues: 1713.6287 Evaluate side-chains 1369 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1282 time to evaluate : 6.137 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.5241 time to fit residues: 94.5034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 594 optimal weight: 8.9990 chunk 486 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 715 optimal weight: 50.0000 chunk 772 optimal weight: 7.9990 chunk 636 optimal weight: 20.0000 chunk 709 optimal weight: 0.5980 chunk 243 optimal weight: 10.0000 chunk 573 optimal weight: 0.9980 overall best weight: 5.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 250 ASN 2 37 ASN 2 214 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 ASN 3 546 GLN ** 4 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 280 GLN 5 21 GLN 5 71 GLN 5 211 GLN 9 23 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN L 248 HIS L 348 HIS L 446 ASN L 471 ASN M 103 GLN N 144 GLN W 124 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Y 105 GLN Z 123 ASN ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 121 ASN f 20 HIS f 75 GLN g 98 GLN i 69 ASN k 184 GLN ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 72 HIS ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 HIS ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.291 67934 Z= 0.592 Angle : 1.589 51.048 91887 Z= 1.025 Chirality : 0.314 6.660 9990 Planarity : 0.005 0.055 11497 Dihedral : 10.229 166.853 9733 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.58 % Favored : 96.40 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -0.67 (0.09), residues: 7950 helix: 0.19 (0.08), residues: 4184 sheet: -0.93 (0.25), residues: 379 loop : -1.09 (0.10), residues: 3387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1338 time to evaluate : 7.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 62 residues processed: 1391 average time/residue: 0.7078 time to fit residues: 1665.0325 Evaluate side-chains 1320 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1258 time to evaluate : 6.172 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5194 time to fit residues: 69.3113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 3.9990 chunk 537 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 341 optimal weight: 40.0000 chunk 480 optimal weight: 9.9990 chunk 717 optimal weight: 20.0000 chunk 759 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 680 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 214 GLN 3 237 ASN 3 311 GLN 3 461 ASN 4 5 GLN 4 313 GLN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN 5 71 GLN 9 23 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN L 170 GLN L 194 ASN L 471 ASN N 144 GLN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Y 105 GLN Z 123 ASN ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN r 125 GLN s 42 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 72 HIS t 77 GLN v 72 ASN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 ASN z 68 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.277 67934 Z= 0.594 Angle : 1.589 51.176 91887 Z= 1.025 Chirality : 0.314 6.618 9990 Planarity : 0.005 0.057 11497 Dihedral : 10.124 167.333 9733 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -0.34 (0.09), residues: 7950 helix: 0.43 (0.08), residues: 4175 sheet: -0.85 (0.25), residues: 387 loop : -0.90 (0.11), residues: 3388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1289 time to evaluate : 6.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 66 residues processed: 1345 average time/residue: 0.7059 time to fit residues: 1613.3691 Evaluate side-chains 1311 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1245 time to evaluate : 6.137 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.5510 time to fit residues: 75.2435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 20.0000 chunk 431 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 565 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 648 optimal weight: 9.9990 chunk 525 optimal weight: 0.0980 chunk 0 optimal weight: 50.0000 chunk 387 optimal weight: 20.0000 chunk 681 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 214 GLN 3 311 GLN 3 336 ASN 3 437 HIS 3 461 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN 5 71 GLN 9 23 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN L 170 GLN L 194 ASN L 471 ASN N 144 GLN W 95 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Y 105 GLN ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 45 ASN p 47 GLN p 49 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 25 HIS t 72 HIS ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 HIS v 72 ASN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.287 67934 Z= 0.599 Angle : 1.590 51.085 91887 Z= 1.026 Chirality : 0.314 6.680 9990 Planarity : 0.005 0.054 11497 Dihedral : 10.101 167.616 9733 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -0.19 (0.09), residues: 7950 helix: 0.52 (0.08), residues: 4195 sheet: -0.77 (0.25), residues: 387 loop : -0.79 (0.11), residues: 3368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1276 time to evaluate : 6.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 57 residues processed: 1329 average time/residue: 0.6897 time to fit residues: 1548.0225 Evaluate side-chains 1283 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1226 time to evaluate : 6.258 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.5475 time to fit residues: 66.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 9.9990 chunk 684 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 446 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 760 optimal weight: 0.6980 chunk 631 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 399 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 373 ASN 2 74 GLN 3 311 GLN 3 313 ASN 3 401 HIS 3 461 ASN ** 4 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN 5 71 GLN 9 23 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN L 194 ASN L 471 ASN L 570 GLN N 144 GLN ** N 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 30 HIS Y 39 ASN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 72 HIS t 77 GLN v 72 ASN ** v 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 136 ASN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.290 67934 Z= 0.583 Angle : 1.583 51.144 91887 Z= 1.023 Chirality : 0.314 6.660 9990 Planarity : 0.005 0.052 11497 Dihedral : 9.979 167.425 9733 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.09), residues: 7950 helix: 0.65 (0.08), residues: 4195 sheet: -0.69 (0.26), residues: 389 loop : -0.69 (0.11), residues: 3366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1277 time to evaluate : 6.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 50 residues processed: 1319 average time/residue: 0.7010 time to fit residues: 1558.9765 Evaluate side-chains 1275 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1225 time to evaluate : 6.159 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.5379 time to fit residues: 58.2533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 433 optimal weight: 2.9990 chunk 555 optimal weight: 8.9990 chunk 430 optimal weight: 3.9990 chunk 640 optimal weight: 10.0000 chunk 424 optimal weight: 0.3980 chunk 757 optimal weight: 0.2980 chunk 474 optimal weight: 20.0000 chunk 461 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 214 GLN 3 311 GLN 3 313 ASN 3 461 ASN ** 4 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 71 GLN 6 82 GLN 9 23 GLN A 83 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN L 194 ASN L 296 ASN L 323 HIS L 471 ASN M 366 ASN N 144 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN p 49 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 72 HIS v 72 ASN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.280 67934 Z= 0.560 Angle : 1.568 51.078 91887 Z= 1.018 Chirality : 0.312 6.584 9990 Planarity : 0.004 0.046 11497 Dihedral : 9.628 166.792 9733 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.10), residues: 7950 helix: 0.85 (0.08), residues: 4180 sheet: -0.62 (0.26), residues: 396 loop : -0.52 (0.11), residues: 3374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1283 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 1309 average time/residue: 0.7109 time to fit residues: 1577.3438 Evaluate side-chains 1263 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1232 time to evaluate : 6.190 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5562 time to fit residues: 40.3128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 452 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 481 optimal weight: 20.0000 chunk 516 optimal weight: 5.9990 chunk 374 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 595 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 356 HIS 2 74 GLN 2 214 GLN 3 311 GLN 3 461 ASN ** 3 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 23 GLN H 317 GLN L 471 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN g 98 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS v 72 ASN v 126 GLN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.278 67934 Z= 0.574 Angle : 1.576 50.942 91887 Z= 1.020 Chirality : 0.314 6.627 9990 Planarity : 0.004 0.047 11497 Dihedral : 9.580 166.795 9733 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.10), residues: 7950 helix: 0.88 (0.08), residues: 4176 sheet: -0.57 (0.26), residues: 391 loop : -0.51 (0.11), residues: 3383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1261 time to evaluate : 6.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 38 residues processed: 1288 average time/residue: 0.7063 time to fit residues: 1531.4978 Evaluate side-chains 1259 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1221 time to evaluate : 6.199 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.5183 time to fit residues: 45.3614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 0.0050 chunk 725 optimal weight: 30.0000 chunk 662 optimal weight: 1.9990 chunk 705 optimal weight: 7.9990 chunk 424 optimal weight: 1.9990 chunk 307 optimal weight: 9.9990 chunk 554 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 637 optimal weight: 10.0000 chunk 667 optimal weight: 8.9990 chunk 703 optimal weight: 10.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 461 ASN ** 4 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN 9 23 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN i 123 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 49 GLN r 25 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS v 72 ASN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 HIS z 68 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.274 67934 Z= 0.559 Angle : 1.568 50.876 91887 Z= 1.017 Chirality : 0.313 6.585 9990 Planarity : 0.004 0.056 11497 Dihedral : 9.340 166.426 9733 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7950 helix: 0.98 (0.08), residues: 4176 sheet: -0.45 (0.26), residues: 388 loop : -0.43 (0.11), residues: 3386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1266 time to evaluate : 6.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 1272 average time/residue: 0.7106 time to fit residues: 1525.2028 Evaluate side-chains 1221 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1210 time to evaluate : 6.262 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5772 time to fit residues: 20.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 20.0000 chunk 746 optimal weight: 8.9990 chunk 455 optimal weight: 20.0000 chunk 354 optimal weight: 2.9990 chunk 518 optimal weight: 9.9990 chunk 783 optimal weight: 9.9990 chunk 720 optimal weight: 8.9990 chunk 623 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 481 optimal weight: 6.9990 chunk 382 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 250 ASN 2 74 GLN 3 461 ASN 3 644 GLN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 23 GLN H 99 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN K 52 HIS ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN M 374 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN e 61 GLN h 24 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS ** t 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 ASN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN z 68 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.289 67934 Z= 0.622 Angle : 1.604 50.969 91887 Z= 1.031 Chirality : 0.315 6.742 9990 Planarity : 0.005 0.053 11497 Dihedral : 9.716 167.396 9733 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.09), residues: 7950 helix: 0.76 (0.08), residues: 4192 sheet: -0.52 (0.26), residues: 390 loop : -0.53 (0.11), residues: 3368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1234 time to evaluate : 6.281 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 1251 average time/residue: 0.7091 time to fit residues: 1496.0670 Evaluate side-chains 1249 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1221 time to evaluate : 6.240 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5328 time to fit residues: 36.3409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 5.9990 chunk 664 optimal weight: 40.0000 chunk 191 optimal weight: 6.9990 chunk 574 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 624 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 641 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 461 ASN ** 4 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 71 GLN 9 23 GLN H 99 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN ** k 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN p 49 GLN ** s 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS ** t 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 ASN v 136 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120235 restraints weight = 88370.471| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.55 r_work: 0.3208 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.281 67934 Z= 0.578 Angle : 1.584 50.995 91887 Z= 1.023 Chirality : 0.314 6.656 9990 Planarity : 0.004 0.055 11497 Dihedral : 9.544 166.896 9733 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 7950 helix: 0.85 (0.08), residues: 4188 sheet: -0.52 (0.26), residues: 390 loop : -0.47 (0.11), residues: 3372 =============================================================================== Job complete usr+sys time: 22917.08 seconds wall clock time: 399 minutes 31.89 seconds (23971.89 seconds total)