Starting phenix.real_space_refine (version: dev) on Sun Feb 26 11:30:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkd_11245/02_2023/6zkd_11245_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 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 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "9 TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "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 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 67450 Number of models: 1 Model: "" Number of chains: 71 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: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} 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: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2498 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 291} Chain breaks: 1 Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1294 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "H" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'DCQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 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 1 365 103.897 54.585 240.865 1.00 26.99 S ATOM 2695 SG CYS 1 362 106.089 54.728 235.434 1.00 40.14 S ATOM 2676 SG CYS 1 359 110.838 55.057 241.230 1.00 42.93 S ATOM 3039 SG CYS 1 405 107.386 48.809 239.865 1.00 37.41 S ATOM 4116 SG CYS 2 103 102.057 49.708 259.711 1.00 47.65 S ATOM 4150 SG CYS 2 108 100.108 47.218 261.892 1.00 64.06 S ATOM 4430 SG CYS 2 144 103.554 46.104 256.038 1.00 61.98 S ATOM 4453 SG CYS 2 148 101.742 43.274 257.558 1.00 57.10 S ATOM 5793 SG CYS 3 114 106.194 72.916 225.922 1.00 32.51 S ATOM 5732 SG CYS 3 105 101.000 76.324 228.037 1.00 36.29 S ATOM 5753 SG CYS 3 108 107.247 77.938 229.526 1.00 21.92 S ATOM 6125 SG CYS 3 156 113.405 65.337 230.480 1.00 27.88 S ATOM 6102 SG CYS 3 153 111.406 68.289 236.181 1.00 28.57 S ATOM 6149 SG CYS 3 159 117.497 69.007 234.344 1.00 74.91 S ATOM 6479 SG CYS 3 203 113.416 71.471 230.602 1.00 29.84 S ATOM 5238 SG CYS 3 41 112.292 58.682 228.704 1.00 29.12 S ATOM 5324 SG CYS 3 52 108.551 59.972 227.996 1.00 32.22 S ATOM 5349 SG CYS 3 55 108.861 55.028 224.442 1.00 27.68 S ATOM 5450 SG CYS 3 69 112.440 55.003 225.767 1.00 31.26 S ATOM 16341 SG CYS 6 149 87.926 96.549 208.875 1.00 60.69 S ATOM 15607 SG CYS 6 54 84.310 96.465 203.254 1.00 82.29 S ATOM 17533 SG CYS 9 116 92.258 97.297 215.171 1.00 44.58 S ATOM 17580 SG CYS 9 122 92.913 92.911 219.865 1.00 27.48 S ATOM 17307 SG CYS 9 87 96.641 92.456 214.425 1.00 22.10 S ATOM 17609 SG CYS 9 126 95.151 89.440 227.115 1.00 15.33 S ATOM 17280 SG CYS 9 83 98.655 91.139 221.917 1.00 29.44 S ATOM 17238 SG CYS 9 77 100.882 92.698 227.697 1.00 39.82 S ATOM 17257 SG CYS 9 80 100.145 86.182 225.868 1.00 26.56 S ATOM 41181 SG CYS b 59 97.174 85.090 242.639 1.00 38.78 S ATOM 41359 SG CYS b 84 99.814 85.402 239.855 1.00 35.75 S ATOM 41381 SG CYS b 87 98.696 87.932 240.910 1.00 47.96 S Time building chain proxies: 28.86, per 1000 atoms: 0.43 Number of scatterers: 67450 At special positions: 0 Unit cell: (176.126, 201.59, 291.775, 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 466 16.00 P 46 15.00 O 12103 8.00 N 11149 7.00 C 43656 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=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.84 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " 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="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="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 6 300 " pdb="FE4 SF4 6 300 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 300 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 300 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 300 " - 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=" SF4 9 403 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " Number of angles added : 3 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 29 sheets defined 51.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.550A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 62 removed outlier: 3.668A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.719A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.905A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 107 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 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: 4.498A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 3.807A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 4.057A 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: 3.689A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.394A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.802A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.840A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 110 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 33 removed outlier: 3.889A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 123 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: 3.509A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 272 removed outlier: 5.345A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 309 removed outlier: 3.839A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 338 removed outlier: 3.760A pdb=" N VAL 3 338 " --> pdb=" O LEU 3 334 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 362 Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 4.332A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER 3 434 " --> pdb=" O ASP 3 431 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.852A 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 480 removed outlier: 3.613A pdb=" N SER 3 480 " --> pdb=" O LYS 3 476 " (cutoff:3.500A) Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 554 through 556 No H-bonds generated for 'chain '3' and resid 554 through 556' Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 631 removed outlier: 3.821A pdb=" N VAL 3 631 " --> pdb=" O PRO 3 628 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 628 through 631' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 671 Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.815A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.014A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix removed outlier: 4.045A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.553A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.035A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.899A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.639A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.676A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.028A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.779A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.984A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 138 removed outlier: 3.842A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 44 Processing helix chain '6' and resid 54 through 63 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 106 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.670A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.769A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.567A 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: 3.591A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.748A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.794A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' 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 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.725A pdb=" N ILE J 5 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.639A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.890A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.313A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.690A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.863A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.694A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.746A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.923A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.629A 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: 3.949A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.879A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.972A 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: 3.983A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.160A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.601A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.396A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.073A 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 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 399 removed outlier: 4.163A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.655A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.872A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.793A 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 508 removed outlier: 3.611A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 4.582A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 5.103A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.112A 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: 4.266A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.700A 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: 3.828A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.654A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.525A 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 171 removed outlier: 3.630A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.278A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (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: 4.994A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.031A 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 246 Processing helix chain 'M' and resid 254 through 266 removed outlier: 5.851A 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 277 removed outlier: 3.923A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.928A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.176A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' 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: 3.853A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.047A 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: 4.020A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.475A 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 171 removed outlier: 4.008A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 221 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.031A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.786A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (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 300 removed outlier: 3.762A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.634A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.789A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.502A 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: 3.681A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.654A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 74 removed outlier: 4.080A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Y 68 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.663A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 113 removed outlier: 4.344A pdb=" N ARG Y 100 " --> pdb=" O ARG Y 97 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS Y 101 " --> pdb=" O ARG Y 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU Y 102 " --> pdb=" O CYS Y 99 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN Y 103 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP Y 107 " --> pdb=" O ALA Y 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Y 110 " --> pdb=" O ASP Y 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP Y 112 " --> pdb=" O CYS Y 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Y 113 " --> pdb=" O VAL Y 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 3.944A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.420A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.612A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 46 removed outlier: 3.699A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU b 46 " --> pdb=" O ASP b 42 " (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 27 through 31 removed outlier: 4.241A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.393A 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 39 removed outlier: 3.845A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.470A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 318 removed outlier: 5.154A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 46 removed outlier: 4.803A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS e 38 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG e 39 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR e 40 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL e 41 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU e 42 " --> pdb=" O ARG e 39 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS e 45 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.183A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 64 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.864A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.117A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.487A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.568A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.746A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 83 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 44 removed outlier: 4.029A 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: 3.585A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.332A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.265A 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: 4.925A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 240 removed outlier: 3.536A pdb=" N TYR k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 253 through 263 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 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 48 through 54 removed outlier: 3.925A 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 87 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 5 through 14 Processing helix chain 'm' and resid 16 through 33 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.725A 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 18 through 20 No H-bonds generated for 'chain 'n' and resid 18 through 20' Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 48 through 51 Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' 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: 3.808A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 15 through 17 No H-bonds generated for 'chain 'p' and resid 15 through 17' Processing helix chain 'p' and resid 19 through 22 Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.900A 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 74 through 78 removed outlier: 3.633A pdb=" N ASN p 78 " --> pdb=" O ASN p 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 74 through 78' Processing helix chain 'p' and resid 83 through 91 Processing helix chain 'p' and resid 95 through 115 Processing helix chain 'q' and resid 31 through 96 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 'q' and resid 138 through 141 No H-bonds generated for 'chain 'q' and resid 138 through 141' 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 92 through 96 removed outlier: 4.300A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 140 removed outlier: 4.002A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.372A 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 45 through 48 No H-bonds generated for 'chain 'u' and resid 45 through 48' 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 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 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 69 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 4.058A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.711A 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 45 Processing helix chain 'y' and resid 11 through 34 removed outlier: 3.727A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU y 15 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.411A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU y 32 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 29 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing helix chain 'z' and resid 66 through 68 No H-bonds generated for 'chain 'z' and resid 66 through 68' Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.982A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 5.933A 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: 6.581A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 removed outlier: 6.273A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL 3 247 " --> pdb=" O ARG 3 243 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 282 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.760A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.993A 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: 8.051A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.720A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.718A 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: 6.455A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.462A 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: 5.878A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.444A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.430A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.796A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.434A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.470A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP k 173 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR k 223 " --> pdb=" O ASP k 173 " (cutoff:3.500A) 2797 hydrogen bonds defined for protein. 7755 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: 21.88 Time building geometry restraints manager: 24.84 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: 28346 1.43 - 1.66: 39914 1.66 - 1.89: 758 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69098 Sorted by residual: bond pdb=" C10 ZMP g 201 " pdb=" S1 ZMP g 201 " ideal model delta sigma weight residual 1.817 1.683 0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.594 0.239 3.80e-02 6.93e+02 3.96e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.326 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" OA3 CDL z 101 " pdb=" PA1 CDL z 101 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.00e-02 1.00e+04 3.60e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.00e-02 1.00e+04 3.52e+01 ... (remaining 69093 not shown) Histogram of bond angle deviations from ideal: 62.31 - 77.27: 74 77.27 - 92.22: 8 92.22 - 107.18: 3255 107.18 - 122.13: 78182 122.13 - 137.09: 11857 Bond angle restraints: 93376 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 72.13 48.47 3.00e+00 1.11e-01 2.61e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 71.19 38.11 3.00e+00 1.11e-01 1.61e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.29 -23.55 1.95e+00 2.62e-01 1.45e+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 91.67 12.66 1.14e+00 7.69e-01 1.23e+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 91.91 12.42 1.14e+00 7.69e-01 1.19e+02 ... (remaining 93371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 40921 33.74 - 67.49: 654 67.49 - 101.23: 43 101.23 - 134.97: 2 134.97 - 168.71: 4 Dihedral angle restraints: 41624 sinusoidal: 17854 harmonic: 23770 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 -131.49 -48.51 0 5.00e+00 4.00e-02 9.41e+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 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" C10 FMN 1 502 " pdb=" C1' FMN 1 502 " pdb=" N10 FMN 1 502 " pdb=" C2' FMN 1 502 " ideal model delta sinusoidal sigma weight residual 257.59 88.88 168.71 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 41621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.228: 10083 4.228 - 8.456: 5 8.456 - 12.683: 0 12.683 - 16.911: 0 16.911 - 21.139: 24 Chirality restraints: 10112 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 -10.58 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S3 SF4 3 802 " pdb=" S4 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.13 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10109 not shown) Planarity restraints: 11640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " -0.049 2.00e-02 2.50e+03 9.25e-02 2.57e+02 pdb=" C1M DCQ H 501 " -0.084 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.028 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " -0.024 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.026 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " 0.037 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " 0.188 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " -0.060 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " 0.194 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " -0.084 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.022 2.00e-02 2.50e+03 3.47e-02 2.41e+01 pdb=" CG TYR 9 40 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.039 2.00e-02 2.50e+03 3.31e-02 2.19e+01 pdb=" CG TYR 6 125 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.000 2.00e-02 2.50e+03 ... (remaining 11637 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.78: 15633 2.78 - 3.37: 73154 3.37 - 3.96: 141864 3.96 - 4.55: 198588 4.55 - 5.14: 288136 Nonbonded interactions: 717375 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.196 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR v 47 " pdb=" O MET v 77 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR d 22 " pdb=" OG SER d 88 " model vdw 2.265 2.440 nonbonded pdb=" O ALA L 245 " pdb=" OG SER L 249 " model vdw 2.267 2.440 ... (remaining 717370 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 46 5.49 5 S 466 5.16 5 C 43656 2.51 5 N 11149 2.21 5 O 12103 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 7.630 Check model and map are aligned: 0.920 Process input model: 157.120 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.460 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.239 69098 Z= 0.520 Angle : 1.023 48.475 93376 Z= 0.542 Chirality : 1.027 21.139 10112 Planarity : 0.008 0.092 11640 Dihedral : 11.895 168.713 26273 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.08), residues: 8039 helix: -1.80 (0.06), residues: 4264 sheet: -1.36 (0.24), residues: 381 loop : -1.60 (0.10), residues: 3394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1667 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1663 time to evaluate : 6.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 1667 average time/residue: 1.6785 time to fit residues: 3591.5022 Evaluate side-chains 1045 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1042 time to evaluate : 6.201 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 8.2358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 7.9990 chunk 602 optimal weight: 10.0000 chunk 334 optimal weight: 30.0000 chunk 205 optimal weight: 9.9990 chunk 406 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 623 optimal weight: 20.0000 chunk 241 optimal weight: 3.9990 chunk 378 optimal weight: 30.0000 chunk 463 optimal weight: 6.9990 chunk 721 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 3 179 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 437 HIS ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 79 HIS 4 149 ASN 4 252 ASN 4 313 GLN 5 211 GLN 6 82 GLN 9 65 HIS A 83 ASN H 194 ASN J 78 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 52 HIS L 25 ASN L 27 HIS L 116 GLN L 135 ASN L 199 GLN L 248 HIS L 323 HIS ** L 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN L 570 GLN M 81 GLN M 83 HIS M 175 ASN M 333 ASN M 366 ASN N 120 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 HIS ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Y 72 GLN Y 142 HIS Z 90 GLN Z 106 GLN Z 114 GLN Z 120 HIS Z 123 ASN a 35 ASN a 55 ASN b 36 ASN d 36 ASN d 103 ASN e 30 GLN f 72 GLN g 125 HIS h 24 GLN h 50 ASN i 12 GLN i 69 ASN i 91 HIS i 122 GLN k 2 GLN k 89 ASN l 97 HIS m 10 ASN o 61 GLN p 47 GLN p 116 GLN q 89 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN s 49 GLN s 109 GLN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN w 57 ASN y 13 HIS y 30 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.283 69098 Z= 0.609 Angle : 1.594 50.931 93376 Z= 1.025 Chirality : 0.311 6.497 10112 Planarity : 0.006 0.069 11640 Dihedral : 11.551 170.994 10140 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.84 (0.09), residues: 8039 helix: -0.12 (0.07), residues: 4273 sheet: -1.09 (0.24), residues: 402 loop : -0.92 (0.10), residues: 3364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1096 time to evaluate : 6.537 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 outliers start: 205 outliers final: 58 residues processed: 1200 average time/residue: 1.5817 time to fit residues: 2465.7177 Evaluate side-chains 1060 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1002 time to evaluate : 6.141 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 32 residues processed: 27 average time/residue: 0.9558 time to fit residues: 46.5420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 600 optimal weight: 9.9990 chunk 491 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 723 optimal weight: 20.0000 chunk 781 optimal weight: 9.9990 chunk 644 optimal weight: 6.9990 chunk 717 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 580 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 250 ASN 3 16 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN A 83 ASN K 50 ASN K 83 ASN L 175 ASN L 442 ASN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN a 35 ASN a 40 ASN b 94 GLN b 95 HIS d 87 HIS e 30 GLN f 72 GLN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 2 GLN l 20 GLN n 32 GLN o 61 GLN p 47 GLN p 78 ASN p 116 GLN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.246 69098 Z= 0.531 Angle : 1.562 50.733 93376 Z= 1.012 Chirality : 0.312 6.446 10112 Planarity : 0.004 0.055 11640 Dihedral : 10.990 170.587 10140 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.05 (0.09), residues: 8039 helix: 0.56 (0.08), residues: 4286 sheet: -0.85 (0.25), residues: 382 loop : -0.59 (0.11), residues: 3371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1056 time to evaluate : 6.191 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: 187 outliers final: 67 residues processed: 1154 average time/residue: 1.6096 time to fit residues: 2417.9032 Evaluate side-chains 1053 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 986 time to evaluate : 6.209 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 39 residues processed: 28 average time/residue: 0.9629 time to fit residues: 48.4999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 20.0000 chunk 543 optimal weight: 4.9990 chunk 375 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 485 optimal weight: 9.9990 chunk 725 optimal weight: 5.9990 chunk 768 optimal weight: 0.0020 chunk 379 optimal weight: 7.9990 chunk 687 optimal weight: 50.0000 chunk 207 optimal weight: 10.0000 overall best weight: 5.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 535 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN K 7 ASN K 50 ASN M 415 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Y 72 GLN b 95 HIS e 30 GLN k 2 GLN k 200 GLN n 32 GLN p 47 GLN p 78 ASN p 125 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN y 30 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 69098 Z= 0.560 Angle : 1.571 50.711 93376 Z= 1.015 Chirality : 0.312 6.476 10112 Planarity : 0.005 0.056 11640 Dihedral : 10.791 170.254 10140 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 8039 helix: 0.87 (0.08), residues: 4278 sheet: -0.73 (0.24), residues: 394 loop : -0.40 (0.11), residues: 3367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1024 time to evaluate : 6.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 83 residues processed: 1140 average time/residue: 1.6353 time to fit residues: 2431.6844 Evaluate side-chains 1064 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 981 time to evaluate : 6.189 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 52 residues processed: 32 average time/residue: 0.9277 time to fit residues: 53.1241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 572 optimal weight: 0.1980 chunk 317 optimal weight: 10.0000 chunk 655 optimal weight: 20.0000 chunk 531 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 392 optimal weight: 2.9990 chunk 689 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN K 50 ASN L 296 ASN N 49 ASN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN a 35 ASN e 30 GLN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 HIS k 2 GLN p 47 GLN p 78 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN t 77 GLN v 137 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69098 Z= 0.534 Angle : 1.560 50.677 93376 Z= 1.011 Chirality : 0.311 6.437 10112 Planarity : 0.004 0.052 11640 Dihedral : 10.569 170.018 10140 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.54 (0.09), residues: 8039 helix: 1.04 (0.08), residues: 4277 sheet: -0.63 (0.25), residues: 393 loop : -0.29 (0.11), residues: 3369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1040 time to evaluate : 6.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 74 residues processed: 1145 average time/residue: 1.6123 time to fit residues: 2418.8119 Evaluate side-chains 1069 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 995 time to evaluate : 6.219 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 53 residues processed: 21 average time/residue: 0.7715 time to fit residues: 34.9217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 20.0000 chunk 692 optimal weight: 30.0000 chunk 151 optimal weight: 10.0000 chunk 451 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 769 optimal weight: 20.0000 chunk 638 optimal weight: 20.0000 chunk 356 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 254 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 535 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN K 50 ASN L 471 ASN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN a 35 ASN d 321 HIS e 30 GLN e 80 ASN k 2 GLN p 78 ASN q 53 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN v 137 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.243 69098 Z= 0.570 Angle : 1.574 50.702 93376 Z= 1.016 Chirality : 0.312 6.478 10112 Planarity : 0.005 0.054 11640 Dihedral : 10.607 170.095 10140 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.59 (0.09), residues: 8039 helix: 1.07 (0.08), residues: 4280 sheet: -0.57 (0.25), residues: 390 loop : -0.25 (0.11), residues: 3369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1010 time to evaluate : 6.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 200 outliers final: 93 residues processed: 1127 average time/residue: 1.6284 time to fit residues: 2407.4406 Evaluate side-chains 1063 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 970 time to evaluate : 6.187 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 68 residues processed: 25 average time/residue: 0.7927 time to fit residues: 40.1088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 438 optimal weight: 40.0000 chunk 561 optimal weight: 8.9990 chunk 435 optimal weight: 20.0000 chunk 647 optimal weight: 20.0000 chunk 429 optimal weight: 5.9990 chunk 766 optimal weight: 30.0000 chunk 479 optimal weight: 6.9990 chunk 467 optimal weight: 30.0000 chunk 353 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 144 HIS A 83 ASN L 170 GLN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 72 GLN a 35 ASN d 296 HIS e 30 GLN f 49 GLN i 122 GLN k 2 GLN l 26 HIS p 78 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN v 137 ASN x 34 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69098 Z= 0.598 Angle : 1.586 50.738 93376 Z= 1.021 Chirality : 0.313 6.510 10112 Planarity : 0.005 0.059 11640 Dihedral : 10.713 170.274 10140 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.55 (0.09), residues: 8039 helix: 1.02 (0.08), residues: 4281 sheet: -0.57 (0.25), residues: 387 loop : -0.26 (0.11), residues: 3371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1003 time to evaluate : 6.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 105 residues processed: 1119 average time/residue: 1.6358 time to fit residues: 2403.6336 Evaluate side-chains 1063 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 958 time to evaluate : 6.292 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 77 residues processed: 28 average time/residue: 0.9177 time to fit residues: 47.9545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 457 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 487 optimal weight: 8.9990 chunk 522 optimal weight: 3.9990 chunk 378 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 602 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 64 GLN Y 72 GLN a 40 ASN e 30 GLN k 2 GLN l 26 HIS p 74 ASN p 78 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN v 66 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69098 Z= 0.543 Angle : 1.571 50.721 93376 Z= 1.015 Chirality : 0.312 6.466 10112 Planarity : 0.004 0.055 11640 Dihedral : 10.556 170.213 10140 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.66 (0.09), residues: 8039 helix: 1.10 (0.08), residues: 4281 sheet: -0.54 (0.25), residues: 388 loop : -0.19 (0.11), residues: 3370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 996 time to evaluate : 6.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 86 residues processed: 1100 average time/residue: 1.6133 time to fit residues: 2333.3623 Evaluate side-chains 1042 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 956 time to evaluate : 6.179 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 73 residues processed: 13 average time/residue: 1.1010 time to fit residues: 29.0522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.0570 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 5.9990 chunk 714 optimal weight: 7.9990 chunk 733 optimal weight: 30.0000 chunk 429 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 645 optimal weight: 9.9990 chunk 675 optimal weight: 5.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 72 GLN a 40 ASN e 30 GLN k 2 GLN l 26 HIS p 74 ASN p 78 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN w 86 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 69098 Z= 0.552 Angle : 1.574 50.712 93376 Z= 1.016 Chirality : 0.312 6.452 10112 Planarity : 0.004 0.053 11640 Dihedral : 10.463 169.798 10140 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.68 (0.09), residues: 8039 helix: 1.11 (0.08), residues: 4285 sheet: -0.52 (0.25), residues: 388 loop : -0.16 (0.11), residues: 3366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 981 time to evaluate : 6.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 85 residues processed: 1074 average time/residue: 1.5992 time to fit residues: 2264.6795 Evaluate side-chains 1038 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 953 time to evaluate : 6.221 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 72 residues processed: 13 average time/residue: 1.0613 time to fit residues: 28.5669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 20.0000 chunk 468 optimal weight: 30.0000 chunk 755 optimal weight: 8.9990 chunk 460 optimal weight: 6.9990 chunk 358 optimal weight: 9.9990 chunk 524 optimal weight: 0.9990 chunk 792 optimal weight: 8.9990 chunk 728 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 487 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 441 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN M 139 GLN N 235 ASN Y 64 GLN Y 72 GLN e 30 GLN k 2 GLN p 78 ASN p 116 GLN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.243 69098 Z= 0.572 Angle : 1.583 50.729 93376 Z= 1.019 Chirality : 0.313 6.471 10112 Planarity : 0.005 0.054 11640 Dihedral : 10.473 169.938 10140 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.64 (0.09), residues: 8039 helix: 1.06 (0.08), residues: 4286 sheet: -0.54 (0.25), residues: 391 loop : -0.17 (0.11), residues: 3362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 958 time to evaluate : 6.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 84 residues processed: 1046 average time/residue: 1.6736 time to fit residues: 2307.3336 Evaluate side-chains 1029 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 945 time to evaluate : 6.237 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 73 residues processed: 12 average time/residue: 1.1296 time to fit residues: 28.2137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 7.9990 chunk 500 optimal weight: 6.9990 chunk 671 optimal weight: 8.9990 chunk 193 optimal weight: 0.0060 chunk 581 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 631 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 648 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN N 235 ASN Y 72 GLN a 40 ASN e 30 GLN k 2 GLN p 78 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN v 28 ASN v 104 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078846 restraints weight = 100878.407| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.38 r_work: 0.2964 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 69098 Z= 0.551 Angle : 1.576 50.713 93376 Z= 1.016 Chirality : 0.312 6.447 10112 Planarity : 0.004 0.052 11640 Dihedral : 10.393 169.867 10140 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.70 (0.09), residues: 8039 helix: 1.10 (0.08), residues: 4283 sheet: -0.52 (0.25), residues: 389 loop : -0.12 (0.11), residues: 3367 =============================================================================== Job complete usr+sys time: 31744.51 seconds wall clock time: 549 minutes 15.42 seconds (32955.42 seconds total)