Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 02:42:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zki_11250/04_2023/6zki_11250_updated.pdb" } resolution = 2.8 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= 0.002 sd= 0.025 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 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 465 5.16 5 C 43676 2.51 5 N 11156 2.21 5 O 12106 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 81": "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 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "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 ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 80": "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 "b TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "v TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67479 Number of models: 1 Model: "" Number of chains: 70 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3427 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 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: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {'3PE': 1, 'DCQ': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'3PE': 3, 'CDL': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 74 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "o" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 196 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "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 1 365 102.710 53.898 241.637 1.00 19.58 S ATOM 2695 SG CYS 1 362 105.034 54.077 236.373 1.00 30.42 S ATOM 2676 SG CYS 1 359 109.733 54.261 242.343 1.00 33.21 S ATOM 3039 SG CYS 1 405 106.280 48.148 240.734 1.00 27.69 S ATOM 4116 SG CYS 2 103 100.312 48.913 260.410 1.00 54.64 S ATOM 4150 SG CYS 2 108 98.142 46.511 262.483 1.00 40.39 S ATOM 4430 SG CYS 2 144 101.894 45.302 256.895 1.00 59.08 S ATOM 4453 SG CYS 2 148 99.956 42.447 258.366 1.00 47.22 S ATOM 5793 SG CYS 3 114 105.147 72.114 226.926 1.00 22.79 S ATOM 5732 SG CYS 3 105 99.828 75.518 228.865 1.00 26.57 S ATOM 5753 SG CYS 3 108 105.951 77.182 230.493 1.00 12.20 S ATOM 6125 SG CYS 3 156 112.331 64.752 231.723 1.00 18.16 S ATOM 6102 SG CYS 3 153 110.267 67.717 237.374 1.00 18.85 S ATOM 6149 SG CYS 3 159 116.366 68.421 235.482 1.00 62.26 S ATOM 6479 SG CYS 3 203 112.203 70.990 231.850 1.00 33.70 S ATOM 5238 SG CYS 3 41 111.402 58.216 229.679 1.00 13.31 S ATOM 5324 SG CYS 3 52 107.666 59.316 229.035 1.00 22.50 S ATOM 5349 SG CYS 3 55 108.078 54.202 225.606 1.00 32.01 S ATOM 5450 SG CYS 3 69 111.676 54.322 226.919 1.00 21.54 S ATOM 16148 SG CYS 6 119 90.390 97.647 204.462 1.00 40.82 S ATOM 16378 SG CYS 6 149 87.064 95.414 209.190 1.00 49.12 S ATOM 15644 SG CYS 6 54 83.668 95.379 203.473 1.00 72.57 S ATOM 17570 SG CYS 9 116 91.122 96.425 215.717 1.00 34.86 S ATOM 17617 SG CYS 9 122 91.658 92.034 220.553 1.00 17.76 S ATOM 17344 SG CYS 9 87 95.657 91.819 215.289 1.00 12.38 S ATOM 17646 SG CYS 9 126 93.856 88.563 227.767 1.00 26.82 S ATOM 17317 SG CYS 9 83 97.515 90.276 222.669 1.00 19.72 S ATOM 17275 SG CYS 9 77 99.589 91.869 228.467 1.00 12.59 S ATOM 17294 SG CYS 9 80 98.923 85.361 226.711 1.00 16.84 S ATOM 41210 SG CYS b 59 95.313 84.357 243.059 1.00 29.06 S ATOM 41388 SG CYS b 84 98.414 84.265 240.706 1.00 21.91 S ATOM 41410 SG CYS b 87 96.615 87.086 241.662 1.00 25.43 S Time building chain proxies: 27.21, per 1000 atoms: 0.40 Number of scatterers: 67479 At special positions: 0 Unit cell: (176.126, 199.468, 292.836, 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 465 16.00 P 46 15.00 O 12106 8.00 N 11156 7.00 C 43676 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=2.01 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.02 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: 24.37 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 337 helices and 29 sheets defined 51.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 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 Processing helix chain '1' and resid 45 through 50 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 81 removed outlier: 3.678A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 184 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: 4.341A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 387 through 399 Processing helix chain '1' and resid 407 through 436 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.720A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.654A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.910A 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: 3.997A 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 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 196 through 202 removed outlier: 4.020A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.852A 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 275 removed outlier: 5.255A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 308 removed outlier: 3.621A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 371 No H-bonds generated for 'chain '3' and resid 369 through 371' 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 432 removed outlier: 3.775A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.836A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 515 No H-bonds generated for 'chain '3' and resid 512 through 515' Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 607 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 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: 3.992A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.548A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 102 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.533A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.062A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.895A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.729A 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: 4.621A 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 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.607A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.116A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.766A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.531A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 3.545A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.826A 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 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 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 177 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 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: 5.650A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 26 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.568A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 31 Proline residue: H 12 - end of helix removed outlier: 3.605A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.566A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.702A pdb=" N ILE H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.672A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) 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 220 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: 3.545A pdb=" N ILE J 5 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.692A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 3.905A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.217A 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: 3.781A 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: 3.500A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.593A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.754A 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 3 through 23 removed outlier: 3.708A 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: 3.963A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.833A 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: 3.912A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.945A 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: 3.537A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.411A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.663A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.733A 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: 4.562A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.032A 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 389 through 399 removed outlier: 4.972A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.656A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.858A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.528A 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: 3.628A 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 547 removed outlier: 3.849A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.864A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.521A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 546 " --> pdb=" O THR L 543 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (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 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.086A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.983A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.593A 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 107 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.424A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 170 removed outlier: 3.715A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.505A pdb=" N ILE M 165 " --> pdb=" O VAL M 162 " (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: 4.948A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 222 Proline residue: M 217 - end of helix removed outlier: 5.369A pdb=" N HIS M 220 " --> pdb=" O PRO M 217 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL M 221 " --> pdb=" O LYS M 218 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU M 222 " --> pdb=" O ALA M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.646A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.057A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.088A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.166A 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 390 through 415 removed outlier: 3.830A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.156A 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 'M' and resid 456 through 458 No H-bonds generated for 'chain 'M' and resid 456 through 458' 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: 4.022A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.528A 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: 3.890A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.890A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.052A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.556A 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: 3.763A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 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: 3.712A 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 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.590A 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: 3.857A 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 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 56 through 74 removed outlier: 3.767A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 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: 3.995A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.696A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 27 removed outlier: 3.639A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 removed outlier: 3.580A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.175A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.327A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 29 through 39 removed outlier: 3.948A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.136A 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 185 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: 5.012A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.615A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 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: 4.293A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.914A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.436A 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: 3.665A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 29 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: 3.909A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 45 removed outlier: 3.547A pdb=" N VAL k 42 " --> pdb=" O ALA k 39 " (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 131 through 140 removed outlier: 3.503A pdb=" N GLU k 136 " --> pdb=" O VAL k 133 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.406A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.477A 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 217 removed outlier: 5.603A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix removed outlier: 4.751A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 15 through 17 No H-bonds generated for 'chain 'l' and resid 15 through 17' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 3.812A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 47 removed outlier: 3.782A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 49 through 52 removed outlier: 3.516A pdb=" N TYR n 52 " --> pdb=" O ALA n 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 49 through 52' Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 2 through 7 removed outlier: 4.027A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.963A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.879A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 71 Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 91 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 removed outlier: 3.530A pdb=" N PHE q 35 " --> pdb=" O GLY q 31 " (cutoff:3.500A) Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 68 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: 4.213A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 100 through 103 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 4.083A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.616A 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 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.025A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 14 removed outlier: 3.720A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 14' Processing helix chain 'y' and resid 16 through 33 removed outlier: 3.708A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 29 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 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: 5.999A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.502A 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: 6.854A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.020A 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: 6.505A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN 2 159 " --> pdb=" O ILE 2 156 " (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: 6.255A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.495A 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: 8.577A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.870A 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: 8.262A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.559A 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 571 through 574 removed outlier: 3.624A pdb=" N ALA 3 571 " --> pdb=" O THR 3 583 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 removed outlier: 3.721A pdb=" N ARG 4 63 " --> pdb=" O HIS 4 79 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.703A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.694A 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: 6.076A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.444A 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: 5.983A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.096A 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: 6.796A 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: 6.482A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.577A 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: 3.525A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.594A 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: 3.592A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.662A 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: 6.551A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2807 hydrogen bonds defined for protein. 7857 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: 23.33 Time building geometry restraints manager: 26.48 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: 28634 1.43 - 1.66: 39661 1.66 - 1.90: 756 1.90 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69131 Sorted by residual: bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.585 0.248 3.80e-02 6.93e+02 4.27e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.324 0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C10 ZMP X 101 " pdb=" S1 ZMP X 101 " ideal model delta sigma weight residual 1.817 1.691 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" OA3 CDL z 101 " pdb=" PA1 CDL z 101 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.00e-02 1.00e+04 3.93e+01 ... (remaining 69126 not shown) Histogram of bond angle deviations from ideal: 62.24 - 77.27: 74 77.27 - 92.30: 8 92.30 - 107.33: 3574 107.33 - 122.37: 80245 122.37 - 137.40: 9525 Bond angle restraints: 93426 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 71.71 48.89 3.00e+00 1.11e-01 2.66e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.62 38.68 3.00e+00 1.11e-01 1.66e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.92 13.41 1.14e+00 7.69e-01 1.38e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.37 -22.63 1.95e+00 2.62e-01 1.34e+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 91.38 12.95 1.14e+00 7.69e-01 1.29e+02 ... (remaining 93421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 40960 34.11 - 68.21: 636 68.21 - 102.32: 42 102.32 - 136.43: 0 136.43 - 170.54: 4 Dihedral angle restraints: 41642 sinusoidal: 17859 harmonic: 23783 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 -129.60 -50.40 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -133.86 -46.14 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA PRO H 60 " pdb=" C PRO H 60 " pdb=" N LEU H 61 " pdb=" CA LEU H 61 " ideal model delta harmonic sigma weight residual 180.00 -137.46 -42.54 0 5.00e+00 4.00e-02 7.24e+01 ... (remaining 41639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.228: 10089 4.228 - 8.456: 5 8.456 - 12.683: 0 12.683 - 16.911: 0 16.911 - 21.139: 24 Chirality restraints: 10118 Sorted by residual: 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 -10.58 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.57 -21.13 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 -10.55 21.11 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10115 not shown) Planarity restraints: 11647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ 6 203 " -0.005 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" C1M DCQ 6 203 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DCQ 6 203 " -0.012 2.00e-02 2.50e+03 pdb=" C3 DCQ 6 203 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DCQ 6 203 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DCQ 6 203 " -0.025 2.00e-02 2.50e+03 pdb=" C6 DCQ 6 203 " 0.019 2.00e-02 2.50e+03 pdb=" C7 DCQ 6 203 " 0.073 2.00e-02 2.50e+03 pdb=" O2 DCQ 6 203 " -0.005 2.00e-02 2.50e+03 pdb=" O3 DCQ 6 203 " -0.032 2.00e-02 2.50e+03 pdb=" O4 DCQ 6 203 " 0.115 2.00e-02 2.50e+03 pdb=" O5 DCQ 6 203 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.034 2.00e-02 2.50e+03 3.13e-02 1.95e+01 pdb=" CG TYR 6 125 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.019 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR 9 40 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.003 2.00e-02 2.50e+03 ... (remaining 11644 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 19430 2.81 - 3.40: 72934 3.40 - 3.98: 141132 3.98 - 4.56: 199220 4.56 - 5.14: 286063 Nonbonded interactions: 718779 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.233 2.440 nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.244 2.440 nonbonded pdb=" O PHE M 105 " pdb=" OG1 THR M 109 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR 4 145 " pdb=" OH TYR 4 181 " model vdw 2.257 2.440 nonbonded pdb=" OG SER 5 119 " pdb=" OE2 GLU 5 131 " model vdw 2.258 2.440 ... (remaining 718774 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 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.140 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 160.740 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.009 0.248 69131 Z= 0.571 Angle : 1.048 48.895 93426 Z= 0.550 Chirality : 1.026 21.139 10118 Planarity : 0.008 0.068 11647 Dihedral : 11.886 170.537 26283 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.07 % 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: -2.73 (0.08), residues: 8046 helix: -1.82 (0.06), residues: 4271 sheet: -1.46 (0.23), residues: 388 loop : -1.65 (0.09), residues: 3387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1680 time to evaluate : 6.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 1683 average time/residue: 1.6970 time to fit residues: 3637.0369 Evaluate side-chains 1112 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1109 time to evaluate : 6.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 1.0280 time to fit residues: 11.4215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 670 optimal weight: 8.9990 chunk 601 optimal weight: 0.7980 chunk 333 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 405 optimal weight: 5.9990 chunk 321 optimal weight: 20.0000 chunk 622 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 378 optimal weight: 7.9990 chunk 463 optimal weight: 6.9990 chunk 721 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 2 155 GLN 3 100 ASN 3 179 ASN ** 3 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 313 ASN 3 546 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 149 ASN 4 252 ASN 5 39 GLN 5 200 ASN ** 6 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 65 HIS A 26 GLN A 83 ASN A 108 GLN H 194 ASN L 135 ASN L 199 GLN L 442 ASN L 446 ASN L 524 ASN L 570 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN M 144 ASN M 169 ASN M 279 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 HIS Y 64 GLN Z 90 GLN Z 106 GLN Z 120 HIS Z 123 ASN a 40 ASN b 74 ASN d 87 HIS d 203 GLN d 288 HIS e 85 GLN f 82 GLN g 125 HIS i 69 ASN i 91 HIS k 21 ASN k 76 ASN l 97 HIS m 10 ASN o 61 GLN ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 74 ASN p 78 ASN q 53 ASN q 75 GLN r 25 GLN s 83 GLN t 17 GLN t 138 GLN u 24 GLN v 132 GLN v 155 HIS ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 30 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.263 69131 Z= 0.561 Angle : 1.584 51.049 93426 Z= 1.021 Chirality : 0.312 6.487 10118 Planarity : 0.006 0.058 11647 Dihedral : 11.520 170.570 10145 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer Outliers : 2.68 % 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: -1.03 (0.09), residues: 8046 helix: -0.23 (0.07), residues: 4262 sheet: -1.09 (0.24), residues: 392 loop : -1.08 (0.10), residues: 3392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1147 time to evaluate : 6.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 75 residues processed: 1244 average time/residue: 1.6481 time to fit residues: 2654.6973 Evaluate side-chains 1129 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1054 time to evaluate : 6.280 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 38 residues processed: 39 average time/residue: 0.9153 time to fit residues: 62.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 400 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 600 optimal weight: 20.0000 chunk 490 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 722 optimal weight: 40.0000 chunk 780 optimal weight: 9.9990 chunk 643 optimal weight: 30.0000 chunk 716 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 579 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS 2 99 HIS 3 100 ASN 3 182 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 28 ASN H 194 ASN K 7 ASN K 52 HIS L 23 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 GLN Z 58 ASN a 40 ASN ** e 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 GLN i 12 GLN i 112 ASN k 180 GLN k 239 GLN m 10 ASN s 83 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 138 GLN v 137 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.242 69131 Z= 0.622 Angle : 1.598 50.863 93426 Z= 1.026 Chirality : 0.312 6.462 10118 Planarity : 0.006 0.056 11647 Dihedral : 11.151 171.737 10145 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer Outliers : 3.20 % 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: -0.22 (0.09), residues: 8046 helix: 0.43 (0.08), residues: 4276 sheet: -0.84 (0.25), residues: 386 loop : -0.69 (0.10), residues: 3384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1081 time to evaluate : 6.435 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 228 outliers final: 95 residues processed: 1210 average time/residue: 1.6473 time to fit residues: 2620.9480 Evaluate side-chains 1124 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1029 time to evaluate : 6.325 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 60 residues processed: 37 average time/residue: 0.8471 time to fit residues: 57.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 713 optimal weight: 9.9990 chunk 543 optimal weight: 3.9990 chunk 374 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 485 optimal weight: 5.9990 chunk 724 optimal weight: 9.9990 chunk 767 optimal weight: 20.0000 chunk 378 optimal weight: 6.9990 chunk 687 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 121 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 GLN ** 6 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 28 ASN A 83 ASN H 194 ASN H 317 GLN K 97 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN N 134 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 135 GLN m 10 ASN ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN s 53 GLN s 83 GLN t 12 GLN t 17 GLN v 137 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69131 Z= 0.561 Angle : 1.570 50.653 93426 Z= 1.015 Chirality : 0.311 6.428 10118 Planarity : 0.005 0.053 11647 Dihedral : 10.754 171.165 10145 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer Outliers : 3.04 % 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: 0.19 (0.09), residues: 8046 helix: 0.78 (0.08), residues: 4275 sheet: -0.73 (0.25), residues: 384 loop : -0.50 (0.11), residues: 3387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1080 time to evaluate : 6.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 217 outliers final: 106 residues processed: 1201 average time/residue: 1.6093 time to fit residues: 2515.5312 Evaluate side-chains 1145 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1039 time to evaluate : 6.254 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 71 residues processed: 36 average time/residue: 0.9005 time to fit residues: 57.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 639 optimal weight: 20.0000 chunk 435 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 571 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 654 optimal weight: 8.9990 chunk 530 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 391 optimal weight: 10.0000 chunk 688 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 GLN A 26 GLN A 28 ASN A 85 ASN H 194 ASN H 317 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN e 61 GLN ** e 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 79 ASN k 180 GLN k 200 GLN m 10 ASN p 47 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.243 69131 Z= 0.551 Angle : 1.566 50.664 93426 Z= 1.013 Chirality : 0.311 6.411 10118 Planarity : 0.004 0.050 11647 Dihedral : 10.455 170.921 10145 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer Outliers : 3.07 % 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: 0.45 (0.09), residues: 8046 helix: 0.99 (0.08), residues: 4289 sheet: -0.64 (0.25), residues: 384 loop : -0.38 (0.11), residues: 3373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1074 time to evaluate : 6.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 115 residues processed: 1199 average time/residue: 1.5949 time to fit residues: 2503.8989 Evaluate side-chains 1150 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1035 time to evaluate : 6.269 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 76 residues processed: 40 average time/residue: 0.8722 time to fit residues: 62.6065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 258 optimal weight: 10.0000 chunk 691 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 450 optimal weight: 0.0040 chunk 189 optimal weight: 9.9990 chunk 768 optimal weight: 10.0000 chunk 637 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 403 optimal weight: 9.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 GLN A 26 GLN A 28 ASN A 83 ASN A 85 ASN J 78 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN N 49 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 GLN b 94 GLN e 75 ASN l 26 HIS m 10 ASN p 47 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 69131 Z= 0.539 Angle : 1.562 50.850 93426 Z= 1.011 Chirality : 0.311 6.452 10118 Planarity : 0.004 0.049 11647 Dihedral : 10.205 170.530 10145 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer Outliers : 2.86 % 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: 0.64 (0.09), residues: 8046 helix: 1.13 (0.08), residues: 4286 sheet: -0.51 (0.24), residues: 404 loop : -0.28 (0.11), residues: 3356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1072 time to evaluate : 6.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 105 residues processed: 1195 average time/residue: 1.6168 time to fit residues: 2528.0212 Evaluate side-chains 1142 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1037 time to evaluate : 6.484 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 76 residues processed: 29 average time/residue: 0.8827 time to fit residues: 48.2258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 740 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 437 optimal weight: 9.9990 chunk 561 optimal weight: 20.0000 chunk 434 optimal weight: 5.9990 chunk 646 optimal weight: 10.0000 chunk 428 optimal weight: 4.9990 chunk 765 optimal weight: 6.9990 chunk 478 optimal weight: 20.0000 chunk 466 optimal weight: 20.0000 chunk 353 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 438 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 621 ASN A 26 GLN A 28 ASN A 85 ASN H 317 GLN ** K 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN m 10 ASN ** o 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN p 125 ASN r 25 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.239 69131 Z= 0.603 Angle : 1.585 50.790 93426 Z= 1.020 Chirality : 0.312 6.429 10118 Planarity : 0.005 0.056 11647 Dihedral : 10.353 170.613 10145 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.58 % Rotamer Outliers : 2.75 % 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: 0.56 (0.09), residues: 8046 helix: 1.05 (0.08), residues: 4281 sheet: -0.46 (0.24), residues: 401 loop : -0.31 (0.11), residues: 3364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1043 time to evaluate : 6.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 127 residues processed: 1160 average time/residue: 1.6294 time to fit residues: 2479.7542 Evaluate side-chains 1148 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1021 time to evaluate : 6.349 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 85 residues processed: 43 average time/residue: 0.9591 time to fit residues: 71.4046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 473 optimal weight: 5.9990 chunk 305 optimal weight: 3.9990 chunk 457 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 486 optimal weight: 20.0000 chunk 521 optimal weight: 8.9990 chunk 378 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 601 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 83 ASN A 85 ASN L 170 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 GLN b 51 GLN h 24 GLN m 10 ASN p 47 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 32 HIS v 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69131 Z= 0.537 Angle : 1.564 50.663 93426 Z= 1.012 Chirality : 0.311 6.395 10118 Planarity : 0.004 0.051 11647 Dihedral : 10.125 170.744 10145 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 8046 helix: 1.18 (0.08), residues: 4295 sheet: -0.36 (0.25), residues: 381 loop : -0.22 (0.11), residues: 3370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1046 time to evaluate : 6.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 111 residues processed: 1164 average time/residue: 1.6057 time to fit residues: 2447.7478 Evaluate side-chains 1124 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1013 time to evaluate : 6.318 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 92 residues processed: 20 average time/residue: 0.9094 time to fit residues: 36.1063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 696 optimal weight: 0.0060 chunk 733 optimal weight: 8.9990 chunk 668 optimal weight: 10.0000 chunk 713 optimal weight: 9.9990 chunk 732 optimal weight: 5.9990 chunk 429 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 chunk 559 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 644 optimal weight: 8.9990 chunk 674 optimal weight: 30.0000 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 85 ASN H 317 GLN L 170 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN M 304 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 GLN h 24 GLN m 10 ASN p 47 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69131 Z= 0.563 Angle : 1.575 50.696 93426 Z= 1.016 Chirality : 0.311 6.404 10118 Planarity : 0.004 0.051 11647 Dihedral : 10.122 170.612 10145 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer Outliers : 2.19 % 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: 0.71 (0.09), residues: 8046 helix: 1.16 (0.08), residues: 4290 sheet: -0.34 (0.25), residues: 383 loop : -0.21 (0.11), residues: 3373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1030 time to evaluate : 6.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 108 residues processed: 1141 average time/residue: 1.6239 time to fit residues: 2429.7232 Evaluate side-chains 1110 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1002 time to evaluate : 6.300 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 90 residues processed: 20 average time/residue: 1.0211 time to fit residues: 38.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 710 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 754 optimal weight: 30.0000 chunk 460 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 chunk 524 optimal weight: 6.9990 chunk 791 optimal weight: 8.9990 chunk 728 optimal weight: 20.0000 chunk 629 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 486 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 85 ASN H 317 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN h 24 GLN m 10 ASN p 47 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 HIS v 66 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69131 Z= 0.560 Angle : 1.576 50.692 93426 Z= 1.017 Chirality : 0.311 6.404 10118 Planarity : 0.004 0.050 11647 Dihedral : 10.092 170.667 10145 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer Outliers : 1.75 % 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: 0.72 (0.09), residues: 8046 helix: 1.16 (0.08), residues: 4280 sheet: -0.30 (0.25), residues: 381 loop : -0.20 (0.11), residues: 3385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16092 Ramachandran restraints generated. 8046 Oldfield, 0 Emsley, 8046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1028 time to evaluate : 6.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 104 residues processed: 1126 average time/residue: 1.6243 time to fit residues: 2395.7037 Evaluate side-chains 1108 residues out of total 7132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1004 time to evaluate : 6.300 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 90 residues processed: 16 average time/residue: 0.9526 time to fit residues: 31.3203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 386 optimal weight: 0.4980 chunk 500 optimal weight: 20.0000 chunk 670 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 580 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 630 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 647 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 85 ASN H 317 GLN L 323 HIS ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN k 239 GLN m 10 ASN p 47 GLN s 83 GLN t 12 GLN ** t 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 58 GLN v 137 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.083925 restraints weight = 96237.094| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.27 r_work: 0.2980 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69131 Z= 0.534 Angle : 1.568 50.672 93426 Z= 1.014 Chirality : 0.311 6.387 10118 Planarity : 0.004 0.050 11647 Dihedral : 9.925 170.531 10145 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer Outliers : 1.98 % 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: 0.81 (0.09), residues: 8046 helix: 1.24 (0.08), residues: 4282 sheet: -0.32 (0.25), residues: 386 loop : -0.16 (0.11), residues: 3378 =============================================================================== Job complete usr+sys time: 33121.97 seconds wall clock time: 574 minutes 13.29 seconds (34453.29 seconds total)