Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 00:38:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zke_11246/04_2023/6zke_11246_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 466 5.16 5 C 43656 2.51 5 N 11149 2.21 5 O 12103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "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 ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67450 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: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2498 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 291} Chain breaks: 1 Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1294 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'3PE': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "H" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'DCQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 276 Unusual residues: {'3PE': 3, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 188 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 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: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 103.550 54.225 240.614 1.00 25.70 S ATOM 2695 SG CYS 1 362 105.960 54.367 235.208 1.00 40.14 S ATOM 2676 SG CYS 1 359 110.707 54.302 241.200 1.00 42.93 S ATOM 3039 SG CYS 1 405 107.132 48.490 239.573 1.00 37.41 S ATOM 4116 SG CYS 2 103 101.427 49.092 259.360 1.00 47.20 S ATOM 4150 SG CYS 2 108 99.313 46.652 261.460 1.00 50.11 S ATOM 4430 SG CYS 2 144 102.940 45.464 255.772 1.00 61.98 S ATOM 4453 SG CYS 2 148 101.028 42.662 257.245 1.00 55.65 S ATOM 5793 SG CYS 3 114 106.094 72.749 226.044 1.00 32.51 S ATOM 5732 SG CYS 3 105 100.889 76.203 228.026 1.00 36.29 S ATOM 5753 SG CYS 3 108 107.033 77.682 229.945 1.00 21.92 S ATOM 6125 SG CYS 3 156 113.117 65.073 230.581 1.00 27.88 S ATOM 6102 SG CYS 3 153 111.176 68.049 236.335 1.00 28.57 S ATOM 6149 SG CYS 3 159 117.212 68.729 234.506 1.00 62.59 S ATOM 6479 SG CYS 3 203 113.207 71.268 230.807 1.00 28.08 S ATOM 5238 SG CYS 3 41 112.205 58.562 228.734 1.00 23.03 S ATOM 5324 SG CYS 3 52 108.415 59.775 227.956 1.00 32.22 S ATOM 5349 SG CYS 3 55 108.878 54.962 224.295 1.00 27.68 S ATOM 5450 SG CYS 3 69 112.417 54.939 225.680 1.00 31.26 S ATOM 15613 SG CYS 6 55 85.053 102.783 205.894 1.00 50.47 S ATOM 16111 SG CYS 6 119 91.233 98.681 203.913 1.00 50.54 S ATOM 16341 SG CYS 6 149 88.100 96.507 208.977 1.00 60.17 S ATOM 15607 SG CYS 6 54 84.593 96.530 203.032 1.00 82.29 S ATOM 17533 SG CYS 9 116 92.189 97.286 215.369 1.00 44.58 S ATOM 17580 SG CYS 9 122 92.809 92.815 220.021 1.00 27.48 S ATOM 17307 SG CYS 9 87 96.646 92.467 214.670 1.00 22.10 S ATOM 17609 SG CYS 9 126 94.975 89.269 227.200 1.00 15.33 S ATOM 17280 SG CYS 9 83 98.539 91.031 222.095 1.00 29.44 S ATOM 17238 SG CYS 9 77 100.786 92.511 227.938 1.00 22.31 S ATOM 17257 SG CYS 9 80 100.017 86.070 225.981 1.00 26.56 S ATOM 41181 SG CYS b 59 96.598 84.866 242.446 1.00 38.78 S ATOM 41359 SG CYS b 84 99.665 84.842 239.996 1.00 29.82 S ATOM 41381 SG CYS b 87 98.013 87.881 240.998 1.00 35.15 S Time building chain proxies: 29.31, per 1000 atoms: 0.43 Number of scatterers: 67450 At special positions: 0 Unit cell: (176.126, 200.529, 290.714, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 466 16.00 P 46 15.00 O 12103 8.00 N 11149 7.00 C 43656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.49 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " 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 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 340 helices and 29 sheets defined 51.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.680A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 51 removed outlier: 3.648A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 62 Processing helix chain '1' and resid 75 through 81 removed outlier: 3.744A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 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: 4.500A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 4.018A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.752A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.582A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.870A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.740A 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 32 Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 196 through 202 removed outlier: 3.831A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.697A 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: 5.213A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 308 removed outlier: 3.736A 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 360 through 362 No H-bonds generated for 'chain '3' and resid 360 through 362' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 432 removed outlier: 3.995A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.927A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 631 removed outlier: 3.680A pdb=" N VAL 3 631 " --> pdb=" O PRO 3 628 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 628 through 631' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 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 15 removed outlier: 3.959A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.066A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix removed outlier: 3.961A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.647A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 3.993A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.837A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.738A 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: 4.557A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.621A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.904A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.815A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.822A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 3.710A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.984A 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 63 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.793A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.700A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.542A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.798A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.697A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 5.496A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.684A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.203A 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: 3.797A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.787A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.615A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.063A 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: 3.987A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.853A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.937A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.964A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.011A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.717A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.619A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.691A 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: 4.329A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 390 Processing helix chain 'L' and resid 392 through 400 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: 3.773A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.508A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 4.162A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.721A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.117A 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: 3.846A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.573A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.606A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.578A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.522A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.367A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.928A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.651A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 246 Processing helix chain 'M' and resid 254 through 266 removed outlier: 5.655A pdb=" N TYR M 259 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix Processing helix chain 'M' and resid 268 through 277 removed outlier: 3.659A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.047A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.114A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.776A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.268A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.174A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.471A 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: 3.825A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.930A 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 232 removed outlier: 4.023A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.662A 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: 3.721A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.668A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.800A 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 79 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.375A 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: 3.807A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.833A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 74 removed outlier: 4.074A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU Y 57 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU Y 58 " --> pdb=" O CYS Y 55 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA Y 66 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU Y 67 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU Y 68 " --> pdb=" O CYS Y 65 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG Y 71 " --> pdb=" O GLU Y 68 " (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 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 4.207A 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: 4.816A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.747A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 44 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: 4.407A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.476A 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: 3.896A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.312A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 300 through 303 Processing helix chain 'd' and resid 310 through 321 removed outlier: 5.240A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 46 removed outlier: 5.148A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS e 38 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG e 39 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR e 40 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL e 41 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU e 42 " --> pdb=" O ARG e 39 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS e 45 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.192A 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: 3.872A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 3.944A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.473A 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 56 Processing helix chain 'i' and resid 3 through 16 Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.752A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.545A 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: 4.444A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 141 removed outlier: 3.642A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.298A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 4.059A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.080A 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 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 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 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 48 through 54 removed outlier: 4.023A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.596A 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 38 removed outlier: 4.035A pdb=" N ARG n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix 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: 3.949A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 17 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.852A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.934A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 74 through 78 removed outlier: 3.502A pdb=" N ASN p 78 " --> pdb=" O ASN p 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 74 through 78' Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 115 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 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 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 140 removed outlier: 3.942A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 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 65 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.012A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (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 34 removed outlier: 3.632A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU y 15 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.449A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU y 32 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 29 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 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: 5.953A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.584A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.704A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.978A 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: 8.099A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.428A 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: 3.521A 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 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: 6.729A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.802A 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: 6.472A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.306A 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: 5.802A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.103A 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: 6.584A 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: 7.490A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.918A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.431A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.642A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC 2790 hydrogen bonds defined for protein. 7692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.59 Time building geometry restraints manager: 23.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.43: 28330 1.43 - 1.66: 39930 1.66 - 1.90: 758 1.90 - 2.13: 0 2.13 - 2.37: 80 Bond restraints: 69098 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.594 0.239 3.80e-02 6.93e+02 3.94e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.329 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.00e-02 1.00e+04 3.63e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.00e-02 1.00e+04 3.60e+01 bond pdb=" OB3 CDL L 704 " pdb=" PB2 CDL L 704 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.00e-02 1.00e+04 3.29e+01 ... (remaining 69093 not shown) Histogram of bond angle deviations from ideal: 62.00 - 77.05: 73 77.05 - 92.11: 7 92.11 - 107.16: 3197 107.16 - 122.21: 78923 122.21 - 137.27: 11176 Bond angle restraints: 93376 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 75.29 45.31 3.00e+00 1.11e-01 2.28e+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 69.35 39.95 3.00e+00 1.11e-01 1.77e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.22 -22.48 1.95e+00 2.62e-01 1.32e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 91.48 12.85 1.14e+00 7.69e-01 1.27e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 91.42 12.91 1.20e+00 6.94e-01 1.16e+02 ... (remaining 93371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 41025 35.65 - 71.30: 566 71.30 - 106.96: 28 106.96 - 142.61: 2 142.61 - 178.26: 3 Dihedral angle restraints: 41624 sinusoidal: 17854 harmonic: 23770 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual 180.00 -130.19 -49.81 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -133.15 -46.85 0 5.00e+00 4.00e-02 8.78e+01 dihedral pdb=" C5' AMP k 501 " pdb=" O5' AMP k 501 " pdb=" P AMP k 501 " pdb=" O3P AMP k 501 " ideal model delta sinusoidal sigma weight residual 300.00 121.74 178.26 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 41621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.229: 10083 4.229 - 8.458: 5 8.458 - 12.686: 0 12.686 - 16.915: 0 16.915 - 21.144: 24 Chirality restraints: 10112 Sorted by residual: chirality pdb="FE2 SF4 9 403 " pdb=" S1 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 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 10.59 -21.14 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10109 not shown) Planarity restraints: 11640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " -0.065 2.00e-02 2.50e+03 1.02e-01 3.10e+02 pdb=" C1M DCQ H 501 " -0.147 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.018 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " 0.018 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.022 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " 0.047 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " 0.226 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " -0.004 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " 0.164 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " -0.087 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.023 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR 9 40 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.029 2.00e-02 2.50e+03 2.51e-02 1.57e+01 pdb=" CG TRP 1 371 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.005 2.00e-02 2.50e+03 ... (remaining 11637 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.83: 21067 2.83 - 3.41: 73537 3.41 - 3.99: 141422 3.99 - 4.56: 199119 4.56 - 5.14: 282425 Nonbonded interactions: 717570 Sorted by model distance: nonbonded pdb=" O PHE M 105 " pdb=" OG1 THR M 109 " model vdw 2.257 2.440 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.268 2.440 nonbonded pdb=" OG SER 5 119 " pdb=" OE2 GLU 5 131 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP g 116 " pdb=" OG SER g 119 " model vdw 2.276 2.440 ... (remaining 717565 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: 0.420 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: 6.940 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 155.470 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.190 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:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.239 69098 Z= 0.529 Angle : 1.021 45.309 93376 Z= 0.538 Chirality : 1.027 21.144 10112 Planarity : 0.008 0.102 11640 Dihedral : 11.876 178.262 26273 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.40 % Favored : 96.59 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.08), residues: 8039 helix: -1.74 (0.06), residues: 4251 sheet: -1.62 (0.23), residues: 399 loop : -1.54 (0.10), residues: 3389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1700 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1695 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 1699 average time/residue: 1.7347 time to fit residues: 3751.2556 Evaluate side-chains 1114 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1113 time to evaluate : 6.225 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 8.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 8.9990 chunk 602 optimal weight: 2.9990 chunk 334 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 406 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 623 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 378 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 721 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 373 ASN 2 55 GLN 2 74 GLN ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 277 GLN 3 546 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 5 144 ASN 5 211 GLN 6 106 GLN 9 65 HIS A 83 ASN H 194 ASN H 317 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 175 ASN L 199 GLN L 442 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 103 GLN M 175 ASN M 304 GLN N 235 ASN W 86 ASN Y 15 GLN Y 29 HIS Z 106 GLN ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 ASN a 55 ASN b 36 ASN b 51 GLN b 94 GLN c 44 ASN d 87 HIS d 184 ASN e 61 GLN e 85 GLN f 49 GLN f 75 GLN g 125 HIS h 24 GLN i 135 GLN k 89 ASN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 180 GLN l 69 GLN l 96 HIS m 61 ASN ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 GLN p 47 GLN r 12 GLN r 25 GLN s 49 GLN t 32 HIS t 50 HIS t 72 HIS t 140 GLN u 6 HIS u 24 GLN v 72 ASN v 137 ASN w 119 GLN x 5 GLN x 34 GLN z 31 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69098 Z= 0.536 Angle : 1.585 51.055 93376 Z= 1.021 Chirality : 0.317 6.630 10112 Planarity : 0.005 0.058 11640 Dihedral : 11.495 173.066 10140 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.09), residues: 8039 helix: -0.08 (0.07), residues: 4308 sheet: -1.13 (0.23), residues: 419 loop : -0.92 (0.10), residues: 3312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1150 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 66 residues processed: 1247 average time/residue: 1.6696 time to fit residues: 2684.6560 Evaluate side-chains 1145 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1079 time to evaluate : 6.138 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 33 residues processed: 33 average time/residue: 0.8478 time to fit residues: 51.8165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 600 optimal weight: 0.9990 chunk 491 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 723 optimal weight: 40.0000 chunk 781 optimal weight: 9.9990 chunk 644 optimal weight: 9.9990 chunk 717 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 580 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 237 ASN 3 581 GLN 5 211 GLN 6 106 GLN A 26 GLN A 28 ASN A 83 ASN H 317 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN L 509 HIS N 235 ASN W 143 ASN Y 15 GLN Y 105 GLN Z 54 GLN c 44 ASN f 70 GLN k 89 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 69 GLN o 61 GLN r 25 GLN s 83 GLN t 32 HIS t 50 HIS t 72 HIS t 77 GLN t 140 GLN u 24 GLN w 86 GLN w 119 GLN x 5 GLN x 34 GLN y 30 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69098 Z= 0.520 Angle : 1.561 50.641 93376 Z= 1.011 Chirality : 0.311 6.470 10112 Planarity : 0.004 0.050 11640 Dihedral : 10.908 171.466 10140 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.09), residues: 8039 helix: 0.60 (0.08), residues: 4302 sheet: -0.84 (0.24), residues: 399 loop : -0.61 (0.11), residues: 3338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1142 time to evaluate : 6.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 74 residues processed: 1244 average time/residue: 1.6281 time to fit residues: 2626.0221 Evaluate side-chains 1133 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1059 time to evaluate : 5.958 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 40 residues processed: 34 average time/residue: 0.9137 time to fit residues: 55.0536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 4.9990 chunk 543 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 chunk 485 optimal weight: 30.0000 chunk 725 optimal weight: 10.0000 chunk 768 optimal weight: 20.0000 chunk 379 optimal weight: 6.9990 chunk 687 optimal weight: 40.0000 chunk 207 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 643 GLN 5 211 GLN A 26 GLN A 28 ASN A 83 ASN A 108 GLN K 52 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN L 509 HIS N 235 ASN Y 63 ASN ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN i 91 HIS k 89 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 GLN q 53 ASN r 25 GLN s 83 GLN t 32 HIS t 50 HIS t 72 HIS t 140 GLN u 6 HIS u 24 GLN x 5 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69098 Z= 0.547 Angle : 1.571 50.688 93376 Z= 1.014 Chirality : 0.312 6.465 10112 Planarity : 0.005 0.050 11640 Dihedral : 10.711 170.336 10140 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.09), residues: 8039 helix: 0.91 (0.08), residues: 4297 sheet: -0.62 (0.24), residues: 398 loop : -0.42 (0.11), residues: 3344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1083 time to evaluate : 6.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 209 outliers final: 92 residues processed: 1197 average time/residue: 1.6426 time to fit residues: 2554.6285 Evaluate side-chains 1127 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1035 time to evaluate : 6.013 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 54 residues processed: 40 average time/residue: 0.8460 time to fit residues: 61.3090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 5.9990 chunk 436 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 572 optimal weight: 0.7980 chunk 317 optimal weight: 4.9990 chunk 655 optimal weight: 5.9990 chunk 531 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 392 optimal weight: 5.9990 chunk 689 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN ** 3 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 102 ASN 5 211 GLN A 26 GLN A 28 ASN A 83 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN L 509 HIS M 83 HIS N 235 ASN a 35 ASN a 40 ASN b 94 GLN f 70 GLN i 69 ASN k 89 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 10 ASN o 61 GLN r 25 GLN s 83 GLN t 32 HIS t 72 HIS t 140 GLN u 24 GLN v 72 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69098 Z= 0.512 Angle : 1.556 50.666 93376 Z= 1.009 Chirality : 0.311 6.424 10112 Planarity : 0.004 0.051 11640 Dihedral : 10.359 169.870 10140 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 8039 helix: 1.13 (0.08), residues: 4301 sheet: -0.56 (0.24), residues: 397 loop : -0.28 (0.11), residues: 3341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1092 time to evaluate : 6.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 88 residues processed: 1202 average time/residue: 1.6536 time to fit residues: 2575.6302 Evaluate side-chains 1124 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1036 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 64 residues processed: 27 average time/residue: 0.9220 time to fit residues: 45.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 7.9990 chunk 692 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 451 optimal weight: 30.0000 chunk 189 optimal weight: 3.9990 chunk 769 optimal weight: 40.0000 chunk 638 optimal weight: 0.7980 chunk 356 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 459 GLN 3 517 ASN 5 211 GLN A 28 ASN A 83 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN N 235 ASN Y 72 GLN Z 90 GLN b 94 GLN d 243 GLN f 70 GLN f 75 GLN h 24 GLN k 89 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 10 ASN o 61 GLN r 12 GLN r 25 GLN s 83 GLN t 72 HIS t 140 GLN x 34 GLN y 30 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 69098 Z= 0.532 Angle : 1.564 50.735 93376 Z= 1.011 Chirality : 0.312 6.442 10112 Planarity : 0.004 0.053 11640 Dihedral : 10.251 169.864 10140 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8039 helix: 1.21 (0.08), residues: 4295 sheet: -0.45 (0.25), residues: 398 loop : -0.19 (0.11), residues: 3346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1055 time to evaluate : 6.180 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 95 residues processed: 1168 average time/residue: 1.6468 time to fit residues: 2496.9428 Evaluate side-chains 1116 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1021 time to evaluate : 6.031 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 64 residues processed: 32 average time/residue: 0.8124 time to fit residues: 49.4919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 561 optimal weight: 20.0000 chunk 435 optimal weight: 20.0000 chunk 647 optimal weight: 0.9990 chunk 429 optimal weight: 10.0000 chunk 766 optimal weight: 9.9990 chunk 479 optimal weight: 20.0000 chunk 467 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 179 ASN 5 211 GLN A 26 GLN A 28 ASN A 83 ASN K 7 ASN K 25 HIS K 83 ASN L 27 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 GLN f 70 GLN f 75 GLN k 89 ASN l 97 HIS o 61 GLN r 25 GLN s 83 GLN t 72 HIS t 140 GLN w 119 GLN x 5 GLN y 30 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.240 69098 Z= 0.577 Angle : 1.582 50.803 93376 Z= 1.018 Chirality : 0.313 6.457 10112 Planarity : 0.005 0.056 11640 Dihedral : 10.417 170.444 10140 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 8039 helix: 1.14 (0.08), residues: 4309 sheet: -0.44 (0.24), residues: 400 loop : -0.18 (0.11), residues: 3330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1045 time to evaluate : 6.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 105 residues processed: 1151 average time/residue: 1.6431 time to fit residues: 2457.3738 Evaluate side-chains 1120 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1015 time to evaluate : 6.087 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 66 residues processed: 39 average time/residue: 0.8744 time to fit residues: 60.8890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 chunk 457 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 487 optimal weight: 2.9990 chunk 522 optimal weight: 6.9990 chunk 378 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 602 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 211 GLN A 26 GLN A 83 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 484 HIS L 509 HIS N 49 ASN N 235 ASN V 78 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN d 243 GLN f 70 GLN f 75 GLN i 135 GLN k 89 ASN n 20 GLN o 61 GLN r 25 GLN s 83 GLN t 32 HIS t 72 HIS t 140 GLN y 30 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 69098 Z= 0.536 Angle : 1.569 50.742 93376 Z= 1.014 Chirality : 0.312 6.442 10112 Planarity : 0.004 0.054 11640 Dihedral : 10.271 170.163 10140 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8039 helix: 1.22 (0.08), residues: 4303 sheet: -0.45 (0.24), residues: 404 loop : -0.12 (0.11), residues: 3332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1039 time to evaluate : 6.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 85 residues processed: 1140 average time/residue: 1.6723 time to fit residues: 2488.3552 Evaluate side-chains 1102 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1017 time to evaluate : 6.060 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 68 residues processed: 18 average time/residue: 0.7085 time to fit residues: 29.7830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.0070 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 6.9990 chunk 714 optimal weight: 0.3980 chunk 733 optimal weight: 8.9990 chunk 429 optimal weight: 10.0000 chunk 311 optimal weight: 0.9980 chunk 560 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 645 optimal weight: 2.9990 chunk 675 optimal weight: 7.9990 overall best weight: 2.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 150 HIS 5 211 GLN A 83 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN L 509 HIS N 235 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN d 243 GLN f 70 GLN f 75 GLN i 135 GLN k 89 ASN n 20 GLN o 61 GLN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN s 83 GLN t 32 HIS t 140 GLN v 104 HIS y 30 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 69098 Z= 0.506 Angle : 1.559 50.547 93376 Z= 1.009 Chirality : 0.310 6.399 10112 Planarity : 0.004 0.054 11640 Dihedral : 9.934 169.194 10140 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 8039 helix: 1.33 (0.08), residues: 4302 sheet: -0.43 (0.24), residues: 405 loop : -0.03 (0.11), residues: 3332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1053 time to evaluate : 6.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 84 residues processed: 1143 average time/residue: 1.6981 time to fit residues: 2533.7144 Evaluate side-chains 1091 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1007 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 68 residues processed: 16 average time/residue: 1.1046 time to fit residues: 33.7393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 8.9990 chunk 468 optimal weight: 7.9990 chunk 755 optimal weight: 0.7980 chunk 460 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 chunk 524 optimal weight: 6.9990 chunk 792 optimal weight: 20.0000 chunk 728 optimal weight: 3.9990 chunk 630 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 487 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 211 GLN 6 106 GLN A 83 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 15 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN b 95 HIS d 243 GLN f 70 GLN f 75 GLN k 89 ASN m 10 ASN o 61 GLN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 83 GLN v 72 ASN v 137 ASN w 119 GLN y 30 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 0.243 69098 Z= 0.527 Angle : 1.569 50.663 93376 Z= 1.013 Chirality : 0.311 6.423 10112 Planarity : 0.004 0.052 11640 Dihedral : 9.922 169.406 10140 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 8039 helix: 1.30 (0.08), residues: 4313 sheet: -0.40 (0.24), residues: 403 loop : -0.01 (0.11), residues: 3323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1012 time to evaluate : 6.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 75 residues processed: 1094 average time/residue: 1.6624 time to fit residues: 2373.3696 Evaluate side-chains 1070 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 995 time to evaluate : 6.064 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 67 residues processed: 9 average time/residue: 0.8824 time to fit residues: 20.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 6.9990 chunk 500 optimal weight: 0.0670 chunk 671 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 581 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 631 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 648 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 211 GLN A 83 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 323 HIS ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Y 15 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN b 95 HIS d 243 GLN f 70 GLN f 75 GLN k 89 ASN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 83 GLN y 30 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079222 restraints weight = 93374.515| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.24 r_work: 0.2977 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69098 Z= 0.518 Angle : 1.566 50.654 93376 Z= 1.012 Chirality : 0.311 6.417 10112 Planarity : 0.004 0.052 11640 Dihedral : 9.836 169.172 10140 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8039 helix: 1.32 (0.08), residues: 4313 sheet: -0.39 (0.25), residues: 403 loop : 0.02 (0.11), residues: 3323 =============================================================================== Job complete usr+sys time: 33593.22 seconds wall clock time: 580 minutes 28.40 seconds (34828.40 seconds total)