Starting phenix.real_space_refine on Fri Jan 19 20:26:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zku_11262/01_2024/6zku_11262_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 34 5.49 5 S 458 5.16 5 C 42360 2.51 5 N 10896 2.21 5 O 11727 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 TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "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 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 65505 Number of models: 1 Model: "" Number of chains: 69 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: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3301 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 384} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4285 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 25, 'TRANS': 514} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "V" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 90 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 103.378 53.612 245.250 1.00 28.77 S ATOM 2695 SG CYS 1 362 106.095 53.563 239.864 1.00 49.30 S ATOM 2676 SG CYS 1 359 110.512 53.786 246.005 1.00 30.74 S ATOM 3039 SG CYS 1 405 107.274 47.928 244.826 1.00 25.22 S ATOM 4116 SG CYS 2 103 101.052 49.672 264.403 1.00 35.65 S ATOM 4150 SG CYS 2 108 98.792 47.387 266.479 1.00 52.02 S ATOM 4430 SG CYS 2 144 102.519 46.054 260.920 1.00 49.79 S ATOM 4453 SG CYS 2 148 100.649 43.210 262.462 1.00 36.32 S ATOM 5793 SG CYS 3 114 106.193 71.235 229.803 1.00 20.32 S ATOM 5732 SG CYS 3 105 100.818 74.701 231.377 1.00 24.10 S ATOM 5753 SG CYS 3 108 106.777 76.521 233.248 1.00 9.73 S ATOM 6125 SG CYS 3 156 113.040 64.035 234.818 1.00 15.69 S ATOM 6102 SG CYS 3 153 111.068 67.269 240.358 1.00 16.38 S ATOM 6149 SG CYS 3 159 117.133 67.763 238.641 1.00 50.40 S ATOM 6479 SG CYS 3 203 113.077 70.272 234.753 1.00 77.02 S ATOM 5238 SG CYS 3 41 112.320 57.304 233.197 1.00 10.84 S ATOM 5324 SG CYS 3 52 108.599 58.478 232.234 1.00 20.03 S ATOM 5349 SG CYS 3 55 109.111 53.421 228.985 1.00 15.49 S ATOM 5450 SG CYS 3 69 112.737 53.568 230.401 1.00 19.07 S ATOM 16022 SG CYS 6 119 91.424 95.980 205.779 1.00 38.35 S ATOM 16252 SG CYS 6 149 87.892 93.834 211.033 1.00 70.13 S ATOM 15518 SG CYS 6 54 84.752 93.651 205.033 1.00 70.10 S ATOM 17444 SG CYS 9 116 92.060 95.097 217.429 1.00 32.39 S ATOM 17491 SG CYS 9 122 92.705 90.828 222.423 1.00 15.40 S ATOM 17218 SG CYS 9 87 96.559 90.431 217.162 1.00 9.91 S ATOM 17520 SG CYS 9 126 94.682 87.633 229.856 1.00 3.14 S ATOM 17191 SG CYS 9 83 98.306 89.312 224.712 1.00 17.85 S ATOM 17149 SG CYS 9 77 100.327 91.067 230.515 1.00 10.12 S ATOM 17168 SG CYS 9 80 99.710 84.514 228.897 1.00 14.37 S ATOM 39723 SG CYS b 59 95.913 84.150 245.448 1.00 26.59 S ATOM 39901 SG CYS b 84 99.181 84.155 243.162 1.00 17.63 S ATOM 39923 SG CYS b 87 97.297 86.906 243.840 1.00 22.96 S Time building chain proxies: 26.05, per 1000 atoms: 0.40 Number of scatterers: 65505 At special positions: 0 Unit cell: (177.24, 197.285, 295.4, 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 458 16.00 P 34 15.00 O 11727 8.00 N 10896 7.00 C 42360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.02 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.73 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 500 " - pdb=" SG CYS 1 362 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " 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 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " Number of angles added : 3 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 334 helices and 28 sheets defined 50.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.53 Creating SS restraints... Processing helix chain '1' and resid 33 through 39 Processing helix chain '1' and resid 45 through 62 removed outlier: 3.667A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.805A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 4.139A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 184 through 187 Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 243 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.415A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 387 through 399 Processing helix chain '1' and resid 407 through 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: 3.898A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.557A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 removed outlier: 4.004A 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 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' 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 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 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: 3.590A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 296 through 308 removed outlier: 3.820A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 removed outlier: 3.563A pdb=" N GLU 3 372 " --> pdb=" O ALA 3 369 " (cutoff:3.500A) No H-bonds generated for '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: 3.641A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.802A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 480 removed outlier: 3.725A pdb=" N SER 3 480 " --> pdb=" O LYS 3 476 " (cutoff:3.500A) Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 650 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 680 removed outlier: 3.662A pdb=" N ALA 3 680 " --> pdb=" O SER 3 676 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 676 through 680' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 11 removed outlier: 4.095A pdb=" N ALA 4 11 " --> pdb=" O VAL 4 8 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 11' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.675A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix removed outlier: 4.037A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 4.070A 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: 3.582A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.124A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.936A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 238 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 261 Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.722A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.221A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.126A 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 57 through 66 Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 138 removed outlier: 3.796A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG 5 132 " --> pdb=" O TRP 5 129 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.775A 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 26 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 94 through 105 removed outlier: 3.515A pdb=" N ALA 6 97 " --> pdb=" O ASN 6 94 " (cutoff:3.500A) Proline residue: 6 98 - end of helix 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 42 removed outlier: 3.700A pdb=" N PHE 9 42 " --> pdb=" O LEU 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 172 removed outlier: 5.681A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.816A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.890A 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: 3.518A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.826A 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 69 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.788A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.827A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' 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 5 through 22 removed outlier: 3.647A pdb=" N SER J 22 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.799A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 4.076A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 106 Processing helix chain 'J' and resid 113 through 116 No H-bonds generated for 'chain 'J' and resid 113 through 116' Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.091A 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 20 removed outlier: 3.516A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 50 Processing helix chain 'K' and resid 54 through 85 removed outlier: 4.163A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.575A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.810A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.187A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.667A 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: 4.035A 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: 3.936A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.140A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.355A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.641A 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 269 removed outlier: 4.947A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 291 removed outlier: 3.682A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.841A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.024A 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 400 removed outlier: 3.901A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.688A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.803A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 508 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 532 removed outlier: 4.013A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix No H-bonds generated for 'chain 'L' and resid 526 through 532' Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.078A 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: 3.742A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.568A 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: 3.612A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.717A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 155 removed outlier: 4.308A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY M 146 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 170 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: 4.969A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 221 Proline residue: M 217 - end of helix removed outlier: 4.057A pdb=" N HIS M 220 " --> 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 248 removed outlier: 4.914A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 277 removed outlier: 3.870A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.872A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.112A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.797A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 446 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 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: 4.236A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 167 Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 232 removed outlier: 3.872A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 252 removed outlier: 3.877A pdb=" N LEU N 243 " --> pdb=" O ILE N 239 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU N 245 " --> pdb=" O THR N 241 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 272 removed outlier: 4.512A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS N 272 " --> pdb=" O GLN N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 301 Processing helix chain 'N' and resid 311 through 316 removed outlier: 4.302A pdb=" N GLN N 316 " --> 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: 3.835A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.705A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.681A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 5.055A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 76 removed outlier: 3.645A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.538A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 4.238A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 removed outlier: 3.506A pdb=" N ALA Z 172 " --> pdb=" O ALA Z 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.954A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.730A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 43 No H-bonds generated for 'chain 'b' and resid 40 through 43' Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 28 through 31 No H-bonds generated for 'chain 'c' and resid 28 through 31' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.478A 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: 4.110A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 56 Processing helix chain 'd' and resid 60 through 62 No H-bonds generated for 'chain 'd' and resid 60 through 62' 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 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 310 through 318 removed outlier: 5.698A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.622A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.421A 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 64 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 4.079A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 67 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.643A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' 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: 3.921A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 83 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 38 through 46 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 71 through 73 No H-bonds generated for 'chain 'k' and resid 71 through 73' Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 117 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 157 Processing helix chain 'k' and resid 160 through 162 No H-bonds generated for 'chain 'k' and resid 160 through 162' Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 217 removed outlier: 5.438A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix removed outlier: 4.298A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 306 through 308 No H-bonds generated for 'chain 'k' and resid 306 through 308' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.103A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 33 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 36 through 47 removed outlier: 4.059A pdb=" N LYS m 39 " --> pdb=" O PRO m 36 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG m 46 " --> pdb=" O MET m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 45 through 52 removed outlier: 4.714A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 17 through 20 removed outlier: 3.719A pdb=" N SER o 20 " --> pdb=" O GLU o 17 " (cutoff:3.500A) No H-bonds generated for '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: 3.866A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 removed outlier: 3.765A pdb=" N TYR p 22 " --> pdb=" O PRO p 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 19 through 22' Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.663A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.601A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 116 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 68 through 73 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 50 removed outlier: 4.664A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 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 142 removed outlier: 3.894A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU t 142 " --> pdb=" O GLN t 138 " (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 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.994A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.589A 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 16 through 33 Processing helix chain 'z' and resid 2 through 29 Proline residue: z 7 - end of helix removed outlier: 3.505A pdb=" N MET z 12 " --> pdb=" O ILE z 9 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix removed outlier: 3.575A pdb=" N ILE z 26 " --> pdb=" O THR z 23 " (cutoff:3.500A) 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: 5.968A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.094A 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: 6.385A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 56 through 58 Processing sheet with id= F, first strand: chain '3' and resid 146 through 148 Processing sheet with id= G, first strand: chain '3' and resid 173 through 175 Processing sheet with id= H, first strand: chain '3' and resid 223 through 228 removed outlier: 3.615A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 282 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.535A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 490 through 493 removed outlier: 8.287A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '3' and resid 571 through 574 removed outlier: 3.656A pdb=" N ALA 3 571 " --> pdb=" O THR 3 583 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '4' and resid 63 through 69 removed outlier: 3.541A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 74 through 82 removed outlier: 6.743A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 172 through 177 Processing sheet with id= Q, first strand: chain '6' and resid 47 through 51 removed outlier: 6.507A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 65 through 67 Processing sheet with id= S, first strand: chain '9' and resid 92 through 98 removed outlier: 6.039A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 3.575A pdb=" N MET L 61 " --> pdb=" O MET L 82 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= V, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.429A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'e' and resid 51 through 57 removed outlier: 3.795A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.331A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.399A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2675 hydrogen bonds defined for protein. 7557 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: 21.41 Time building geometry restraints manager: 22.79 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: 27632 1.43 - 1.66: 38671 1.66 - 1.89: 746 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 67129 Sorted by residual: bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.325 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.592 0.241 3.80e-02 6.93e+02 4.01e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.00e-02 1.00e+04 3.46e+01 bond pdb=" OA3 CDL z 101 " pdb=" PA1 CDL z 101 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.00e-02 1.00e+04 3.45e+01 bond pdb=" O5D NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 1.757 1.556 0.201 3.50e-02 8.16e+02 3.30e+01 ... (remaining 67124 not shown) Histogram of bond angle deviations from ideal: 62.44 - 77.48: 72 77.48 - 92.52: 8 92.52 - 107.55: 3755 107.55 - 122.59: 79761 122.59 - 137.63: 7196 Bond angle restraints: 90792 Sorted by residual: angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.75 -24.01 1.95e+00 2.62e-01 1.51e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.91 13.42 1.14e+00 7.69e-01 1.39e+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 91.04 13.29 1.20e+00 6.94e-01 1.23e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 92.26 12.07 1.14e+00 7.69e-01 1.12e+02 angle pdb=" S1 FES 2 300 " pdb="FE1 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 92.35 11.98 1.20e+00 6.94e-01 9.97e+01 ... (remaining 90787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 39991 34.30 - 68.61: 654 68.61 - 102.91: 57 102.91 - 137.21: 2 137.21 - 171.52: 4 Dihedral angle restraints: 40708 sinusoidal: 17493 harmonic: 23215 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual 180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -132.64 -47.36 0 5.00e+00 4.00e-02 8.97e+01 dihedral pdb=" CA SER J 85 " pdb=" C SER J 85 " pdb=" N ASN J 86 " pdb=" CA ASN J 86 " ideal model delta harmonic sigma weight residual -180.00 -137.53 -42.47 0 5.00e+00 4.00e-02 7.22e+01 ... (remaining 40705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.222: 9824 4.222 - 8.444: 4 8.444 - 12.666: 0 12.666 - 16.889: 0 16.889 - 21.111: 24 Chirality restraints: 9852 Sorted by residual: chirality pdb="FE1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " pdb=" S4 SF4 3 802 " both_signs ideal model delta sigma weight residual False -10.55 10.56 -21.11 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.55 21.11 2.00e-01 2.50e+01 1.11e+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 -10.54 21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 9849 not shown) Planarity restraints: 11369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.035 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR 6 125 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.020 2.00e-02 2.50e+03 2.92e-02 1.71e+01 pdb=" CG TYR 9 40 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.025 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP A 106 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.003 2.00e-02 2.50e+03 ... (remaining 11366 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 17494 2.80 - 3.39: 69905 3.39 - 3.97: 134273 3.97 - 4.56: 188946 4.56 - 5.14: 274405 Nonbonded interactions: 685023 Sorted by model distance: nonbonded pdb=" OH TYR v 47 " pdb=" O MET v 77 " model vdw 2.218 2.440 nonbonded pdb=" OG SER k 22 " pdb=" O GLY k 119 " model vdw 2.232 2.440 nonbonded pdb=" O PHE M 105 " pdb=" OG1 THR M 109 " model vdw 2.251 2.440 nonbonded pdb=" O ALA L 245 " pdb=" OG SER L 249 " model vdw 2.256 2.440 nonbonded pdb=" OE2 GLU 5 31 " pdb=" OH TYR f 46 " model vdw 2.256 2.440 ... (remaining 685018 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 4.770 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 155.760 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.240 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 67129 Z= 0.569 Angle : 1.031 24.011 90792 Z= 0.553 Chirality : 1.038 21.111 9852 Planarity : 0.008 0.079 11369 Dihedral : 12.304 171.516 25712 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.09 % Favored : 95.90 % Rotamer: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.08), residues: 7846 helix: -1.93 (0.06), residues: 4108 sheet: -1.39 (0.24), residues: 395 loop : -1.94 (0.09), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP 1 371 HIS 0.019 0.003 HIS 4 200 PHE 0.064 0.004 PHE 4 171 TYR 0.078 0.004 TYR 6 125 ARG 0.026 0.001 ARG Y 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1922 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1918 time to evaluate : 5.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7990 (ttmt) REVERT: 1 54 ASP cc_start: 0.8038 (m-30) cc_final: 0.7653 (t70) REVERT: 1 339 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.6790 (mtm110) REVERT: 2 93 LYS cc_start: 0.8690 (mttm) cc_final: 0.8262 (mtmt) REVERT: 3 314 ASP cc_start: 0.8137 (m-30) cc_final: 0.7731 (m-30) REVERT: 3 418 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.7710 (ttp-110) REVERT: 3 427 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7474 (mmmt) REVERT: 3 447 LYS cc_start: 0.8752 (mttm) cc_final: 0.8352 (mtmm) REVERT: 3 476 LYS cc_start: 0.8594 (tttm) cc_final: 0.8050 (tppp) REVERT: 3 611 LEU cc_start: 0.8983 (mt) cc_final: 0.8775 (mt) REVERT: 3 643 GLN cc_start: 0.7561 (tp40) cc_final: 0.7311 (mm-40) REVERT: 3 647 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8099 (mt-10) REVERT: 3 669 LYS cc_start: 0.8101 (ttpm) cc_final: 0.7880 (ptmm) REVERT: 4 77 ASP cc_start: 0.8538 (t0) cc_final: 0.8331 (t0) REVERT: 4 182 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8808 (tm-30) REVERT: 5 178 ASP cc_start: 0.8614 (t70) cc_final: 0.8413 (t0) REVERT: 5 204 GLU cc_start: 0.8788 (tt0) cc_final: 0.8451 (tt0) REVERT: 6 25 ARG cc_start: 0.6597 (ttt180) cc_final: 0.6141 (mpt180) REVERT: 6 68 ASP cc_start: 0.8841 (t70) cc_final: 0.8609 (t70) REVERT: 9 11 SER cc_start: 0.8655 (m) cc_final: 0.8320 (p) REVERT: 9 13 ASP cc_start: 0.8136 (p0) cc_final: 0.7593 (p0) REVERT: 9 15 LYS cc_start: 0.8132 (tptp) cc_final: 0.7421 (ttmt) REVERT: 9 19 ASP cc_start: 0.8658 (m-30) cc_final: 0.8282 (t0) REVERT: A 15 THR cc_start: 0.8419 (m) cc_final: 0.7937 (m) REVERT: A 16 LEU cc_start: 0.8264 (tp) cc_final: 0.7960 (mp) REVERT: H 1 MET cc_start: 0.6756 (tpp) cc_final: 0.6553 (tpt) REVERT: J 1 MET cc_start: 0.3810 (tmt) cc_final: 0.2410 (tpp) REVERT: J 103 MET cc_start: 0.5745 (ttt) cc_final: 0.5424 (tpp) REVERT: J 173 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7386 (ttp-170) REVERT: L 45 ILE cc_start: 0.7361 (mm) cc_final: 0.7127 (mm) REVERT: L 139 GLN cc_start: 0.8424 (tt0) cc_final: 0.8121 (tt0) REVERT: L 205 ASN cc_start: 0.7517 (t0) cc_final: 0.7178 (p0) REVERT: L 269 ASN cc_start: 0.7718 (m110) cc_final: 0.7505 (m-40) REVERT: L 290 MET cc_start: 0.5690 (ttp) cc_final: 0.4659 (tmm) REVERT: L 364 LYS cc_start: 0.5706 (mttt) cc_final: 0.5439 (mppt) REVERT: L 407 TRP cc_start: 0.6499 (t-100) cc_final: 0.6243 (t-100) REVERT: L 410 LEU cc_start: 0.7282 (tt) cc_final: 0.6815 (mt) REVERT: L 453 SER cc_start: 0.7043 (p) cc_final: 0.6667 (m) REVERT: L 466 PHE cc_start: 0.5258 (t80) cc_final: 0.4995 (t80) REVERT: L 480 MET cc_start: 0.4664 (mtp) cc_final: 0.4462 (tpt) REVERT: M 19 LYS cc_start: 0.7054 (mttp) cc_final: 0.6792 (mmtt) REVERT: M 98 MET cc_start: 0.8020 (mmp) cc_final: 0.7795 (mmp) REVERT: M 158 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8184 (tp) REVERT: M 334 TYR cc_start: 0.8596 (t80) cc_final: 0.8227 (t80) REVERT: N 229 SER cc_start: 0.8361 (p) cc_final: 0.8148 (m) REVERT: N 315 TRP cc_start: 0.6230 (m-10) cc_final: 0.5782 (m-10) REVERT: W 37 VAL cc_start: 0.8157 (t) cc_final: 0.7782 (m) REVERT: X 14 ARG cc_start: 0.6413 (mtp180) cc_final: 0.5296 (mpt180) REVERT: Y 54 ARG cc_start: 0.7468 (mmp80) cc_final: 0.6958 (mtp-110) REVERT: Y 148 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7208 (mp0) REVERT: Z 31 TYR cc_start: 0.5933 (m-80) cc_final: 0.5514 (m-10) REVERT: Z 40 VAL cc_start: 0.7592 (t) cc_final: 0.7388 (t) REVERT: Z 66 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7250 (tt0) REVERT: Z 72 ASP cc_start: 0.7774 (p0) cc_final: 0.7532 (p0) REVERT: Z 112 CYS cc_start: 0.7947 (t) cc_final: 0.7687 (t) REVERT: Z 142 TYR cc_start: 0.8655 (m-80) cc_final: 0.8420 (m-80) REVERT: b 51 GLN cc_start: 0.8087 (mm110) cc_final: 0.7856 (mm-40) REVERT: b 78 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7232 (tt0) REVERT: c 109 LYS cc_start: 0.7957 (mttm) cc_final: 0.7463 (mmpt) REVERT: d 77 ASP cc_start: 0.8335 (t0) cc_final: 0.8123 (t0) REVERT: d 123 GLU cc_start: 0.7904 (pt0) cc_final: 0.7488 (tm-30) REVERT: d 140 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7222 (mmtm) REVERT: d 226 LYS cc_start: 0.8375 (mmtp) cc_final: 0.8077 (mtmm) REVERT: d 246 PHE cc_start: 0.8096 (m-80) cc_final: 0.7822 (m-80) REVERT: d 250 HIS cc_start: 0.6703 (m170) cc_final: 0.6223 (m170) REVERT: e 26 SER cc_start: 0.8351 (m) cc_final: 0.8112 (m) REVERT: e 34 ASP cc_start: 0.8315 (m-30) cc_final: 0.8005 (m-30) REVERT: f 45 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7840 (tttt) REVERT: f 66 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8246 (mtmm) REVERT: f 93 MET cc_start: 0.8452 (mmm) cc_final: 0.8162 (mtp) REVERT: g 56 LYS cc_start: 0.8196 (tmmt) cc_final: 0.7544 (tppt) REVERT: g 63 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.8055 (tpp-160) REVERT: g 79 ASP cc_start: 0.8174 (m-30) cc_final: 0.7902 (m-30) REVERT: h 32 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7947 (pttp) REVERT: h 108 ASP cc_start: 0.8396 (t70) cc_final: 0.8196 (t70) REVERT: i 1 MET cc_start: 0.4812 (tpt) cc_final: 0.4589 (ttm) REVERT: i 2 GLU cc_start: 0.7421 (pt0) cc_final: 0.7060 (pt0) REVERT: i 8 LYS cc_start: 0.8186 (mttt) cc_final: 0.7866 (mttp) REVERT: i 32 ASP cc_start: 0.9057 (t70) cc_final: 0.8812 (t70) REVERT: j 6 LEU cc_start: 0.5662 (mm) cc_final: 0.5424 (mt) REVERT: j 16 LEU cc_start: 0.8552 (mt) cc_final: 0.8276 (mt) REVERT: j 66 ASP cc_start: 0.7447 (p0) cc_final: 0.7032 (m-30) REVERT: k 20 GLU cc_start: 0.7553 (pp20) cc_final: 0.7048 (tp30) REVERT: k 25 ILE cc_start: 0.7541 (mt) cc_final: 0.6999 (pp) REVERT: k 51 PHE cc_start: 0.7431 (m-10) cc_final: 0.6948 (m-80) REVERT: k 60 ASP cc_start: 0.6882 (m-30) cc_final: 0.6472 (m-30) REVERT: k 143 PHE cc_start: 0.4475 (m-10) cc_final: 0.3575 (m-80) REVERT: k 185 LYS cc_start: 0.5646 (mtmp) cc_final: 0.5199 (pptt) REVERT: k 291 ARG cc_start: 0.6369 (tmm160) cc_final: 0.6094 (ttp80) REVERT: l 27 ARG cc_start: 0.8441 (mmt-90) cc_final: 0.8108 (mmp80) REVERT: l 81 GLN cc_start: 0.7731 (tp40) cc_final: 0.7515 (tp-100) REVERT: m 14 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7886 (mmtp) REVERT: m 78 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7210 (mm-30) REVERT: o 54 LEU cc_start: 0.6405 (mt) cc_final: 0.6094 (tp) REVERT: o 62 PHE cc_start: 0.8395 (t80) cc_final: 0.8140 (t80) REVERT: p 109 ASP cc_start: 0.7110 (m-30) cc_final: 0.6837 (m-30) REVERT: p 119 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7536 (mmpt) REVERT: q 27 ARG cc_start: 0.7759 (ptm160) cc_final: 0.5143 (tpt-90) REVERT: q 130 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7444 (tp30) REVERT: r 18 ARG cc_start: 0.7341 (tpt170) cc_final: 0.7122 (tpt90) REVERT: r 82 HIS cc_start: 0.8495 (t70) cc_final: 0.8146 (t-170) REVERT: s 57 TYR cc_start: 0.4865 (m-80) cc_final: 0.4609 (m-80) REVERT: s 62 LEU cc_start: 0.8094 (tp) cc_final: 0.7887 (tm) REVERT: s 80 LYS cc_start: 0.7474 (mmpt) cc_final: 0.6853 (tptp) REVERT: s 108 LEU cc_start: 0.6282 (mt) cc_final: 0.5972 (mp) REVERT: t 79 TYR cc_start: 0.6835 (t80) cc_final: 0.6565 (t80) REVERT: u 16 GLN cc_start: 0.7150 (tt0) cc_final: 0.6827 (tt0) REVERT: u 31 THR cc_start: 0.6911 (m) cc_final: 0.6560 (p) REVERT: v 71 LEU cc_start: 0.6201 (tp) cc_final: 0.5917 (tt) REVERT: v 72 ASN cc_start: 0.6068 (m-40) cc_final: 0.5814 (m-40) REVERT: v 80 ASP cc_start: 0.6805 (m-30) cc_final: 0.6374 (m-30) REVERT: w 49 LYS cc_start: 0.6640 (ptpt) cc_final: 0.6371 (ptmm) REVERT: w 58 MET cc_start: 0.7838 (tmm) cc_final: 0.7435 (ttp) REVERT: w 59 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7671 (mtt-85) REVERT: w 85 MET cc_start: 0.7735 (ptm) cc_final: 0.7175 (mpp) REVERT: x 39 VAL cc_start: 0.8658 (m) cc_final: 0.8353 (t) REVERT: y 42 LEU cc_start: 0.8159 (mt) cc_final: 0.7724 (mt) REVERT: y 44 TYR cc_start: 0.7915 (m-80) cc_final: 0.7691 (m-80) outliers start: 4 outliers final: 4 residues processed: 1922 average time/residue: 1.5612 time to fit residues: 3835.5528 Evaluate side-chains 1233 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1228 time to evaluate : 5.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain M residue 158 LEU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 282 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 655 optimal weight: 9.9990 chunk 588 optimal weight: 5.9990 chunk 326 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 396 optimal weight: 1.9990 chunk 314 optimal weight: 8.9990 chunk 608 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 452 optimal weight: 0.8980 chunk 704 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 356 HIS 1 373 ASN 1 435 GLN 1 437 HIS 2 121 GLN 3 82 ASN 3 179 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 441 GLN 4 5 GLN 4 54 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 313 GLN 5 69 ASN 5 144 ASN 9 6 ASN 9 65 HIS 9 170 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN H 317 GLN J 46 ASN K 50 ASN K 52 HIS K 92 ASN L 23 ASN L 31 ASN L 194 ASN L 210 ASN L 248 HIS L 270 ASN L 470 ASN M 81 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN M 333 ASN M 415 GLN N 120 GLN N 172 GLN N 273 ASN W 124 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN Z 114 GLN Z 130 GLN b 36 ASN b 74 ASN d 36 ASN d 87 HIS e 85 GLN e 92 ASN f 49 GLN g 125 HIS h 20 GLN i 12 GLN i 91 HIS i 116 ASN i 135 GLN k 107 GLN k 180 GLN k 287 HIS ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 70 GLN o 61 GLN t 11 HIS u 13 GLN u 24 GLN v 87 ASN w 57 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.258 67129 Z= 0.516 Angle : 1.608 51.054 90792 Z= 1.036 Chirality : 0.316 6.492 9852 Planarity : 0.005 0.058 11369 Dihedral : 12.271 172.406 9905 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.48 % Allowed : 11.68 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.09), residues: 7846 helix: -0.33 (0.07), residues: 4134 sheet: -1.00 (0.25), residues: 395 loop : -1.39 (0.10), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 4 10 HIS 0.006 0.001 HIS b 68 PHE 0.027 0.002 PHE 4 171 TYR 0.028 0.002 TYR 6 125 ARG 0.009 0.001 ARG L 436 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1322 time to evaluate : 5.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7945 (ttmp) REVERT: 1 54 ASP cc_start: 0.8108 (m-30) cc_final: 0.7776 (t0) REVERT: 1 281 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: 1 339 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.6704 (mtm110) REVERT: 2 93 LYS cc_start: 0.8719 (mttm) cc_final: 0.8168 (mtmm) REVERT: 3 314 ASP cc_start: 0.8116 (m-30) cc_final: 0.7792 (m-30) REVERT: 3 418 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7660 (ttp-110) REVERT: 3 447 LYS cc_start: 0.8776 (mttm) cc_final: 0.8431 (mtmm) REVERT: 3 476 LYS cc_start: 0.8430 (tttm) cc_final: 0.7938 (tttt) REVERT: 3 643 GLN cc_start: 0.7316 (tp40) cc_final: 0.6973 (tp-100) REVERT: 3 647 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7387 (tp30) REVERT: 3 669 LYS cc_start: 0.8130 (ttpm) cc_final: 0.7818 (ptmm) REVERT: 4 47 LEU cc_start: 0.7735 (tt) cc_final: 0.7481 (tm) REVERT: 4 77 ASP cc_start: 0.8285 (t0) cc_final: 0.8030 (t0) REVERT: 4 182 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8804 (tm-30) REVERT: 4 290 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8420 (mtp-110) REVERT: 6 25 ARG cc_start: 0.6378 (ttt180) cc_final: 0.6152 (mpt180) REVERT: 6 68 ASP cc_start: 0.8854 (t70) cc_final: 0.8637 (t70) REVERT: 9 11 SER cc_start: 0.8692 (m) cc_final: 0.8335 (p) REVERT: 9 13 ASP cc_start: 0.8095 (p0) cc_final: 0.7673 (p0) REVERT: 9 15 LYS cc_start: 0.8046 (tptp) cc_final: 0.7408 (ttmt) REVERT: 9 19 ASP cc_start: 0.8616 (m-30) cc_final: 0.8230 (t0) REVERT: A 16 LEU cc_start: 0.8185 (tp) cc_final: 0.7746 (mp) REVERT: A 19 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8093 (p) REVERT: A 87 MET cc_start: 0.8565 (tmt) cc_final: 0.8187 (tmt) REVERT: H 234 MET cc_start: 0.8574 (tpp) cc_final: 0.8369 (mmm) REVERT: J 1 MET cc_start: 0.3748 (tmt) cc_final: 0.3212 (ppp) REVERT: J 103 MET cc_start: 0.5670 (ttt) cc_final: 0.5129 (mpp) REVERT: K 9 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8440 (mtp) REVERT: K 37 MET cc_start: 0.8561 (tmm) cc_final: 0.8230 (ttp) REVERT: L 29 PHE cc_start: 0.3690 (OUTLIER) cc_final: 0.3038 (t80) REVERT: L 45 ILE cc_start: 0.7407 (mm) cc_final: 0.7183 (mm) REVERT: L 139 GLN cc_start: 0.8434 (tt0) cc_final: 0.8033 (tt0) REVERT: L 205 ASN cc_start: 0.7487 (t0) cc_final: 0.7138 (p0) REVERT: L 235 SER cc_start: 0.6803 (m) cc_final: 0.6448 (t) REVERT: L 251 THR cc_start: 0.6967 (m) cc_final: 0.6589 (p) REVERT: L 283 MET cc_start: 0.6924 (tpt) cc_final: 0.6544 (tpt) REVERT: L 290 MET cc_start: 0.5582 (ttp) cc_final: 0.4720 (tmm) REVERT: L 331 THR cc_start: 0.6495 (OUTLIER) cc_final: 0.6172 (m) REVERT: L 358 LYS cc_start: 0.6724 (mptt) cc_final: 0.6508 (mptp) REVERT: L 364 LYS cc_start: 0.5621 (mttt) cc_final: 0.5361 (mppt) REVERT: L 377 SER cc_start: 0.6222 (OUTLIER) cc_final: 0.5705 (t) REVERT: M 19 LYS cc_start: 0.7100 (mttp) cc_final: 0.6819 (mmtt) REVERT: M 98 MET cc_start: 0.8016 (mmp) cc_final: 0.7625 (mmp) REVERT: N 280 THR cc_start: 0.8724 (m) cc_final: 0.8455 (p) REVERT: N 329 MET cc_start: 0.8291 (mtm) cc_final: 0.8010 (mmp) REVERT: W 37 VAL cc_start: 0.8185 (t) cc_final: 0.7855 (m) REVERT: W 99 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: X 14 ARG cc_start: 0.6082 (mtp180) cc_final: 0.5237 (mpt180) REVERT: Y 18 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7908 (mtpt) REVERT: Y 109 CYS cc_start: 0.8463 (t) cc_final: 0.8081 (m) REVERT: Y 123 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: Y 144 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6266 (mtm180) REVERT: Y 148 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7181 (mp0) REVERT: Z 42 ARG cc_start: 0.6715 (tmt170) cc_final: 0.6437 (tmt170) REVERT: Z 66 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7289 (tt0) REVERT: Z 112 CYS cc_start: 0.7961 (t) cc_final: 0.7702 (t) REVERT: b 37 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: b 51 GLN cc_start: 0.8092 (mm110) cc_final: 0.7868 (mm-40) REVERT: b 78 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7308 (tt0) REVERT: c 106 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: c 109 LYS cc_start: 0.8044 (mttm) cc_final: 0.7561 (mmpt) REVERT: d 77 ASP cc_start: 0.8333 (t0) cc_final: 0.8107 (t0) REVERT: d 140 LYS cc_start: 0.7598 (mtmm) cc_final: 0.7332 (mmtm) REVERT: d 181 TYR cc_start: 0.8969 (t80) cc_final: 0.8740 (t80) REVERT: d 226 LYS cc_start: 0.8437 (mmtp) cc_final: 0.8133 (mtmm) REVERT: d 246 PHE cc_start: 0.8134 (m-80) cc_final: 0.7792 (m-80) REVERT: d 250 HIS cc_start: 0.6435 (m170) cc_final: 0.6228 (m170) REVERT: e 26 SER cc_start: 0.8306 (m) cc_final: 0.8078 (m) REVERT: e 39 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8574 (mmm-85) REVERT: e 88 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7676 (mtt180) REVERT: f 44 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8123 (ttm170) REVERT: f 93 MET cc_start: 0.8447 (mmm) cc_final: 0.8221 (mtp) REVERT: g 56 LYS cc_start: 0.8137 (tmmt) cc_final: 0.7602 (tppt) REVERT: g 98 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8739 (mt0) REVERT: h 17 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7314 (mmm160) REVERT: h 32 LYS cc_start: 0.8498 (mmtt) cc_final: 0.7890 (pttp) REVERT: h 108 ASP cc_start: 0.8363 (t70) cc_final: 0.8131 (t70) REVERT: h 109 GLU cc_start: 0.8179 (tt0) cc_final: 0.7976 (tt0) REVERT: i 2 GLU cc_start: 0.7568 (pt0) cc_final: 0.7183 (pt0) REVERT: i 32 ASP cc_start: 0.9083 (t70) cc_final: 0.8879 (t70) REVERT: i 71 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7888 (ttmt) REVERT: i 107 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7768 (ptmt) REVERT: j 14 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5196 (mtp85) REVERT: j 16 LEU cc_start: 0.8399 (mt) cc_final: 0.8140 (mt) REVERT: j 57 GLU cc_start: 0.6974 (tp30) cc_final: 0.6447 (tp30) REVERT: j 66 ASP cc_start: 0.7535 (p0) cc_final: 0.6928 (m-30) REVERT: k 20 GLU cc_start: 0.7388 (pp20) cc_final: 0.6905 (tp30) REVERT: k 67 LYS cc_start: 0.7109 (mttp) cc_final: 0.6850 (mmpt) REVERT: k 72 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.5875 (pmm-80) REVERT: k 76 ASN cc_start: 0.7449 (t0) cc_final: 0.7196 (t0) REVERT: k 131 ASP cc_start: 0.6392 (t70) cc_final: 0.5955 (t70) REVERT: k 185 LYS cc_start: 0.5566 (mtmp) cc_final: 0.5007 (pptt) REVERT: k 319 LEU cc_start: 0.7105 (mt) cc_final: 0.6890 (mm) REVERT: l 27 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8168 (mmp80) REVERT: m 9 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7947 (tmmm) REVERT: m 14 LYS cc_start: 0.7970 (mtmt) cc_final: 0.7730 (mmtp) REVERT: o 54 LEU cc_start: 0.6296 (mt) cc_final: 0.6000 (tp) REVERT: o 58 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6243 (mp) REVERT: o 62 PHE cc_start: 0.8470 (t80) cc_final: 0.8135 (t80) REVERT: p 119 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7527 (mmpt) REVERT: q 92 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: r 82 HIS cc_start: 0.8560 (t70) cc_final: 0.8191 (t-170) REVERT: r 86 LYS cc_start: 0.7543 (tttt) cc_final: 0.7208 (tptm) REVERT: r 87 TYR cc_start: 0.6964 (m-80) cc_final: 0.6741 (m-80) REVERT: s 19 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.5905 (mp) REVERT: s 80 LYS cc_start: 0.7321 (mmpt) cc_final: 0.6840 (tptp) REVERT: s 103 ARG cc_start: 0.6524 (tmt90) cc_final: 0.6291 (tpt90) REVERT: t 37 ARG cc_start: 0.6096 (tpp-160) cc_final: 0.5746 (mtp-110) REVERT: t 79 TYR cc_start: 0.7045 (t80) cc_final: 0.6733 (t80) REVERT: u 16 GLN cc_start: 0.7185 (tt0) cc_final: 0.6850 (tt0) REVERT: u 31 THR cc_start: 0.7150 (m) cc_final: 0.6849 (p) REVERT: u 39 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.4836 (ttm-80) REVERT: v 27 TYR cc_start: 0.5123 (m-80) cc_final: 0.4912 (m-10) REVERT: v 77 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4927 (mpp) REVERT: v 80 ASP cc_start: 0.6958 (m-30) cc_final: 0.6641 (m-30) REVERT: v 132 GLN cc_start: 0.6460 (mt0) cc_final: 0.6019 (mt0) REVERT: w 58 MET cc_start: 0.8004 (tmm) cc_final: 0.7662 (ttp) REVERT: w 59 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7482 (ttt-90) REVERT: w 85 MET cc_start: 0.7768 (ptm) cc_final: 0.6931 (mpp) REVERT: w 95 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7029 (mtp180) REVERT: x 38 ASP cc_start: 0.6526 (m-30) cc_final: 0.6260 (m-30) REVERT: y 10 HIS cc_start: 0.5822 (OUTLIER) cc_final: 0.4927 (p-80) REVERT: y 38 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7448 (ttp-170) REVERT: y 44 TYR cc_start: 0.8004 (m-80) cc_final: 0.7698 (m-80) REVERT: z 68 ASN cc_start: 0.8726 (t0) cc_final: 0.8324 (t0) outliers start: 243 outliers final: 85 residues processed: 1446 average time/residue: 1.4548 time to fit residues: 2724.1889 Evaluate side-chains 1271 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1159 time to evaluate : 5.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 2 residue 136 LEU Chi-restraints excluded: chain 2 residue 162 GLU Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 232 ASP Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 425 SER Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 4 residue 75 LYS Chi-restraints excluded: chain 4 residue 165 THR Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 12 MET Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 377 SER Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 330 THR Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 99 GLU Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain Y residue 144 ARG Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 126 LYS Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 37 GLU Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain e residue 17 GLU Chi-restraints excluded: chain e residue 39 ARG Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 44 ARG Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain h residue 49 SER Chi-restraints excluded: chain i residue 53 LYS Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain i residue 107 LYS Chi-restraints excluded: chain j residue 14 ARG Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 72 ARG Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 216 GLU Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 9 LYS Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain n residue 63 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 58 LEU Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain t residue 127 LEU Chi-restraints excluded: chain u residue 39 ARG Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain y residue 10 HIS Chi-restraints excluded: chain y residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 391 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 586 optimal weight: 2.9990 chunk 479 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 705 optimal weight: 30.0000 chunk 762 optimal weight: 5.9990 chunk 628 optimal weight: 9.9990 chunk 700 optimal weight: 40.0000 chunk 240 optimal weight: 0.0970 chunk 566 optimal weight: 8.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 435 GLN 1 437 HIS 3 237 ASN 3 444 GLN ** 3 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN A 10 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN J 46 ASN K 52 HIS L 116 GLN ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN M 30 HIS ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 172 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 36 ASN e 85 GLN f 72 GLN i 12 GLN i 46 ASN i 116 ASN i 135 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 81 GLN p 49 GLN t 11 HIS u 50 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 67129 Z= 0.517 Angle : 1.598 50.649 90792 Z= 1.031 Chirality : 0.316 6.464 9852 Planarity : 0.005 0.061 11369 Dihedral : 11.765 171.815 9897 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.01 % Allowed : 13.06 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.09), residues: 7846 helix: 0.28 (0.08), residues: 4143 sheet: -0.80 (0.25), residues: 394 loop : -1.12 (0.11), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 272 HIS 0.008 0.001 HIS t 168 PHE 0.023 0.002 PHE 4 171 TYR 0.020 0.002 TYR 6 125 ARG 0.012 0.001 ARG s 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1223 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7924 (ttmp) REVERT: 1 54 ASP cc_start: 0.8202 (m-30) cc_final: 0.7878 (t0) REVERT: 1 281 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: 1 339 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.6786 (mtm110) REVERT: 1 432 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8106 (ptp90) REVERT: 2 93 LYS cc_start: 0.8828 (mttm) cc_final: 0.8287 (mtmm) REVERT: 3 314 ASP cc_start: 0.7912 (m-30) cc_final: 0.7624 (m-30) REVERT: 3 418 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7606 (ttp-110) REVERT: 3 447 LYS cc_start: 0.8801 (mttm) cc_final: 0.8432 (mtmm) REVERT: 3 515 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7781 (mtp180) REVERT: 3 643 GLN cc_start: 0.7216 (tp40) cc_final: 0.6425 (tp-100) REVERT: 3 647 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8018 (mt-10) REVERT: 3 669 LYS cc_start: 0.8209 (ttpm) cc_final: 0.7955 (ptmm) REVERT: 4 47 LEU cc_start: 0.7757 (tt) cc_final: 0.7500 (tm) REVERT: 4 182 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8852 (tm-30) REVERT: 4 290 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8438 (mtp-110) REVERT: 6 25 ARG cc_start: 0.6304 (ttt180) cc_final: 0.6080 (mpt180) REVERT: 9 11 SER cc_start: 0.8681 (m) cc_final: 0.8310 (p) REVERT: 9 13 ASP cc_start: 0.8145 (p0) cc_final: 0.7757 (p0) REVERT: 9 15 LYS cc_start: 0.8041 (tptp) cc_final: 0.7404 (ttmt) REVERT: 9 19 ASP cc_start: 0.8618 (m-30) cc_final: 0.8187 (t0) REVERT: 9 110 ASP cc_start: 0.8385 (m-30) cc_final: 0.8159 (m-30) REVERT: A 16 LEU cc_start: 0.8159 (tp) cc_final: 0.7739 (mp) REVERT: A 19 THR cc_start: 0.8303 (m) cc_final: 0.8078 (p) REVERT: A 83 ASN cc_start: 0.8318 (t0) cc_final: 0.8080 (t0) REVERT: A 87 MET cc_start: 0.8572 (tmt) cc_final: 0.8328 (tmt) REVERT: H 234 MET cc_start: 0.8558 (tpp) cc_final: 0.8349 (mmm) REVERT: H 253 GLU cc_start: 0.8391 (mp0) cc_final: 0.8174 (mp0) REVERT: J 1 MET cc_start: 0.3654 (tmt) cc_final: 0.3013 (ppp) REVERT: J 103 MET cc_start: 0.5787 (ttt) cc_final: 0.5256 (mpp) REVERT: K 9 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: K 37 MET cc_start: 0.8566 (tmm) cc_final: 0.8202 (ttp) REVERT: L 29 PHE cc_start: 0.4035 (OUTLIER) cc_final: 0.3531 (t80) REVERT: L 139 GLN cc_start: 0.8500 (tt0) cc_final: 0.8268 (tt0) REVERT: L 179 ASP cc_start: 0.7367 (m-30) cc_final: 0.7062 (m-30) REVERT: L 205 ASN cc_start: 0.7517 (t0) cc_final: 0.7229 (p0) REVERT: L 235 SER cc_start: 0.6804 (m) cc_final: 0.6432 (t) REVERT: L 251 THR cc_start: 0.7301 (m) cc_final: 0.6877 (p) REVERT: L 283 MET cc_start: 0.6899 (tpt) cc_final: 0.6485 (tpt) REVERT: L 290 MET cc_start: 0.5611 (ttp) cc_final: 0.4786 (tmt) REVERT: M 19 LYS cc_start: 0.7112 (mttp) cc_final: 0.6795 (mmtt) REVERT: M 98 MET cc_start: 0.7972 (mmp) cc_final: 0.7430 (mmp) REVERT: M 119 TYR cc_start: 0.8261 (t80) cc_final: 0.8011 (t80) REVERT: N 71 MET cc_start: 0.8327 (tpp) cc_final: 0.8043 (tpt) REVERT: N 242 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5368 (pp) REVERT: N 280 THR cc_start: 0.8766 (m) cc_final: 0.8530 (p) REVERT: N 290 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7217 (mm) REVERT: N 315 TRP cc_start: 0.6169 (m-10) cc_final: 0.5356 (m-10) REVERT: N 329 MET cc_start: 0.8297 (mtm) cc_final: 0.8001 (mmp) REVERT: W 37 VAL cc_start: 0.8188 (t) cc_final: 0.7852 (m) REVERT: W 99 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: X 14 ARG cc_start: 0.5773 (mtp180) cc_final: 0.4997 (mpt180) REVERT: X 15 VAL cc_start: 0.4697 (t) cc_final: 0.4327 (p) REVERT: Y 3 ILE cc_start: 0.7430 (mt) cc_final: 0.6962 (tp) REVERT: Y 109 CYS cc_start: 0.8419 (t) cc_final: 0.8089 (m) REVERT: Y 123 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: Y 148 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7190 (mp0) REVERT: Z 66 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7255 (tt0) REVERT: Z 112 CYS cc_start: 0.7848 (t) cc_final: 0.7600 (t) REVERT: Z 129 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6743 (tp40) REVERT: b 37 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: b 51 GLN cc_start: 0.8114 (mm110) cc_final: 0.7858 (mm-40) REVERT: b 78 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7297 (tt0) REVERT: c 106 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: c 109 LYS cc_start: 0.8060 (mttm) cc_final: 0.7565 (mmpt) REVERT: d 77 ASP cc_start: 0.8352 (t0) cc_final: 0.8067 (t0) REVERT: d 140 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7383 (mmtm) REVERT: d 181 TYR cc_start: 0.8987 (t80) cc_final: 0.8740 (t80) REVERT: d 226 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8134 (mtmm) REVERT: d 246 PHE cc_start: 0.8128 (m-80) cc_final: 0.7708 (m-80) REVERT: d 250 HIS cc_start: 0.6409 (m170) cc_final: 0.6177 (m170) REVERT: e 26 SER cc_start: 0.8293 (m) cc_final: 0.8066 (m) REVERT: e 88 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7661 (mtt180) REVERT: f 93 MET cc_start: 0.8423 (mmm) cc_final: 0.8172 (mtp) REVERT: g 56 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7721 (tppt) REVERT: g 86 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8262 (mtmm) REVERT: g 99 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8190 (ttp80) REVERT: h 32 LYS cc_start: 0.8573 (mmtt) cc_final: 0.7930 (pttp) REVERT: h 39 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8334 (tmtm) REVERT: i 2 GLU cc_start: 0.7469 (pt0) cc_final: 0.7112 (pt0) REVERT: i 32 ASP cc_start: 0.9174 (t70) cc_final: 0.8954 (t0) REVERT: i 71 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7852 (ttmt) REVERT: j 14 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5259 (mtp85) REVERT: j 16 LEU cc_start: 0.8469 (mt) cc_final: 0.8147 (mt) REVERT: j 57 GLU cc_start: 0.7180 (tp30) cc_final: 0.6730 (tp30) REVERT: j 66 ASP cc_start: 0.7533 (p0) cc_final: 0.7073 (m-30) REVERT: k 20 GLU cc_start: 0.7451 (pp20) cc_final: 0.6926 (tp30) REVERT: k 51 PHE cc_start: 0.6666 (m-80) cc_final: 0.6427 (m-80) REVERT: k 60 ASP cc_start: 0.7097 (m-30) cc_final: 0.6889 (m-30) REVERT: k 67 LYS cc_start: 0.7167 (mttp) cc_final: 0.6931 (mmpt) REVERT: k 72 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5921 (pmm-80) REVERT: k 76 ASN cc_start: 0.7211 (t0) cc_final: 0.6625 (t0) REVERT: k 101 TYR cc_start: 0.7127 (t80) cc_final: 0.6911 (t80) REVERT: k 185 LYS cc_start: 0.5592 (mtmp) cc_final: 0.5070 (pttp) REVERT: k 192 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.4790 (OUTLIER) REVERT: k 245 LYS cc_start: 0.5374 (ttpt) cc_final: 0.4991 (tttt) REVERT: k 302 ARG cc_start: 0.4872 (mpt180) cc_final: 0.4628 (mpt180) REVERT: k 319 LEU cc_start: 0.7123 (mt) cc_final: 0.6894 (mm) REVERT: l 27 ARG cc_start: 0.8423 (mmt-90) cc_final: 0.8188 (mmp80) REVERT: m 9 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7905 (tmmm) REVERT: m 21 SER cc_start: 0.8884 (m) cc_final: 0.8438 (m) REVERT: o 54 LEU cc_start: 0.6331 (mt) cc_final: 0.6022 (tp) REVERT: o 58 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6239 (mp) REVERT: o 62 PHE cc_start: 0.8475 (t80) cc_final: 0.8086 (t80) REVERT: p 119 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7495 (mmpt) REVERT: q 27 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7794 (ptm160) REVERT: q 92 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: r 82 HIS cc_start: 0.8556 (t70) cc_final: 0.8238 (t-170) REVERT: r 87 TYR cc_start: 0.7022 (m-80) cc_final: 0.6725 (m-80) REVERT: s 17 GLU cc_start: 0.4839 (OUTLIER) cc_final: 0.3462 (pp20) REVERT: s 19 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6483 (mm) REVERT: s 21 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5275 (ppp) REVERT: t 63 LEU cc_start: 0.4059 (tt) cc_final: 0.3794 (tm) REVERT: t 79 TYR cc_start: 0.6964 (t80) cc_final: 0.6727 (t80) REVERT: u 16 GLN cc_start: 0.7206 (tt0) cc_final: 0.6936 (tt0) REVERT: v 77 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.5175 (mpp) REVERT: v 80 ASP cc_start: 0.7021 (m-30) cc_final: 0.6665 (m-30) REVERT: v 132 GLN cc_start: 0.6666 (mt0) cc_final: 0.6251 (mt0) REVERT: w 58 MET cc_start: 0.8077 (tmm) cc_final: 0.7555 (ttp) REVERT: w 59 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7501 (mtt-85) REVERT: w 85 MET cc_start: 0.7763 (ptm) cc_final: 0.6893 (mpp) REVERT: w 95 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7074 (mtp180) REVERT: x 38 ASP cc_start: 0.6444 (m-30) cc_final: 0.6186 (m-30) REVERT: y 10 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.4972 (p-80) REVERT: y 38 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7408 (ttp-170) REVERT: z 68 ASN cc_start: 0.8724 (t0) cc_final: 0.8466 (t0) outliers start: 280 outliers final: 125 residues processed: 1376 average time/residue: 1.4408 time to fit residues: 2565.7336 Evaluate side-chains 1290 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1138 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 114 ASP Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 136 LEU Chi-restraints excluded: chain 2 residue 162 GLU Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 232 ASP Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 425 SER Chi-restraints excluded: chain 3 residue 515 ARG Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 4 residue 8 VAL Chi-restraints excluded: chain 4 residue 75 LYS Chi-restraints excluded: chain 4 residue 165 THR Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 4 residue 407 LYS Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 9 residue 12 MET Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 377 SER Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 330 THR Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 99 GLU Chi-restraints excluded: chain W residue 108 LEU Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 126 LYS Chi-restraints excluded: chain Z residue 129 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 37 GLU Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 296 HIS Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain e residue 17 GLU Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain h residue 39 LYS Chi-restraints excluded: chain h residue 49 SER Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain j residue 14 ARG Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 72 ARG Chi-restraints excluded: chain k residue 183 ILE Chi-restraints excluded: chain k residue 192 MET Chi-restraints excluded: chain k residue 216 GLU Chi-restraints excluded: chain k residue 239 GLN Chi-restraints excluded: chain k residue 284 ILE Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 9 LYS Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain n residue 63 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 58 LEU Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 21 MET Chi-restraints excluded: chain s residue 65 PHE Chi-restraints excluded: chain t residue 127 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain w residue 56 TRP Chi-restraints excluded: chain y residue 10 HIS Chi-restraints excluded: chain y residue 18 VAL Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain z residue 67 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 697 optimal weight: 20.0000 chunk 530 optimal weight: 3.9990 chunk 366 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 474 optimal weight: 10.0000 chunk 708 optimal weight: 10.0000 chunk 750 optimal weight: 0.3980 chunk 370 optimal weight: 9.9990 chunk 671 optimal weight: 30.0000 chunk 202 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 435 GLN ** 3 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 HIS ** L 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 172 GLN N 289 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 GLN i 12 GLN i 135 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 81 GLN p 49 GLN t 11 HIS ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 13 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 67129 Z= 0.512 Angle : 1.592 50.613 90792 Z= 1.028 Chirality : 0.315 6.453 9852 Planarity : 0.005 0.063 11369 Dihedral : 11.388 174.843 9897 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.19 % Allowed : 13.79 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: -0.19 (0.09), residues: 7846 helix: 0.59 (0.08), residues: 4151 sheet: -0.74 (0.26), residues: 383 loop : -0.89 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 272 HIS 0.008 0.001 HIS t 168 PHE 0.022 0.002 PHE L 44 TYR 0.024 0.002 TYR k 58 ARG 0.008 0.001 ARG Z 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15692 Ramachandran restraints generated. 7846 Oldfield, 0 Emsley, 7846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1196 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 34 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7930 (ttmp) REVERT: 1 281 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: 1 339 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.6788 (mtm110) REVERT: 1 432 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8098 (ptp90) REVERT: 2 93 LYS cc_start: 0.8881 (mttm) cc_final: 0.8373 (mtmt) REVERT: 3 119 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9048 (mt0) REVERT: 3 147 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8700 (ttpp) REVERT: 3 314 ASP cc_start: 0.7914 (m-30) cc_final: 0.7618 (m-30) REVERT: 3 341 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: 3 346 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: 3 347 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: 3 418 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7644 (ttp80) REVERT: 3 447 LYS cc_start: 0.8805 (mttm) cc_final: 0.8438 (mtmm) REVERT: 3 515 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7811 (mtp180) REVERT: 3 521 MET cc_start: 0.8803 (ttt) cc_final: 0.8558 (ttt) REVERT: 3 669 LYS cc_start: 0.8227 (ttpm) cc_final: 0.7975 (ptmm) REVERT: 4 47 LEU cc_start: 0.7771 (tt) cc_final: 0.7522 (tm) REVERT: 4 182 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8893 (tm-30) REVERT: 4 290 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8439 (mtp-110) REVERT: 6 25 ARG cc_start: 0.6330 (ttt180) cc_final: 0.6085 (mpt180) REVERT: 9 11 SER cc_start: 0.8694 (m) cc_final: 0.8292 (p) REVERT: 9 13 ASP cc_start: 0.8136 (p0) cc_final: 0.7741 (OUTLIER) REVERT: 9 15 LYS cc_start: 0.8034 (tptp) cc_final: 0.7412 (ttmt) REVERT: 9 19 ASP cc_start: 0.8616 (m-30) cc_final: 0.8180 (t0) REVERT: 9 110 ASP cc_start: 0.8399 (m-30) cc_final: 0.8168 (m-30) REVERT: A 16 LEU cc_start: 0.8172 (tp) cc_final: 0.7765 (mp) REVERT: A 19 THR cc_start: 0.8300 (m) cc_final: 0.8085 (p) REVERT: H 117 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8692 (mt) REVERT: H 253 GLU cc_start: 0.8430 (mp0) cc_final: 0.8204 (mp0) REVERT: J 1 MET cc_start: 0.3539 (tmt) cc_final: 0.2994 (ppp) REVERT: J 103 MET cc_start: 0.5883 (ttt) cc_final: 0.5225 (mpp) REVERT: K 9 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: K 37 MET cc_start: 0.8540 (tmm) cc_final: 0.8221 (ttp) REVERT: L 29 PHE cc_start: 0.4218 (OUTLIER) cc_final: 0.3755 (t80) REVERT: L 139 GLN cc_start: 0.8577 (tt0) cc_final: 0.8337 (tt0) REVERT: L 205 ASN cc_start: 0.7561 (t0) cc_final: 0.7251 (p0) REVERT: L 235 SER cc_start: 0.6881 (m) cc_final: 0.6453 (t) REVERT: L 251 THR cc_start: 0.7133 (m) cc_final: 0.6827 (p) REVERT: L 283 MET cc_start: 0.6711 (tpt) cc_final: 0.6317 (tpt) REVERT: L 290 MET cc_start: 0.5667 (ttp) cc_final: 0.4824 (tmt) REVERT: L 445 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.5467 (pp20) REVERT: M 19 LYS cc_start: 0.7092 (mttp) cc_final: 0.6744 (mmtt) REVERT: M 98 MET cc_start: 0.7943 (mmp) cc_final: 0.7431 (mmp) REVERT: M 119 TYR cc_start: 0.8293 (t80) cc_final: 0.8037 (t80) REVERT: M 206 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8180 (mmtp) REVERT: N 242 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5346 (pp) REVERT: N 280 THR cc_start: 0.8725 (m) cc_final: 0.8473 (p) REVERT: N 290 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7030 (mm) REVERT: N 315 TRP cc_start: 0.6142 (m-10) cc_final: 0.5237 (m-10) REVERT: N 329 MET cc_start: 0.8226 (mtm) cc_final: 0.7924 (mmp) REVERT: W 37 VAL cc_start: 0.8204 (t) cc_final: 0.7883 (m) REVERT: W 99 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: W 143 ASN cc_start: 0.7352 (p0) cc_final: 0.6937 (p0) REVERT: X 14 ARG cc_start: 0.5751 (mtp180) cc_final: 0.4993 (mpt180) REVERT: X 15 VAL cc_start: 0.4656 (t) cc_final: 0.4276 (p) REVERT: X 75 GLU cc_start: 0.6043 (mt-10) cc_final: 0.5476 (tt0) REVERT: Y 3 ILE cc_start: 0.7475 (mt) cc_final: 0.7038 (tp) REVERT: Y 109 CYS cc_start: 0.8442 (t) cc_final: 0.8155 (m) REVERT: Y 123 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: Y 148 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7166 (mp0) REVERT: Z 32 LEU cc_start: 0.8116 (mp) cc_final: 0.7894 (mp) REVERT: Z 66 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7286 (tt0) REVERT: Z 112 CYS cc_start: 0.7841 (t) cc_final: 0.7620 (t) REVERT: Z 129 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6747 (tp40) REVERT: a 63 MET cc_start: 0.8446 (mmm) cc_final: 0.7827 (mmm) REVERT: b 37 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: b 51 GLN cc_start: 0.8075 (mm110) cc_final: 0.7848 (mm-40) REVERT: b 78 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7417 (tt0) REVERT: c 109 LYS cc_start: 0.8070 (mttm) cc_final: 0.7590 (mmpt) REVERT: d 77 ASP cc_start: 0.8362 (t0) cc_final: 0.8067 (t0) REVERT: d 140 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7403 (mmtm) REVERT: d 181 TYR cc_start: 0.9011 (t80) cc_final: 0.8769 (t80) REVERT: d 226 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8152 (mtmm) REVERT: d 246 PHE cc_start: 0.8087 (m-80) cc_final: 0.7724 (m-80) REVERT: d 250 HIS cc_start: 0.6453 (m170) cc_final: 0.6251 (m170) REVERT: e 26 SER cc_start: 0.8299 (m) cc_final: 0.8073 (m) REVERT: e 88 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7665 (mtt180) REVERT: f 104 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: g 56 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7721 (tppt) REVERT: g 86 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8260 (mtmm) REVERT: g 99 ARG cc_start: 0.8525 (ttm110) cc_final: 0.8209 (ttp80) REVERT: h 17 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7450 (mmm160) REVERT: h 32 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8228 (mtmt) REVERT: h 39 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8356 (tmtm) REVERT: i 2 GLU cc_start: 0.7452 (pt0) cc_final: 0.7118 (pt0) REVERT: i 32 ASP cc_start: 0.9179 (t70) cc_final: 0.8976 (t0) REVERT: i 71 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7807 (ttmt) REVERT: i 107 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7835 (ptmt) REVERT: j 16 LEU cc_start: 0.8451 (mt) cc_final: 0.8124 (mt) REVERT: j 23 ASP cc_start: 0.6919 (p0) cc_final: 0.6702 (p0) REVERT: j 66 ASP cc_start: 0.7593 (p0) cc_final: 0.7089 (m-30) REVERT: k 20 GLU cc_start: 0.7476 (pp20) cc_final: 0.6910 (tp30) REVERT: k 51 PHE cc_start: 0.6695 (m-80) cc_final: 0.6471 (m-80) REVERT: k 60 ASP cc_start: 0.6936 (m-30) cc_final: 0.6723 (m-30) REVERT: k 67 LYS cc_start: 0.7204 (mttp) cc_final: 0.6936 (mmpt) REVERT: k 72 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.5916 (pmm-80) REVERT: k 185 LYS cc_start: 0.5657 (mtmp) cc_final: 0.5196 (pptt) REVERT: k 245 LYS cc_start: 0.5332 (ttpt) cc_final: 0.4984 (tttt) REVERT: k 319 LEU cc_start: 0.7086 (mt) cc_final: 0.6859 (mm) REVERT: l 24 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8421 (mm110) REVERT: l 27 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8191 (mmp80) REVERT: m 9 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7894 (tmmm) REVERT: m 14 LYS cc_start: 0.8368 (mmpt) cc_final: 0.8146 (mtmt) REVERT: m 21 SER cc_start: 0.8819 (m) cc_final: 0.8384 (m) REVERT: o 54 LEU cc_start: 0.6244 (mt) cc_final: 0.5947 (tp) REVERT: o 58 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6302 (mp) REVERT: p 106 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7948 (p) REVERT: p 119 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7497 (mmpt) REVERT: q 27 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7832 (ptm160) REVERT: q 92 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: r 82 HIS cc_start: 0.8571 (t70) cc_final: 0.8284 (t-170) REVERT: s 17 GLU cc_start: 0.4971 (OUTLIER) cc_final: 0.3612 (pp20) REVERT: s 19 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6471 (mm) REVERT: s 21 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5381 (ppp) REVERT: s 43 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: s 80 LYS cc_start: 0.7039 (tmmt) cc_final: 0.6615 (tptp) REVERT: t 63 LEU cc_start: 0.3980 (tt) cc_final: 0.3733 (tm) REVERT: u 16 GLN cc_start: 0.7222 (tt0) cc_final: 0.6965 (tt0) REVERT: v 27 TYR cc_start: 0.4685 (m-10) cc_final: 0.4467 (m-10) REVERT: v 77 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5201 (mpp) REVERT: v 80 ASP cc_start: 0.7036 (m-30) cc_final: 0.6816 (m-30) REVERT: w 58 MET cc_start: 0.8086 (tmm) cc_final: 0.7556 (ttp) REVERT: w 59 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7492 (mtt-85) REVERT: w 85 MET cc_start: 0.7729 (ptm) cc_final: 0.6856 (mpp) REVERT: w 95 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7090 (mtp180) REVERT: x 38 ASP cc_start: 0.6137 (m-30) cc_final: 0.5883 (m-30) REVERT: y 10 HIS cc_start: 0.5674 (OUTLIER) cc_final: 0.4801 (p-80) REVERT: y 38 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7444 (ttp80) REVERT: y 44 TYR cc_start: 0.7995 (m-80) cc_final: 0.7642 (m-80) REVERT: z 68 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8446 (t0) outliers start: 292 outliers final: 135 residues processed: 1362 average time/residue: 1.4486 time to fit residues: 2552.6006 Evaluate side-chains 1299 residues out of total 6975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1126 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 136 LEU Chi-restraints excluded: chain 2 residue 162 GLU Chi-restraints excluded: chain 3 residue 119 GLN Chi-restraints excluded: chain 3 residue 147 LYS Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 232 ASP Chi-restraints excluded: chain 3 residue 341 ASP Chi-restraints excluded: chain 3 residue 346 GLU Chi-restraints excluded: chain 3 residue 347 GLU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 425 SER Chi-restraints excluded: chain 3 residue 515 ARG Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 4 residue 8 VAL Chi-restraints excluded: chain 4 residue 75 LYS Chi-restraints excluded: chain 4 residue 165 THR Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 4 residue 407 LYS Chi-restraints excluded: chain 4 residue 417 ILE Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 154 GLU Chi-restraints excluded: chain 9 residue 12 MET Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 297 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 377 SER Chi-restraints excluded: chain L residue 413 LEU Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 206 LYS Chi-restraints excluded: chain M residue 355 MET Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 14 MET Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 330 THR Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 99 GLU Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 126 LYS Chi-restraints excluded: chain Z residue 129 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 37 GLU Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 296 HIS Chi-restraints excluded: chain d residue 340 VAL Chi-restraints excluded: chain e residue 17 GLU Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 104 GLU Chi-restraints excluded: chain g residue 17 LYS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain h residue 17 ARG Chi-restraints excluded: chain h residue 39 LYS Chi-restraints excluded: chain h residue 49 SER Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain i residue 107 LYS Chi-restraints excluded: chain j residue 14 ARG Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 72 ARG Chi-restraints excluded: chain k residue 146 LYS Chi-restraints excluded: chain k residue 183 ILE Chi-restraints excluded: chain k residue 216 GLU Chi-restraints excluded: chain k residue 239 GLN Chi-restraints excluded: chain k residue 284 ILE Chi-restraints excluded: chain l residue 42 CYS Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 9 LYS Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 63 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 58 LEU Chi-restraints excluded: chain p residue 43 LYS Chi-restraints excluded: chain p residue 94 ILE Chi-restraints excluded: chain p residue 106 THR Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 21 MET Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 50 LEU Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain w residue 56 TRP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain y residue 10 HIS Chi-restraints excluded: chain y residue 18 VAL Chi-restraints excluded: chain z residue 67 GLU Chi-restraints excluded: chain z residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.397 > 50: distance: 143 - 148: 34.044 distance: 148 - 149: 40.471 distance: 149 - 150: 11.639 distance: 150 - 151: 14.868 distance: 150 - 156: 41.966 distance: 152 - 153: 39.696 distance: 156 - 157: 39.647 distance: 157 - 158: 4.906 distance: 157 - 160: 55.527 distance: 158 - 159: 36.451 distance: 158 - 164: 34.233 distance: 160 - 161: 27.166 distance: 161 - 162: 42.253 distance: 161 - 163: 26.805 distance: 164 - 165: 55.407 distance: 165 - 166: 53.386 distance: 166 - 167: 56.934 distance: 166 - 176: 29.172 distance: 168 - 169: 39.821 distance: 169 - 170: 39.860 distance: 169 - 171: 40.775 distance: 170 - 172: 55.204 distance: 171 - 173: 34.466 distance: 173 - 174: 40.554 distance: 174 - 175: 40.992 distance: 176 - 177: 12.052 distance: 177 - 178: 14.809 distance: 177 - 180: 24.500 distance: 180 - 181: 56.804 distance: 180 - 182: 41.102 distance: 183 - 184: 56.122 distance: 184 - 185: 57.007 distance: 184 - 187: 4.328 distance: 185 - 189: 40.186 distance: 187 - 188: 36.983 distance: 190 - 191: 39.211 distance: 191 - 192: 40.777 distance: 191 - 197: 40.203 distance: 193 - 194: 40.343 distance: 197 - 198: 14.057 distance: 197 - 203: 56.790 distance: 198 - 199: 15.790 distance: 198 - 201: 24.864 distance: 199 - 204: 40.591 distance: 201 - 202: 39.132 distance: 205 - 206: 40.736 distance: 206 - 207: 40.604 distance: 208 - 210: 41.272 distance: 213 - 214: 39.429 distance: 218 - 220: 55.887 distance: 219 - 221: 40.356 distance: 220 - 221: 39.191 distance: 224 - 225: 36.134 distance: 224 - 230: 34.169 distance: 226 - 227: 39.124