Starting phenix.real_space_refine on Sat Jan 20 04:06:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkt_11261/01_2024/6zkt_11261_neut_updated.pdb" } resolution = 2.8 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= 0.015 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 464 5.16 5 C 42876 2.51 5 N 11018 2.21 5 O 11872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 "9 TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 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 "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66294 Number of models: 1 Model: "" Number of chains: 67 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3381 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 336 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 226 Unusual residues: {'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "N" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "m" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "o" 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: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 103.369 53.821 242.698 1.00 37.46 S ATOM 2695 SG CYS 1 362 106.537 53.908 237.291 1.00 35.21 S ATOM 2676 SG CYS 1 359 110.879 53.963 243.508 1.00 38.00 S ATOM 3039 SG CYS 1 405 107.732 48.270 241.811 1.00 32.48 S ATOM 4116 SG CYS 2 103 101.280 49.675 261.594 1.00 45.24 S ATOM 4150 SG CYS 2 108 99.253 47.325 263.880 1.00 60.13 S ATOM 4430 SG CYS 2 144 102.871 45.990 258.169 1.00 75.52 S ATOM 4453 SG CYS 2 148 101.267 43.144 259.768 1.00 44.20 S ATOM 5793 SG CYS 3 114 106.341 71.947 227.666 1.00 27.58 S ATOM 5732 SG CYS 3 105 100.978 75.393 229.435 1.00 31.36 S ATOM 5753 SG CYS 3 108 106.921 77.251 231.170 1.00 16.99 S ATOM 6125 SG CYS 3 156 113.184 64.630 232.518 1.00 22.95 S ATOM 6102 SG CYS 3 153 111.286 67.760 238.176 1.00 23.64 S ATOM 6149 SG CYS 3 159 117.275 68.516 236.351 1.00 57.66 S ATOM 6479 SG CYS 3 203 113.287 70.822 232.492 1.00 20.59 S ATOM 5238 SG CYS 3 41 112.631 58.166 230.856 1.00 18.10 S ATOM 5324 SG CYS 3 52 108.799 59.206 230.061 1.00 27.29 S ATOM 5349 SG CYS 3 55 109.433 54.187 226.620 1.00 22.75 S ATOM 5450 SG CYS 3 69 112.961 54.367 227.935 1.00 39.00 S ATOM 16102 SG CYS 6 119 91.460 96.991 204.427 1.00 45.61 S ATOM 16332 SG CYS 6 149 88.324 94.889 209.179 1.00 46.98 S ATOM 15598 SG CYS 6 54 84.655 94.746 203.458 1.00 77.36 S ATOM 17524 SG CYS 9 116 92.105 96.003 215.777 1.00 39.65 S ATOM 17571 SG CYS 9 122 92.729 91.621 220.642 1.00 22.55 S ATOM 17298 SG CYS 9 87 96.648 91.312 215.410 1.00 17.17 S ATOM 17600 SG CYS 9 126 94.687 88.448 228.050 1.00 10.40 S ATOM 17271 SG CYS 9 83 98.300 90.022 222.911 1.00 24.51 S ATOM 17229 SG CYS 9 77 100.378 91.822 228.760 1.00 36.26 S ATOM 17248 SG CYS 9 80 99.762 85.285 226.889 1.00 21.63 S ATOM 40512 SG CYS b 59 96.087 84.551 243.515 1.00 33.85 S ATOM 40690 SG CYS b 84 99.120 84.343 241.358 1.00 24.89 S ATOM 40712 SG CYS b 87 97.346 87.547 241.880 1.00 30.22 S Time building chain proxies: 26.38, per 1000 atoms: 0.40 Number of scatterers: 66294 At special positions: 0 Unit cell: (177.24, 197.285, 293.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 464 16.00 P 34 15.00 O 11872 8.00 N 11018 7.00 C 42876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.29 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 500 " 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="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 119 " pdb="FE2 SF4 9 201 " - pdb=" NE2 HIS 9 65 " pdb=" SF4 9 202 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 336 helices and 28 sheets defined 50.6% 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 36 No H-bonds generated for 'chain '1' and resid 33 through 36' Processing helix chain '1' and resid 45 through 62 removed outlier: 3.741A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.831A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.880A 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 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.327A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.660A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.604A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.531A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.846A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 32 Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 196 through 202 removed outlier: 3.659A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 275 removed outlier: 5.036A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY 3 273 " --> pdb=" O PHE 3 269 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 3 274 " --> pdb=" O ALA 3 270 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS 3 275 " --> pdb=" O TYR 3 271 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 307 removed outlier: 3.799A 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 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 3.954A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.867A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 534 through 536 No H-bonds generated for 'chain '3' and resid 534 through 536' Processing helix chain '3' and resid 554 through 556 No H-bonds generated for 'chain '3' and resid 554 through 556' Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 4.308A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.056A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix removed outlier: 3.932A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 125 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.555A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 3.886A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.822A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 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 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.644A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.047A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 3.847A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.553A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 3.667A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG 5 132 " --> pdb=" O TRP 5 129 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.949A 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 97 through 105 Processing helix chain '6' and resid 118 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: 3.637A pdb=" N PHE 9 42 " --> pdb=" O LEU 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 144 through 147 Processing helix chain '9' and resid 151 through 175 removed outlier: 5.795A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.641A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 Processing helix chain 'H' and resid 2 through 31 Proline residue: H 12 - end of helix removed outlier: 3.556A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.595A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.658A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 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 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' 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 3 through 21 removed outlier: 4.591A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 45 Processing helix chain 'J' and resid 50 through 74 removed outlier: 4.169A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET J 74 " --> pdb=" O TYR J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 89 No H-bonds generated for 'chain 'J' and resid 86 through 89' Processing helix chain 'J' and resid 91 through 106 Processing helix chain 'J' and resid 110 through 116 removed outlier: 3.580A pdb=" N GLU J 114 " --> pdb=" O ASP J 110 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.242A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.753A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 85 removed outlier: 4.031A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.642A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.819A 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: 4.066A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.943A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.893A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.711A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.874A 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 232 through 238 removed outlier: 3.926A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.217A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.624A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.364A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 4.057A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.780A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.894A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.498A 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 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 529 through 532 No H-bonds generated for 'chain 'L' and resid 529 through 532' Processing helix chain 'L' and resid 537 through 547 removed outlier: 3.698A pdb=" N LEU L 542 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER L 545 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN L 546 " --> pdb=" O LEU L 542 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 553 No H-bonds generated for 'chain 'L' and resid 550 through 553' Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 564 through 575 removed outlier: 3.793A pdb=" N ALA L 569 " --> pdb=" O THR L 565 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 575 " --> pdb=" O MET L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 598 removed outlier: 3.744A pdb=" N THR L 594 " --> pdb=" O SER L 590 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.118A 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: 3.902A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.630A 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: 3.656A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.635A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.953A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY M 146 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU M 147 " --> pdb=" O ASN M 144 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY M 156 " --> pdb=" O THR M 153 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.616A pdb=" N LEU M 164 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN M 169 " --> pdb=" O TYR M 166 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.724A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 No H-bonds generated for 'chain 'M' and resid 216 through 219' Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.810A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.191A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.119A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.116A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.689A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 3.771A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.246A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.553A 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: 4.285A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 252 removed outlier: 3.982A pdb=" N LEU N 245 " --> pdb=" O THR N 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 271 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 301 Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.919A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.790A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 98 removed outlier: 3.610A pdb=" N CYS V 94 " --> pdb=" O LEU V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 110 through 114 Processing helix chain 'V' and resid 117 through 130 removed outlier: 3.660A pdb=" N LEU V 123 " --> pdb=" O LEU V 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS V 125 " --> pdb=" O ALA V 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.435A 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: 3.653A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'X' and resid 8 through 19 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 74 Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.539A 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 57 removed outlier: 5.262A pdb=" N ARG Z 42 " --> pdb=" O LEU Z 38 " (cutoff:3.500A) Proline residue: Z 43 - end of helix Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 3.889A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 No H-bonds generated for 'chain 'Z' and resid 120 through 123' Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 removed outlier: 3.726A pdb=" N ALA Z 172 " --> pdb=" O ALA Z 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 50 through 58 Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.581A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 44 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.105A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 80 No H-bonds generated for 'chain 'c' and resid 78 through 80' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 30 through 39 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 122 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 318 removed outlier: 4.699A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.642A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 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: 4.217A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 64 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 4.031A 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: 4.540A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.562A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.018A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.698A 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 10 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.186A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS k 45 " --> pdb=" O VAL k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 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 removed outlier: 3.586A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.591A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 217 removed outlier: 5.692A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix removed outlier: 4.349A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 238 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 271 through 274 Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 48 through 54 removed outlier: 4.233A 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 98 No H-bonds generated for 'chain 'l' and resid 95 through 98' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 32 through 34 No H-bonds generated for 'chain 'm' and resid 32 through 34' Processing helix chain 'm' and resid 38 through 47 removed outlier: 3.601A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 18 through 20 No H-bonds generated for 'chain 'n' and resid 18 through 20' Processing helix chain 'n' and resid 27 through 38 removed outlier: 4.217A pdb=" N ARG n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 removed outlier: 3.566A pdb=" N ARG n 51 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 2 through 7 removed outlier: 3.886A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.654A pdb=" N SER o 20 " --> pdb=" O GLU o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 47 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.935A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 15 through 17 No H-bonds generated for 'chain 'p' and resid 15 through 17' Processing helix chain 'p' and resid 19 through 21 No H-bonds generated for 'chain 'p' and resid 19 through 21' Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.757A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 83 through 92 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 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 25 Processing helix chain 'r' and resid 68 through 72 Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 3 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 92 through 95 removed outlier: 4.396A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 92 through 95' Processing helix chain 't' and resid 100 through 103 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 139 removed outlier: 4.079A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.098A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 14 removed outlier: 3.644A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 14' Processing helix chain 'y' and resid 16 through 31 Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 29 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 6.190A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.071A 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: 6.772A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 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: 3.624A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 283 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.489A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.991A 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: 8.527A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.478A 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 572 through 574 Processing sheet with id= M, first strand: chain '4' and resid 47 through 51 removed outlier: 6.323A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 361 through 369 Processing sheet with id= O, first strand: chain '5' and resid 74 through 82 removed outlier: 6.740A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.964A 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: 6.439A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.340A 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: 5.830A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.215A 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: 6.689A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= V, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.668A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.675A 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: 3.814A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.627A 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: 3.679A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.570A 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: 6.350A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP k 173 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR k 223 " --> pdb=" O ASP k 173 " (cutoff:3.500A) 2693 hydrogen bonds defined for protein. 7569 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: 22.70 Time building geometry restraints manager: 22.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 28433 1.43 - 1.67: 38665 1.67 - 1.90: 756 1.90 - 2.14: 0 2.14 - 2.37: 80 Bond restraints: 67934 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.591 0.242 3.80e-02 6.93e+02 4.04e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.331 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" OA3 CDL h 201 " pdb=" PA1 CDL h 201 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.67e+01 bond pdb=" OB3 CDL L1003 " pdb=" PB2 CDL L1003 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.00e-02 1.00e+04 3.31e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.339 0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 67929 not shown) Histogram of bond angle deviations from ideal: 62.46 - 77.46: 71 77.46 - 92.46: 9 92.46 - 107.46: 3637 107.46 - 122.45: 79552 122.45 - 137.45: 8618 Bond angle restraints: 91887 Sorted by residual: angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.69 -23.95 1.95e+00 2.62e-01 1.50e+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 90.97 13.36 1.14e+00 7.69e-01 1.37e+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 90.96 13.37 1.20e+00 6.94e-01 1.24e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 91.65 12.68 1.14e+00 7.69e-01 1.24e+02 angle pdb="FE1 FES 2 300 " pdb=" S2 FES 2 300 " pdb="FE2 FES 2 300 " ideal model delta sigma weight residual 75.66 87.83 -12.17 1.14e+00 7.69e-01 1.14e+02 ... (remaining 91882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 40519 35.10 - 70.20: 621 70.20 - 105.29: 41 105.29 - 140.39: 1 140.39 - 175.49: 5 Dihedral angle restraints: 41187 sinusoidal: 17672 harmonic: 23515 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -129.29 -50.71 0 5.00e+00 4.00e-02 1.03e+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 -132.32 -47.68 0 5.00e+00 4.00e-02 9.09e+01 dihedral pdb=" CA LEU N 302 " pdb=" C LEU N 302 " pdb=" N THR N 303 " pdb=" CA THR N 303 " ideal model delta harmonic sigma weight residual 180.00 -137.04 -42.96 0 5.00e+00 4.00e-02 7.38e+01 ... (remaining 41184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.234: 9962 4.234 - 8.468: 4 8.468 - 12.701: 0 12.701 - 16.935: 0 16.935 - 21.169: 24 Chirality restraints: 9990 Sorted by residual: chirality pdb="FE4 SF4 9 201 " pdb=" S1 SF4 9 201 " pdb=" S2 SF4 9 201 " pdb=" S3 SF4 9 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 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 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9987 not shown) Planarity restraints: 11497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.024 2.00e-02 2.50e+03 3.50e-02 2.45e+01 pdb=" CG TYR 9 40 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.039 2.00e-02 2.50e+03 3.07e-02 1.89e+01 pdb=" CG TYR 6 125 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.030 2.00e-02 2.50e+03 2.55e-02 1.62e+01 pdb=" CG TRP 1 371 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.001 2.00e-02 2.50e+03 ... (remaining 11494 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 15495 2.79 - 3.38: 71360 3.38 - 3.96: 137883 3.96 - 4.55: 192040 4.55 - 5.14: 281358 Nonbonded interactions: 698136 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.200 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR d 22 " pdb=" OG SER d 88 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR v 47 " pdb=" O MET v 77 " model vdw 2.263 2.440 nonbonded pdb=" O VAL J 126 " pdb=" OG1 THR q 136 " model vdw 2.267 2.440 ... (remaining 698131 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: 0.460 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: 0.080 Extract box with map and model: 4.910 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 156.600 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 67934 Z= 0.500 Angle : 1.001 23.955 91887 Z= 0.536 Chirality : 1.034 21.169 9990 Planarity : 0.008 0.065 11497 Dihedral : 12.196 175.492 25996 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.08), residues: 7950 helix: -1.94 (0.06), residues: 4164 sheet: -1.36 (0.24), residues: 383 loop : -1.87 (0.09), residues: 3403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP 1 371 HIS 0.020 0.003 HIS 4 200 PHE 0.058 0.004 PHE 4 171 TYR 0.078 0.003 TYR 9 40 ARG 0.026 0.001 ARG Y 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1931 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1926 time to evaluate : 5.559 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 15 LEU cc_start: 0.8258 (tp) cc_final: 0.7938 (tp) REVERT: 1 34 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7674 (tppt) REVERT: 1 61 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8036 (mtpp) REVERT: 1 73 PHE cc_start: 0.7570 (t80) cc_final: 0.6884 (m-10) REVERT: 1 114 ASP cc_start: 0.8240 (m-30) cc_final: 0.7975 (t0) REVERT: 1 154 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7578 (ttp80) REVERT: 1 178 VAL cc_start: 0.8637 (t) cc_final: 0.8413 (m) REVERT: 1 281 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7923 (mm-30) REVERT: 1 309 LYS cc_start: 0.8326 (tmtp) cc_final: 0.8124 (ttmt) REVERT: 1 326 GLN cc_start: 0.7248 (pt0) cc_final: 0.6852 (tp-100) REVERT: 1 356 HIS cc_start: 0.8091 (m-70) cc_final: 0.7196 (t70) REVERT: 1 431 GLN cc_start: 0.8004 (pt0) cc_final: 0.7604 (pp30) REVERT: 2 29 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7436 (ttpt) REVERT: 2 71 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7772 (mt-10) REVERT: 2 114 ASP cc_start: 0.7818 (m-30) cc_final: 0.7287 (p0) REVERT: 2 117 LEU cc_start: 0.8163 (tp) cc_final: 0.7921 (tm) REVERT: 2 127 LYS cc_start: 0.7444 (ptpt) cc_final: 0.6867 (mttp) REVERT: 2 180 LYS cc_start: 0.6657 (mtmm) cc_final: 0.6121 (mmmm) REVERT: 2 204 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6836 (tp30) REVERT: 3 16 GLN cc_start: 0.7986 (tt0) cc_final: 0.7662 (tp40) REVERT: 3 19 MET cc_start: 0.8561 (mmm) cc_final: 0.8356 (mmm) REVERT: 3 61 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7920 (mmtt) REVERT: 3 188 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7833 (mm-30) REVERT: 3 246 GLU cc_start: 0.8828 (tt0) cc_final: 0.8302 (tp30) REVERT: 3 297 GLU cc_start: 0.8064 (mp0) cc_final: 0.7425 (mt-10) REVERT: 3 329 ILE cc_start: 0.8423 (tp) cc_final: 0.8138 (tt) REVERT: 3 418 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7771 (mmm-85) REVERT: 3 450 MET cc_start: 0.8618 (ttt) cc_final: 0.8394 (ttt) REVERT: 3 462 ASP cc_start: 0.8364 (p0) cc_final: 0.8009 (p0) REVERT: 3 475 GLN cc_start: 0.6784 (mm110) cc_final: 0.5530 (pp30) REVERT: 3 533 THR cc_start: 0.8499 (p) cc_final: 0.8143 (t) REVERT: 3 640 ASN cc_start: 0.8128 (t0) cc_final: 0.7755 (t0) REVERT: 3 642 PHE cc_start: 0.8562 (m-80) cc_final: 0.8302 (m-80) REVERT: 3 643 GLN cc_start: 0.7473 (tp40) cc_final: 0.7078 (tt0) REVERT: 3 669 LYS cc_start: 0.7788 (ttpm) cc_final: 0.7420 (ttpt) REVERT: 4 74 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.7509 (mmm160) REVERT: 4 75 LYS cc_start: 0.8979 (tttm) cc_final: 0.8421 (ttmt) REVERT: 4 282 GLU cc_start: 0.8320 (tt0) cc_final: 0.8057 (mt-10) REVERT: 4 327 ASP cc_start: 0.8536 (t0) cc_final: 0.8205 (t70) REVERT: 5 147 ASP cc_start: 0.8147 (t0) cc_final: 0.7930 (t70) REVERT: 6 81 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7058 (mmt90) REVERT: 6 178 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8079 (mtm-85) REVERT: 9 36 MET cc_start: 0.8784 (tpp) cc_final: 0.8567 (tpt) REVERT: 9 112 ASP cc_start: 0.8758 (t0) cc_final: 0.8551 (t0) REVERT: 9 176 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7841 (mtt180) REVERT: A 1 MET cc_start: 0.6793 (tpt) cc_final: 0.6587 (tpp) REVERT: H 31 MET cc_start: 0.9028 (mtt) cc_final: 0.8812 (mtp) REVERT: H 184 MET cc_start: 0.8822 (mtm) cc_final: 0.8490 (mtm) REVERT: H 202 GLU cc_start: 0.5726 (mt-10) cc_final: 0.4757 (tp30) REVERT: H 220 PHE cc_start: 0.6558 (t80) cc_final: 0.6299 (t80) REVERT: H 251 MET cc_start: 0.8416 (mtp) cc_final: 0.8076 (mtt) REVERT: J 1 MET cc_start: 0.4141 (tmt) cc_final: 0.3391 (mtp) REVERT: J 55 MET cc_start: 0.8661 (mmp) cc_final: 0.8436 (mmm) REVERT: J 74 MET cc_start: 0.7967 (mtp) cc_final: 0.7689 (mtp) REVERT: J 99 MET cc_start: 0.2667 (mtp) cc_final: 0.2182 (mmp) REVERT: K 6 MET cc_start: 0.7529 (ttp) cc_final: 0.7230 (mtt) REVERT: K 34 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8256 (tp30) REVERT: L 24 PHE cc_start: 0.6508 (m-10) cc_final: 0.6110 (t80) REVERT: L 53 MET cc_start: 0.7859 (ptm) cc_final: 0.7494 (ptm) REVERT: L 89 PHE cc_start: 0.8032 (t80) cc_final: 0.7699 (t80) REVERT: L 109 HIS cc_start: 0.6920 (t-90) cc_final: 0.6151 (p90) REVERT: L 229 LEU cc_start: 0.7844 (mt) cc_final: 0.7568 (mp) REVERT: L 283 MET cc_start: 0.7972 (tpt) cc_final: 0.7524 (ttp) REVERT: L 354 GLN cc_start: 0.6473 (mt0) cc_final: 0.6121 (mt0) REVERT: L 407 TRP cc_start: 0.7025 (t-100) cc_final: 0.6694 (t-100) REVERT: L 410 LEU cc_start: 0.7576 (tt) cc_final: 0.7369 (tm) REVERT: L 463 PHE cc_start: 0.7505 (m-80) cc_final: 0.7193 (m-80) REVERT: L 475 MET cc_start: 0.7015 (mmm) cc_final: 0.6815 (mmm) REVERT: L 480 MET cc_start: 0.6547 (mtp) cc_final: 0.5764 (ppp) REVERT: L 544 MET cc_start: 0.2908 (tmm) cc_final: 0.2116 (mpp) REVERT: L 573 MET cc_start: 0.2702 (mmp) cc_final: 0.1912 (mmm) REVERT: M 98 MET cc_start: 0.8773 (mmp) cc_final: 0.8560 (mmp) REVERT: M 184 GLN cc_start: 0.8374 (mm110) cc_final: 0.8104 (mm-40) REVERT: M 186 MET cc_start: 0.7544 (ttm) cc_final: 0.7343 (ttm) REVERT: M 194 PHE cc_start: 0.8121 (m-80) cc_final: 0.7888 (m-10) REVERT: M 200 MET cc_start: 0.8481 (mmm) cc_final: 0.8169 (mmm) REVERT: M 214 LEU cc_start: 0.8488 (mm) cc_final: 0.8170 (mt) REVERT: M 259 TYR cc_start: 0.8168 (m-80) cc_final: 0.7813 (m-80) REVERT: M 267 TRP cc_start: 0.8259 (t-100) cc_final: 0.8006 (t-100) REVERT: M 325 MET cc_start: 0.7994 (ttt) cc_final: 0.7771 (ttt) REVERT: M 437 MET cc_start: 0.8860 (mmp) cc_final: 0.8631 (mmp) REVERT: N 11 MET cc_start: 0.7983 (mmp) cc_final: 0.7522 (mtm) REVERT: N 68 MET cc_start: 0.8954 (mmt) cc_final: 0.8751 (mmp) REVERT: N 71 MET cc_start: 0.8838 (tpp) cc_final: 0.8598 (tpp) REVERT: N 88 LYS cc_start: 0.8081 (ptmt) cc_final: 0.7872 (pttt) REVERT: N 93 MET cc_start: 0.8509 (tpt) cc_final: 0.8261 (tpt) REVERT: N 270 MET cc_start: 0.8951 (mtp) cc_final: 0.8661 (mtp) REVERT: V 126 MET cc_start: 0.4463 (mtt) cc_final: 0.3924 (mpt) REVERT: V 130 GLU cc_start: 0.5465 (mp0) cc_final: 0.4670 (mt-10) REVERT: W 7 ARG cc_start: 0.5635 (mtm110) cc_final: 0.5408 (mtm180) REVERT: W 19 LYS cc_start: 0.8078 (mtpm) cc_final: 0.7448 (tmmm) REVERT: W 68 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7888 (tttm) REVERT: W 77 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7339 (ttp-110) REVERT: W 98 SER cc_start: 0.8372 (p) cc_final: 0.8016 (p) REVERT: W 107 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7193 (tt0) REVERT: W 130 LYS cc_start: 0.8386 (pttp) cc_final: 0.8033 (pttt) REVERT: W 134 ASP cc_start: 0.8246 (t0) cc_final: 0.7904 (t0) REVERT: X 7 THR cc_start: 0.4434 (p) cc_final: 0.4095 (m) REVERT: X 9 GLU cc_start: 0.6936 (tt0) cc_final: 0.6576 (tp30) REVERT: X 68 GLU cc_start: 0.6259 (pt0) cc_final: 0.5409 (mt-10) REVERT: X 71 MET cc_start: 0.5563 (mmt) cc_final: 0.5193 (mpp) REVERT: X 84 LYS cc_start: 0.6273 (mmtp) cc_final: 0.5830 (mttp) REVERT: Y 79 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7696 (pm20) REVERT: Y 131 LYS cc_start: 0.7296 (tptp) cc_final: 0.6922 (tmtm) REVERT: Z 31 TYR cc_start: 0.6738 (m-80) cc_final: 0.6475 (m-10) REVERT: Z 61 TYR cc_start: 0.7105 (m-80) cc_final: 0.6779 (m-80) REVERT: Z 66 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7512 (pp20) REVERT: Z 72 ASP cc_start: 0.8014 (p0) cc_final: 0.7791 (p0) REVERT: Z 126 LYS cc_start: 0.7607 (ttpm) cc_final: 0.7397 (ptpp) REVERT: Z 162 MET cc_start: 0.7893 (mtp) cc_final: 0.7646 (mtp) REVERT: Z 167 LYS cc_start: 0.7091 (tttm) cc_final: 0.6871 (ttmt) REVERT: a 63 MET cc_start: 0.7169 (mmm) cc_final: 0.6820 (mtp) REVERT: a 71 GLU cc_start: 0.7982 (tt0) cc_final: 0.7669 (mp0) REVERT: b 22 ASP cc_start: 0.8424 (t0) cc_final: 0.8196 (t70) REVERT: b 46 GLU cc_start: 0.7763 (mt-10) cc_final: 0.6812 (mm-30) REVERT: b 50 SER cc_start: 0.9034 (t) cc_final: 0.8774 (t) REVERT: b 94 GLN cc_start: 0.7582 (pt0) cc_final: 0.7086 (tt0) REVERT: c 13 VAL cc_start: 0.7431 (t) cc_final: 0.7223 (p) REVERT: c 15 GLU cc_start: 0.5706 (mm-30) cc_final: 0.5322 (pp20) REVERT: d 60 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.8171 (mtt180) REVERT: d 77 ASP cc_start: 0.8292 (t0) cc_final: 0.7813 (t0) REVERT: d 79 ASP cc_start: 0.8162 (t0) cc_final: 0.7948 (m-30) REVERT: d 82 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7303 (tmm160) REVERT: d 86 GLU cc_start: 0.8020 (pt0) cc_final: 0.7783 (tp30) REVERT: d 139 ILE cc_start: 0.8032 (mm) cc_final: 0.7605 (tp) REVERT: d 141 SER cc_start: 0.8366 (t) cc_final: 0.7982 (p) REVERT: d 154 LYS cc_start: 0.7704 (tttm) cc_final: 0.7314 (ttpp) REVERT: d 158 GLU cc_start: 0.8046 (pt0) cc_final: 0.7730 (mt-10) REVERT: d 240 ASP cc_start: 0.7671 (p0) cc_final: 0.6910 (m-30) REVERT: d 281 ARG cc_start: 0.6884 (ptp90) cc_final: 0.6520 (ptm160) REVERT: e 42 GLU cc_start: 0.7533 (pm20) cc_final: 0.6737 (mp0) REVERT: e 45 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7631 (mtpp) REVERT: e 63 LYS cc_start: 0.9001 (tppp) cc_final: 0.8744 (tptt) REVERT: e 72 GLN cc_start: 0.7959 (mm110) cc_final: 0.6787 (tt0) REVERT: e 91 GLU cc_start: 0.7464 (pt0) cc_final: 0.7167 (pp20) REVERT: f 57 ILE cc_start: 0.8580 (mt) cc_final: 0.8297 (mp) REVERT: f 61 GLU cc_start: 0.6679 (tp30) cc_final: 0.6244 (tp30) REVERT: f 66 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7443 (mtmt) REVERT: f 69 GLU cc_start: 0.8019 (mp0) cc_final: 0.7802 (mp0) REVERT: f 70 GLN cc_start: 0.8458 (pt0) cc_final: 0.8007 (pt0) REVERT: f 84 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7684 (mt-10) REVERT: f 91 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7817 (mtt-85) REVERT: g 29 ARG cc_start: 0.8429 (ttm110) cc_final: 0.7606 (ttp80) REVERT: g 33 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8205 (tt0) REVERT: g 41 GLU cc_start: 0.7674 (tp30) cc_final: 0.7306 (tp30) REVERT: g 56 LYS cc_start: 0.8378 (tmmt) cc_final: 0.7924 (tptp) REVERT: g 60 ASP cc_start: 0.8371 (m-30) cc_final: 0.7996 (m-30) REVERT: g 87 MET cc_start: 0.8882 (mtt) cc_final: 0.8605 (mtp) REVERT: h 17 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7345 (mpp-170) REVERT: h 47 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7861 (mtp180) REVERT: h 102 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7776 (ttp80) REVERT: i 1 MET cc_start: 0.4830 (tpt) cc_final: 0.3526 (mtm) REVERT: i 12 GLN cc_start: 0.8122 (pt0) cc_final: 0.7716 (mt0) REVERT: i 15 SER cc_start: 0.7952 (t) cc_final: 0.7744 (p) REVERT: i 25 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7687 (ttt90) REVERT: i 50 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8079 (tp30) REVERT: i 71 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7877 (tttp) REVERT: i 112 ASN cc_start: 0.8784 (t0) cc_final: 0.8334 (t0) REVERT: i 122 GLN cc_start: 0.8523 (mp10) cc_final: 0.8273 (mt0) REVERT: j 8 LEU cc_start: 0.6078 (tt) cc_final: 0.5850 (mp) REVERT: j 18 VAL cc_start: 0.7553 (t) cc_final: 0.7314 (m) REVERT: j 24 LYS cc_start: 0.7303 (ttmp) cc_final: 0.7063 (ttmt) REVERT: j 54 MET cc_start: 0.7188 (mmt) cc_final: 0.6852 (mmt) REVERT: j 77 VAL cc_start: 0.7480 (p) cc_final: 0.7209 (m) REVERT: j 80 ILE cc_start: 0.8234 (mt) cc_final: 0.7969 (mm) REVERT: k 45 LYS cc_start: 0.6732 (mmtt) cc_final: 0.6321 (mtmm) REVERT: k 141 GLN cc_start: 0.6911 (mm110) cc_final: 0.6600 (mm110) REVERT: k 150 ASP cc_start: 0.8041 (m-30) cc_final: 0.7841 (m-30) REVERT: k 191 GLU cc_start: 0.6753 (tt0) cc_final: 0.6508 (tp30) REVERT: k 201 ASP cc_start: 0.6783 (m-30) cc_final: 0.6374 (m-30) REVERT: k 261 MET cc_start: 0.8598 (mmm) cc_final: 0.8370 (mmm) REVERT: k 265 ASP cc_start: 0.7764 (t0) cc_final: 0.7549 (t0) REVERT: k 288 GLN cc_start: 0.7846 (tt0) cc_final: 0.7610 (tt0) REVERT: k 293 PHE cc_start: 0.8541 (t80) cc_final: 0.8285 (t80) REVERT: k 318 TRP cc_start: 0.7545 (p-90) cc_final: 0.7281 (p-90) REVERT: l 12 ASP cc_start: 0.8196 (t0) cc_final: 0.7942 (t0) REVERT: l 27 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.8125 (mmt90) REVERT: l 73 LYS cc_start: 0.8028 (tttm) cc_final: 0.7774 (ttpp) REVERT: m 10 ASN cc_start: 0.7677 (t0) cc_final: 0.7211 (m-40) REVERT: m 14 LYS cc_start: 0.7365 (mtmt) cc_final: 0.7087 (tppt) REVERT: n 13 MET cc_start: 0.4403 (ttt) cc_final: 0.3895 (mpp) REVERT: n 62 PHE cc_start: 0.6422 (t80) cc_final: 0.6212 (t80) REVERT: o 45 ASP cc_start: 0.7916 (t70) cc_final: 0.7699 (t0) REVERT: o 55 SER cc_start: 0.7707 (m) cc_final: 0.7467 (t) REVERT: o 97 HIS cc_start: 0.7481 (m90) cc_final: 0.7246 (m-70) REVERT: o 110 ARG cc_start: 0.7151 (ptm-80) cc_final: 0.6903 (ptt90) REVERT: p 35 ARG cc_start: 0.6762 (mtm-85) cc_final: 0.6385 (mtp180) REVERT: p 97 LEU cc_start: 0.7416 (mt) cc_final: 0.7157 (tp) REVERT: q 85 MET cc_start: 0.8701 (mtp) cc_final: 0.8442 (mtp) REVERT: q 89 ASN cc_start: 0.8514 (m-40) cc_final: 0.8172 (m110) REVERT: q 122 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7980 (mt-10) REVERT: q 131 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7290 (mt-10) REVERT: r 71 PHE cc_start: 0.7705 (t80) cc_final: 0.7371 (t80) REVERT: s 6 ARG cc_start: 0.4840 (mtm110) cc_final: 0.4189 (mtt90) REVERT: s 103 ARG cc_start: 0.5421 (tmt90) cc_final: 0.5017 (tmm-80) REVERT: s 121 MET cc_start: 0.3651 (tpt) cc_final: 0.2573 (ttm) REVERT: t 50 HIS cc_start: 0.5480 (m-70) cc_final: 0.5098 (m-70) REVERT: t 56 MET cc_start: 0.2689 (mmm) cc_final: 0.2453 (ttt) REVERT: t 83 GLU cc_start: 0.8142 (mp0) cc_final: 0.7705 (mt-10) REVERT: t 120 LYS cc_start: 0.6350 (ttmt) cc_final: 0.5999 (mtmt) REVERT: t 134 ARG cc_start: 0.6496 (mtm180) cc_final: 0.5978 (tpt170) REVERT: u 41 TRP cc_start: 0.6595 (t-100) cc_final: 0.6043 (t-100) REVERT: v 59 ASP cc_start: 0.6999 (t0) cc_final: 0.6713 (t0) REVERT: v 70 ARG cc_start: 0.5973 (mtt180) cc_final: 0.5695 (mmt90) REVERT: v 77 MET cc_start: 0.8098 (mtt) cc_final: 0.7791 (mtp) REVERT: v 141 GLU cc_start: 0.7197 (mp0) cc_final: 0.6949 (mp0) REVERT: v 149 GLU cc_start: 0.6037 (tt0) cc_final: 0.5798 (tm-30) REVERT: w 94 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7932 (mt-10) REVERT: x 37 GLU cc_start: 0.7720 (tt0) cc_final: 0.7290 (tp30) REVERT: z 25 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7603 (mtt180) REVERT: z 59 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.8232 (mtm180) outliers start: 5 outliers final: 5 residues processed: 1930 average time/residue: 1.6156 time to fit residues: 3978.5293 Evaluate side-chains 1290 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1285 time to evaluate : 5.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain v residue 145 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 10.0000 chunk 595 optimal weight: 0.3980 chunk 330 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 318 optimal weight: 0.7980 chunk 616 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 458 optimal weight: 30.0000 chunk 713 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 356 HIS 1 373 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 313 ASN 3 546 GLN 4 50 ASN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 409 HIS 5 69 ASN 5 200 ASN A 108 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 HIS K 52 HIS K 92 ASN L 136 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 390 ASN ** W 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 HIS Y 72 GLN Y 94 GLN Y 139 ASN Y 142 HIS Z 55 HIS Z 58 ASN Z 106 GLN Z 130 GLN a 35 ASN b 36 ASN c 67 ASN d 37 HIS d 87 HIS d 184 ASN e 85 GLN ** f 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 ASN g 50 GLN g 107 HIS g 125 HIS i 123 GLN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 141 GLN k 180 GLN l 6 GLN l 26 HIS l 69 GLN l 81 GLN l 97 HIS m 51 ASN o 61 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 116 GLN q 53 ASN s 42 GLN s 43 GLN s 75 ASN u 13 GLN ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 136 ASN x 34 GLN y 30 ASN z 31 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.268 67934 Z= 0.538 Angle : 1.586 50.784 91887 Z= 1.025 Chirality : 0.312 6.510 9990 Planarity : 0.005 0.059 11497 Dihedral : 12.098 176.150 10011 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.17 % Allowed : 10.37 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 7950 helix: -0.27 (0.07), residues: 4195 sheet: -1.09 (0.24), residues: 401 loop : -1.28 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 1 371 HIS 0.018 0.001 HIS 9 65 PHE 0.025 0.002 PHE 4 171 TYR 0.027 0.002 TYR N 291 ARG 0.008 0.001 ARG w 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1376 time to evaluate : 5.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 34 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7749 (tppt) REVERT: 1 61 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8069 (mtpp) REVERT: 1 73 PHE cc_start: 0.7449 (t80) cc_final: 0.6835 (m-10) REVERT: 1 154 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7607 (ttp80) REVERT: 1 178 VAL cc_start: 0.8564 (t) cc_final: 0.8330 (m) REVERT: 1 188 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: 1 248 GLU cc_start: 0.7881 (tt0) cc_final: 0.7225 (pp20) REVERT: 1 249 ARG cc_start: 0.7900 (mtp-110) cc_final: 0.7437 (mtm110) REVERT: 1 281 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7906 (mm-30) REVERT: 1 309 LYS cc_start: 0.8382 (tmtp) cc_final: 0.8116 (ttmt) REVERT: 1 326 GLN cc_start: 0.7144 (pt0) cc_final: 0.6733 (tp-100) REVERT: 1 356 HIS cc_start: 0.8068 (m90) cc_final: 0.7270 (t-90) REVERT: 1 376 MET cc_start: 0.8850 (mmm) cc_final: 0.8628 (mmm) REVERT: 1 431 GLN cc_start: 0.7997 (pt0) cc_final: 0.7621 (pp30) REVERT: 1 436 GLN cc_start: 0.7679 (pt0) cc_final: 0.6770 (pp30) REVERT: 2 29 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7292 (ttpt) REVERT: 2 114 ASP cc_start: 0.7814 (m-30) cc_final: 0.7285 (p0) REVERT: 2 117 LEU cc_start: 0.8276 (tp) cc_final: 0.7985 (tm) REVERT: 2 127 LYS cc_start: 0.7330 (ptpt) cc_final: 0.6776 (mttp) REVERT: 2 158 ASP cc_start: 0.7637 (m-30) cc_final: 0.7423 (m-30) REVERT: 2 180 LYS cc_start: 0.6733 (mtmm) cc_final: 0.6226 (mmmm) REVERT: 2 204 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6697 (tp30) REVERT: 3 16 GLN cc_start: 0.8014 (tt0) cc_final: 0.7679 (tp40) REVERT: 3 61 LYS cc_start: 0.8390 (mtmt) cc_final: 0.7793 (mmtt) REVERT: 3 188 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7722 (mm-30) REVERT: 3 246 GLU cc_start: 0.8875 (tt0) cc_final: 0.8310 (tp30) REVERT: 3 260 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: 3 297 GLU cc_start: 0.8145 (mp0) cc_final: 0.7571 (mt-10) REVERT: 3 329 ILE cc_start: 0.8344 (tp) cc_final: 0.8014 (tt) REVERT: 3 347 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: 3 418 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7611 (mmt-90) REVERT: 3 462 ASP cc_start: 0.8422 (p0) cc_final: 0.8150 (p0) REVERT: 3 475 GLN cc_start: 0.6841 (mm110) cc_final: 0.5653 (pp30) REVERT: 3 533 THR cc_start: 0.8540 (p) cc_final: 0.8184 (t) REVERT: 3 640 ASN cc_start: 0.8083 (t0) cc_final: 0.7772 (t0) REVERT: 3 643 GLN cc_start: 0.7444 (tp40) cc_final: 0.7083 (tt0) REVERT: 3 673 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: 4 74 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.7573 (mmm160) REVERT: 4 75 LYS cc_start: 0.8826 (tttm) cc_final: 0.8159 (ttmt) REVERT: 4 282 GLU cc_start: 0.8294 (tt0) cc_final: 0.8038 (mt-10) REVERT: 4 327 ASP cc_start: 0.8459 (t0) cc_final: 0.7968 (t70) REVERT: 5 186 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: 6 62 MET cc_start: 0.9004 (ttp) cc_final: 0.8792 (ttp) REVERT: 6 81 ARG cc_start: 0.7442 (mtp180) cc_final: 0.7023 (tpp80) REVERT: 6 178 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8031 (mtm-85) REVERT: 9 36 MET cc_start: 0.8957 (tpp) cc_final: 0.8684 (tpt) REVERT: 9 112 ASP cc_start: 0.8826 (t0) cc_final: 0.8581 (t0) REVERT: A 1 MET cc_start: 0.6843 (tpt) cc_final: 0.6516 (tpp) REVERT: H 184 MET cc_start: 0.8837 (mtm) cc_final: 0.8611 (mtm) REVERT: H 202 GLU cc_start: 0.5944 (mt-10) cc_final: 0.4929 (tp30) REVERT: H 251 MET cc_start: 0.8294 (mtp) cc_final: 0.7989 (mtt) REVERT: J 1 MET cc_start: 0.3805 (tmt) cc_final: 0.2902 (mmt) REVERT: J 74 MET cc_start: 0.7933 (mtp) cc_final: 0.7705 (mtp) REVERT: J 99 MET cc_start: 0.2691 (mtp) cc_final: 0.1773 (mmm) REVERT: K 6 MET cc_start: 0.7550 (ttp) cc_final: 0.7197 (mtt) REVERT: L 24 PHE cc_start: 0.6511 (m-10) cc_final: 0.6055 (t80) REVERT: L 88 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7062 (mpp) REVERT: L 89 PHE cc_start: 0.8000 (t80) cc_final: 0.7576 (t80) REVERT: L 109 HIS cc_start: 0.7011 (t-90) cc_final: 0.6262 (p90) REVERT: L 128 MET cc_start: 0.8580 (tpt) cc_final: 0.8376 (tpt) REVERT: L 300 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7884 (mmmt) REVERT: L 327 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7874 (tp) REVERT: L 354 GLN cc_start: 0.6355 (mt0) cc_final: 0.6067 (mt0) REVERT: L 359 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6611 (tpp) REVERT: L 407 TRP cc_start: 0.6831 (t-100) cc_final: 0.6267 (t-100) REVERT: L 411 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6446 (mpm) REVERT: L 413 LEU cc_start: 0.7789 (mt) cc_final: 0.7497 (mt) REVERT: L 463 PHE cc_start: 0.7493 (m-80) cc_final: 0.7040 (m-80) REVERT: L 479 GLN cc_start: 0.5809 (mt0) cc_final: 0.5491 (tt0) REVERT: L 488 MET cc_start: 0.6321 (mpp) cc_final: 0.4943 (ptp) REVERT: L 489 THR cc_start: 0.7597 (m) cc_final: 0.7145 (t) REVERT: L 544 MET cc_start: 0.2637 (tmm) cc_final: 0.1880 (mpp) REVERT: M 184 GLN cc_start: 0.8369 (mm110) cc_final: 0.8089 (mm-40) REVERT: M 194 PHE cc_start: 0.8003 (m-80) cc_final: 0.7762 (m-10) REVERT: M 195 MET cc_start: 0.8253 (tmm) cc_final: 0.8039 (tpt) REVERT: M 214 LEU cc_start: 0.8451 (mm) cc_final: 0.8193 (mt) REVERT: M 259 TYR cc_start: 0.8171 (m-80) cc_final: 0.7787 (m-80) REVERT: M 325 MET cc_start: 0.7960 (ttt) cc_final: 0.7717 (ttt) REVERT: M 437 MET cc_start: 0.8853 (mmp) cc_final: 0.8579 (mmp) REVERT: N 11 MET cc_start: 0.7994 (mmp) cc_final: 0.7440 (mtm) REVERT: N 51 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7588 (mtt90) REVERT: N 71 MET cc_start: 0.8843 (tpp) cc_final: 0.8573 (tpp) REVERT: N 236 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7482 (mtmt) REVERT: N 254 LEU cc_start: 0.8018 (tt) cc_final: 0.7774 (tp) REVERT: N 270 MET cc_start: 0.8880 (mtp) cc_final: 0.8564 (mtp) REVERT: V 119 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4615 (mm) REVERT: V 130 GLU cc_start: 0.5296 (mp0) cc_final: 0.4745 (mt-10) REVERT: W 7 ARG cc_start: 0.5531 (mtm110) cc_final: 0.5329 (mtm180) REVERT: W 19 LYS cc_start: 0.8196 (mtpm) cc_final: 0.7977 (ttpt) REVERT: W 77 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7338 (ttp-110) REVERT: W 98 SER cc_start: 0.8230 (p) cc_final: 0.7977 (p) REVERT: W 107 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7104 (tt0) REVERT: W 130 LYS cc_start: 0.8329 (pttp) cc_final: 0.8013 (pttt) REVERT: W 134 ASP cc_start: 0.8290 (t0) cc_final: 0.7934 (t0) REVERT: X 7 THR cc_start: 0.4315 (p) cc_final: 0.3852 (m) REVERT: X 9 GLU cc_start: 0.6702 (tt0) cc_final: 0.6085 (tp30) REVERT: X 13 ASP cc_start: 0.6092 (m-30) cc_final: 0.5462 (m-30) REVERT: X 52 MET cc_start: 0.6993 (ttt) cc_final: 0.6730 (ttm) REVERT: X 62 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7301 (mt) REVERT: X 68 GLU cc_start: 0.6273 (pt0) cc_final: 0.5480 (mt-10) REVERT: Y 79 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7711 (mp0) REVERT: Y 131 LYS cc_start: 0.7259 (tptp) cc_final: 0.6940 (tmtm) REVERT: Y 141 TYR cc_start: 0.8002 (m-80) cc_final: 0.7774 (m-80) REVERT: Z 31 TYR cc_start: 0.6523 (m-80) cc_final: 0.6294 (m-10) REVERT: Z 54 GLN cc_start: 0.7246 (mp10) cc_final: 0.6494 (mm-40) REVERT: Z 61 TYR cc_start: 0.7196 (m-80) cc_final: 0.6889 (m-80) REVERT: Z 66 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7514 (pp20) REVERT: a 63 MET cc_start: 0.7295 (mmm) cc_final: 0.6983 (mtp) REVERT: a 71 GLU cc_start: 0.7996 (tt0) cc_final: 0.7624 (mp0) REVERT: b 22 ASP cc_start: 0.8459 (t0) cc_final: 0.8205 (t70) REVERT: b 46 GLU cc_start: 0.7908 (mt-10) cc_final: 0.6989 (mm-30) REVERT: b 78 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: b 94 GLN cc_start: 0.7562 (pt0) cc_final: 0.7146 (tt0) REVERT: c 13 VAL cc_start: 0.7367 (t) cc_final: 0.7066 (p) REVERT: c 15 GLU cc_start: 0.5607 (mm-30) cc_final: 0.5356 (mp0) REVERT: d 60 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8121 (mtt180) REVERT: d 77 ASP cc_start: 0.8284 (t0) cc_final: 0.7788 (t0) REVERT: d 79 ASP cc_start: 0.8132 (t0) cc_final: 0.7908 (m-30) REVERT: d 86 GLU cc_start: 0.7862 (pt0) cc_final: 0.7582 (tp30) REVERT: d 102 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7634 (ttpp) REVERT: d 139 ILE cc_start: 0.8063 (mm) cc_final: 0.7677 (tp) REVERT: d 154 LYS cc_start: 0.7788 (tttm) cc_final: 0.7412 (ttpp) REVERT: d 158 GLU cc_start: 0.8100 (pt0) cc_final: 0.7709 (mt-10) REVERT: d 162 GLU cc_start: 0.8230 (mp0) cc_final: 0.7795 (mm-30) REVERT: d 240 ASP cc_start: 0.7333 (p0) cc_final: 0.6761 (m-30) REVERT: d 306 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6717 (mt0) REVERT: e 42 GLU cc_start: 0.7462 (pm20) cc_final: 0.6724 (mp0) REVERT: e 45 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7595 (mtpp) REVERT: e 63 LYS cc_start: 0.8947 (tppp) cc_final: 0.8676 (tptt) REVERT: e 72 GLN cc_start: 0.7957 (mm110) cc_final: 0.6756 (tt0) REVERT: e 84 ASP cc_start: 0.7247 (m-30) cc_final: 0.7021 (m-30) REVERT: e 91 GLU cc_start: 0.7428 (pt0) cc_final: 0.7124 (pp20) REVERT: f 57 ILE cc_start: 0.8533 (mt) cc_final: 0.8244 (mp) REVERT: f 84 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7596 (mt-10) REVERT: g 29 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7603 (ttp80) REVERT: g 33 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8186 (tt0) REVERT: g 41 GLU cc_start: 0.7913 (tp30) cc_final: 0.7547 (tp30) REVERT: g 56 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7932 (tptp) REVERT: g 60 ASP cc_start: 0.8351 (m-30) cc_final: 0.7965 (m-30) REVERT: g 87 MET cc_start: 0.8842 (mtt) cc_final: 0.8594 (mtp) REVERT: h 17 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7424 (mtm-85) REVERT: h 47 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7774 (mtp180) REVERT: h 102 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7896 (ttp80) REVERT: i 1 MET cc_start: 0.4920 (tpt) cc_final: 0.3605 (mtm) REVERT: i 8 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6786 (ttmt) REVERT: i 12 GLN cc_start: 0.7907 (pt0) cc_final: 0.7515 (mt0) REVERT: i 15 SER cc_start: 0.7859 (t) cc_final: 0.7657 (p) REVERT: i 25 ARG cc_start: 0.7965 (ttt90) cc_final: 0.7742 (ttt90) REVERT: i 42 ASP cc_start: 0.8554 (p0) cc_final: 0.8350 (p0) REVERT: i 71 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7974 (tttp) REVERT: i 112 ASN cc_start: 0.8873 (t0) cc_final: 0.8451 (t0) REVERT: i 122 GLN cc_start: 0.8555 (mp10) cc_final: 0.8331 (mt0) REVERT: j 8 LEU cc_start: 0.6205 (tt) cc_final: 0.5997 (mp) REVERT: j 18 VAL cc_start: 0.7470 (t) cc_final: 0.7207 (m) REVERT: j 52 MET cc_start: 0.7820 (mtm) cc_final: 0.7413 (mtm) REVERT: j 54 MET cc_start: 0.7170 (mmt) cc_final: 0.6943 (mmt) REVERT: j 56 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5531 (m-30) REVERT: j 77 VAL cc_start: 0.7340 (p) cc_final: 0.7065 (m) REVERT: k 45 LYS cc_start: 0.6716 (mmtt) cc_final: 0.6494 (mtpp) REVERT: k 92 ASN cc_start: 0.7957 (t0) cc_final: 0.7732 (t0) REVERT: k 138 MET cc_start: 0.8401 (mtm) cc_final: 0.7887 (mtp) REVERT: k 143 PHE cc_start: 0.7689 (m-10) cc_final: 0.7382 (m-80) REVERT: k 185 LYS cc_start: 0.7251 (mtpt) cc_final: 0.6691 (mmtp) REVERT: k 192 MET cc_start: 0.7601 (mtt) cc_final: 0.7204 (mtt) REVERT: k 201 ASP cc_start: 0.6887 (m-30) cc_final: 0.6596 (m-30) REVERT: k 261 MET cc_start: 0.8569 (mmm) cc_final: 0.8347 (mmm) REVERT: k 293 PHE cc_start: 0.8596 (t80) cc_final: 0.8362 (t80) REVERT: k 318 TRP cc_start: 0.7448 (p-90) cc_final: 0.7058 (p-90) REVERT: l 12 ASP cc_start: 0.8233 (t0) cc_final: 0.7925 (t70) REVERT: l 23 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8463 (tm-30) REVERT: l 73 LYS cc_start: 0.7953 (tttm) cc_final: 0.7703 (ttpt) REVERT: m 10 ASN cc_start: 0.7641 (t0) cc_final: 0.7107 (m-40) REVERT: m 14 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7144 (tppt) REVERT: n 13 MET cc_start: 0.4388 (ttt) cc_final: 0.3895 (mpp) REVERT: o 16 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6247 (t70) REVERT: o 45 ASP cc_start: 0.8051 (t70) cc_final: 0.7779 (t0) REVERT: o 55 SER cc_start: 0.7727 (m) cc_final: 0.7491 (t) REVERT: o 97 HIS cc_start: 0.7481 (m90) cc_final: 0.7210 (m-70) REVERT: q 89 ASN cc_start: 0.8574 (m-40) cc_final: 0.8243 (m110) REVERT: q 91 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: q 120 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6838 (mmp) REVERT: q 122 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7952 (mt-10) REVERT: r 71 PHE cc_start: 0.7910 (t80) cc_final: 0.7455 (t80) REVERT: r 102 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6631 (ttp80) REVERT: r 107 ASP cc_start: 0.8293 (m-30) cc_final: 0.8009 (m-30) REVERT: s 6 ARG cc_start: 0.4810 (mtm110) cc_final: 0.4306 (mtt90) REVERT: s 71 ASP cc_start: 0.5764 (m-30) cc_final: 0.5533 (m-30) REVERT: s 100 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: s 103 ARG cc_start: 0.5502 (tmt90) cc_final: 0.5288 (tmt170) REVERT: s 121 MET cc_start: 0.3640 (tpt) cc_final: 0.3186 (mtp) REVERT: t 50 HIS cc_start: 0.5541 (m-70) cc_final: 0.5158 (m-70) REVERT: t 56 MET cc_start: 0.2807 (mmm) cc_final: 0.2565 (ttt) REVERT: t 79 TYR cc_start: 0.8127 (t80) cc_final: 0.7662 (t80) REVERT: t 83 GLU cc_start: 0.8152 (mp0) cc_final: 0.7729 (mt-10) REVERT: t 134 ARG cc_start: 0.6532 (mtm180) cc_final: 0.6032 (tpt170) REVERT: t 137 LYS cc_start: 0.5806 (pttp) cc_final: 0.5491 (ttpt) REVERT: u 41 TRP cc_start: 0.6578 (t-100) cc_final: 0.6062 (t-100) REVERT: v 59 ASP cc_start: 0.6909 (t0) cc_final: 0.6685 (t0) REVERT: v 70 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5728 (mmt90) REVERT: v 77 MET cc_start: 0.8144 (mtt) cc_final: 0.7909 (mtp) REVERT: v 108 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: v 115 MET cc_start: 0.7403 (mmt) cc_final: 0.7170 (mmt) REVERT: v 141 GLU cc_start: 0.7250 (mp0) cc_final: 0.6985 (mp0) REVERT: v 149 GLU cc_start: 0.6027 (tt0) cc_final: 0.5762 (tm-30) REVERT: w 109 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7085 (tp30) REVERT: x 30 TYR cc_start: 0.7973 (t80) cc_final: 0.7748 (t80) REVERT: x 44 ARG cc_start: 0.7714 (tmm160) cc_final: 0.6993 (ttp-170) REVERT: z 23 THR cc_start: 0.8850 (t) cc_final: 0.8552 (m) REVERT: z 25 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7447 (mtt180) REVERT: z 59 ARG cc_start: 0.8569 (mmt-90) cc_final: 0.8247 (mtm180) outliers start: 224 outliers final: 65 residues processed: 1478 average time/residue: 1.5297 time to fit residues: 2946.9444 Evaluate side-chains 1310 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1222 time to evaluate : 5.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 188 GLU Chi-restraints excluded: chain 1 residue 253 THR Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 2 residue 170 GLU Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 341 ASP Chi-restraints excluded: chain 3 residue 347 GLU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 77 ASP Chi-restraints excluded: chain 5 residue 186 GLU Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 300 LYS Chi-restraints excluded: chain L residue 307 SER Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 321 LYS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 65 CYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 98 ARG Chi-restraints excluded: chain Y residue 99 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 39 LYS Chi-restraints excluded: chain f residue 72 GLN Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain i residue 32 ASP Chi-restraints excluded: chain i residue 111 THR Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 56 ASP Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 78 SER Chi-restraints excluded: chain k residue 289 SER Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain o residue 16 ASP Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 94 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain p residue 115 ILE Chi-restraints excluded: chain q residue 91 GLU Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 80 ILE Chi-restraints excluded: chain t residue 89 SER Chi-restraints excluded: chain v residue 108 PHE Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 594 optimal weight: 0.0770 chunk 486 optimal weight: 40.0000 chunk 196 optimal weight: 20.0000 chunk 715 optimal weight: 7.9990 chunk 772 optimal weight: 10.0000 chunk 636 optimal weight: 20.0000 chunk 709 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 573 optimal weight: 20.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 361 GLN 2 112 ASN 2 121 GLN 3 517 ASN 3 546 GLN 4 5 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 52 HIS K 92 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 ASN L 136 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 GLN L 270 ASN L 323 HIS ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN W 95 GLN W 124 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Y 150 ASN d 180 ASN e 61 GLN ** f 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 ASN g 50 GLN h 24 GLN i 31 ASN i 52 ASN i 69 ASN i 123 GLN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 GLN l 69 GLN l 96 HIS m 51 ASN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 116 GLN s 42 GLN s 43 GLN ** t 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 13 GLN ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 28 ASN v 136 ASN x 46 ASN y 30 ASN z 44 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.282 67934 Z= 0.542 Angle : 1.580 51.007 91887 Z= 1.021 Chirality : 0.315 6.624 9990 Planarity : 0.005 0.050 11497 Dihedral : 11.384 172.101 10004 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.81 % Allowed : 11.89 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.09), residues: 7950 helix: 0.35 (0.08), residues: 4214 sheet: -0.79 (0.24), residues: 404 loop : -0.97 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 125 HIS 0.016 0.001 HIS 9 65 PHE 0.024 0.002 PHE 4 171 TYR 0.034 0.002 TYR r 87 ARG 0.008 0.001 ARG Z 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1286 time to evaluate : 5.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 34 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7808 (tppt) REVERT: 1 73 PHE cc_start: 0.7488 (t80) cc_final: 0.6833 (m-10) REVERT: 1 178 VAL cc_start: 0.8604 (t) cc_final: 0.8319 (m) REVERT: 1 248 GLU cc_start: 0.7864 (tt0) cc_final: 0.7256 (pp20) REVERT: 1 249 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7262 (mtm110) REVERT: 1 281 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7923 (mm-30) REVERT: 1 309 LYS cc_start: 0.8378 (tmtp) cc_final: 0.8065 (ttmt) REVERT: 1 326 GLN cc_start: 0.7229 (pt0) cc_final: 0.6687 (tp-100) REVERT: 1 356 HIS cc_start: 0.8120 (m90) cc_final: 0.7292 (t70) REVERT: 1 376 MET cc_start: 0.8928 (mmm) cc_final: 0.8656 (mmm) REVERT: 1 385 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7638 (mpp-170) REVERT: 1 431 GLN cc_start: 0.7968 (pt0) cc_final: 0.7665 (pp30) REVERT: 1 436 GLN cc_start: 0.7686 (pt0) cc_final: 0.6763 (pp30) REVERT: 2 29 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7268 (ttpt) REVERT: 2 114 ASP cc_start: 0.7816 (m-30) cc_final: 0.7261 (p0) REVERT: 2 117 LEU cc_start: 0.8261 (tp) cc_final: 0.8019 (tm) REVERT: 2 127 LYS cc_start: 0.7300 (ptpt) cc_final: 0.6743 (mttp) REVERT: 2 180 LYS cc_start: 0.6693 (mtmm) cc_final: 0.6236 (mmmm) REVERT: 2 204 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6690 (tp30) REVERT: 3 16 GLN cc_start: 0.7947 (tt0) cc_final: 0.7615 (tp40) REVERT: 3 61 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7782 (mmtt) REVERT: 3 135 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8051 (ptt90) REVERT: 3 188 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7776 (mm-30) REVERT: 3 246 GLU cc_start: 0.8896 (tt0) cc_final: 0.8369 (tp30) REVERT: 3 297 GLU cc_start: 0.8232 (mp0) cc_final: 0.7649 (mt-10) REVERT: 3 329 ILE cc_start: 0.8361 (tp) cc_final: 0.8005 (tt) REVERT: 3 418 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7644 (mmt-90) REVERT: 3 461 ASN cc_start: 0.7911 (m-40) cc_final: 0.7625 (m-40) REVERT: 3 462 ASP cc_start: 0.8340 (p0) cc_final: 0.7906 (p0) REVERT: 3 475 GLN cc_start: 0.6872 (mm110) cc_final: 0.5682 (pp30) REVERT: 3 533 THR cc_start: 0.8518 (p) cc_final: 0.8237 (t) REVERT: 3 605 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: 3 642 PHE cc_start: 0.8647 (m-80) cc_final: 0.8328 (m-80) REVERT: 3 643 GLN cc_start: 0.7509 (tp40) cc_final: 0.6782 (mt0) REVERT: 3 673 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: 4 74 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7546 (mmm160) REVERT: 4 75 LYS cc_start: 0.8776 (tttm) cc_final: 0.7985 (ttmt) REVERT: 4 227 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: 4 282 GLU cc_start: 0.8409 (tt0) cc_final: 0.8161 (mt-10) REVERT: 4 327 ASP cc_start: 0.8395 (t0) cc_final: 0.7858 (t70) REVERT: 5 49 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8451 (tt0) REVERT: 6 81 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7166 (mmt90) REVERT: 6 178 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: 9 32 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: 9 36 MET cc_start: 0.8973 (tpp) cc_final: 0.8614 (tpt) REVERT: 9 112 ASP cc_start: 0.8787 (t0) cc_final: 0.8544 (t0) REVERT: A 1 MET cc_start: 0.6891 (tpt) cc_final: 0.6564 (tpp) REVERT: H 184 MET cc_start: 0.8810 (mtm) cc_final: 0.8594 (mtm) REVERT: H 202 GLU cc_start: 0.6032 (mt-10) cc_final: 0.4973 (tp30) REVERT: H 227 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: H 251 MET cc_start: 0.8208 (mtp) cc_final: 0.7901 (mtt) REVERT: J 98 LEU cc_start: 0.3681 (OUTLIER) cc_final: 0.3444 (mt) REVERT: K 6 MET cc_start: 0.7476 (ttp) cc_final: 0.7214 (mtt) REVERT: L 24 PHE cc_start: 0.6628 (m-10) cc_final: 0.6034 (t80) REVERT: L 55 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7619 (mp) REVERT: L 88 MET cc_start: 0.7472 (mpm) cc_final: 0.7230 (mpp) REVERT: L 89 PHE cc_start: 0.7948 (t80) cc_final: 0.7549 (t80) REVERT: L 109 HIS cc_start: 0.6844 (t-90) cc_final: 0.6194 (p90) REVERT: L 113 ASN cc_start: 0.7302 (m110) cc_final: 0.7089 (m-40) REVERT: L 354 GLN cc_start: 0.6319 (mt0) cc_final: 0.6047 (mt0) REVERT: L 359 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6632 (tpp) REVERT: L 407 TRP cc_start: 0.6831 (t-100) cc_final: 0.6248 (t-100) REVERT: L 411 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6396 (mpm) REVERT: L 413 LEU cc_start: 0.7882 (mt) cc_final: 0.7595 (mt) REVERT: L 449 PHE cc_start: 0.6395 (m-10) cc_final: 0.6146 (m-10) REVERT: L 463 PHE cc_start: 0.7626 (m-80) cc_final: 0.7179 (m-80) REVERT: L 488 MET cc_start: 0.6097 (mpp) cc_final: 0.5020 (ptm) REVERT: L 544 MET cc_start: 0.3066 (tmm) cc_final: 0.2021 (mpp) REVERT: L 573 MET cc_start: 0.2109 (mmp) cc_final: 0.1063 (mmm) REVERT: M 19 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7027 (tptm) REVERT: M 184 GLN cc_start: 0.8395 (mm110) cc_final: 0.8123 (mm-40) REVERT: M 194 PHE cc_start: 0.8008 (m-80) cc_final: 0.7716 (m-10) REVERT: M 214 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8141 (mt) REVERT: M 259 TYR cc_start: 0.8178 (m-80) cc_final: 0.7753 (m-80) REVERT: M 325 MET cc_start: 0.7897 (ttt) cc_final: 0.7546 (ttt) REVERT: M 437 MET cc_start: 0.8755 (mmp) cc_final: 0.8491 (mmp) REVERT: M 458 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8018 (pp) REVERT: N 11 MET cc_start: 0.8062 (mmp) cc_final: 0.7461 (mtm) REVERT: N 51 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7564 (mtt90) REVERT: N 71 MET cc_start: 0.8844 (tpp) cc_final: 0.8520 (tpp) REVERT: N 183 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7863 (p) REVERT: N 236 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7622 (mtmt) REVERT: N 254 LEU cc_start: 0.8128 (tt) cc_final: 0.7915 (tp) REVERT: N 270 MET cc_start: 0.8775 (mtp) cc_final: 0.8533 (mtp) REVERT: V 119 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4733 (mm) REVERT: V 130 GLU cc_start: 0.5250 (mp0) cc_final: 0.4720 (mt-10) REVERT: W 19 LYS cc_start: 0.8213 (mtpm) cc_final: 0.7916 (ttpt) REVERT: W 68 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7781 (ttmt) REVERT: W 77 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7387 (ttp-110) REVERT: W 98 SER cc_start: 0.8223 (p) cc_final: 0.8003 (p) REVERT: W 107 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7155 (tt0) REVERT: W 134 ASP cc_start: 0.8292 (t0) cc_final: 0.8015 (t0) REVERT: X 7 THR cc_start: 0.4434 (p) cc_final: 0.4004 (m) REVERT: X 9 GLU cc_start: 0.6665 (tt0) cc_final: 0.6049 (tp30) REVERT: X 52 MET cc_start: 0.6932 (ttt) cc_final: 0.6707 (ttm) REVERT: X 68 GLU cc_start: 0.6090 (pt0) cc_final: 0.5556 (mt-10) REVERT: Y 131 LYS cc_start: 0.7256 (tptp) cc_final: 0.6929 (tmtm) REVERT: Y 141 TYR cc_start: 0.8096 (m-80) cc_final: 0.7752 (m-80) REVERT: Z 31 TYR cc_start: 0.6565 (m-80) cc_final: 0.6274 (m-80) REVERT: Z 54 GLN cc_start: 0.7217 (mp10) cc_final: 0.6580 (mm-40) REVERT: Z 66 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7569 (pp20) REVERT: Z 72 ASP cc_start: 0.7966 (p0) cc_final: 0.7674 (p0) REVERT: Z 126 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6941 (ptpp) REVERT: Z 129 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: a 63 MET cc_start: 0.7287 (mmm) cc_final: 0.6986 (mtp) REVERT: a 71 GLU cc_start: 0.8031 (tt0) cc_final: 0.7701 (mp0) REVERT: b 46 GLU cc_start: 0.7834 (mt-10) cc_final: 0.6915 (mm-30) REVERT: b 78 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: b 94 GLN cc_start: 0.7452 (pt0) cc_final: 0.7033 (tt0) REVERT: c 15 GLU cc_start: 0.5595 (mm-30) cc_final: 0.5273 (mp0) REVERT: d 60 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8174 (mtt180) REVERT: d 77 ASP cc_start: 0.8248 (t0) cc_final: 0.7788 (t0) REVERT: d 79 ASP cc_start: 0.8159 (t0) cc_final: 0.7945 (m-30) REVERT: d 82 ARG cc_start: 0.7923 (ttp-110) cc_final: 0.7243 (tmt-80) REVERT: d 98 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: d 102 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7639 (ttpp) REVERT: d 139 ILE cc_start: 0.7961 (mm) cc_final: 0.7572 (tp) REVERT: d 162 GLU cc_start: 0.8340 (mp0) cc_final: 0.7881 (mm-30) REVERT: d 240 ASP cc_start: 0.7180 (p0) cc_final: 0.6688 (m-30) REVERT: d 306 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6754 (mt0) REVERT: e 26 SER cc_start: 0.8703 (m) cc_final: 0.8430 (m) REVERT: e 42 GLU cc_start: 0.7494 (pm20) cc_final: 0.6804 (mp0) REVERT: e 45 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7542 (mtpp) REVERT: e 63 LYS cc_start: 0.8979 (tppp) cc_final: 0.8717 (tptt) REVERT: e 72 GLN cc_start: 0.7983 (mm110) cc_final: 0.6779 (tt0) REVERT: e 84 ASP cc_start: 0.7266 (m-30) cc_final: 0.7044 (m-30) REVERT: e 91 GLU cc_start: 0.7244 (pt0) cc_final: 0.6968 (pp20) REVERT: f 57 ILE cc_start: 0.8514 (mt) cc_final: 0.8227 (mp) REVERT: f 84 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7577 (mt-10) REVERT: g 29 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7583 (ttp80) REVERT: g 33 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8195 (tt0) REVERT: g 41 GLU cc_start: 0.7821 (tp30) cc_final: 0.7508 (tp30) REVERT: g 56 LYS cc_start: 0.8425 (tmmt) cc_final: 0.8018 (tptp) REVERT: g 60 ASP cc_start: 0.8344 (m-30) cc_final: 0.7952 (m-30) REVERT: g 87 MET cc_start: 0.8869 (mtt) cc_final: 0.8628 (mtp) REVERT: h 17 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7408 (mtt90) REVERT: h 47 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7849 (mtp180) REVERT: h 102 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7814 (ttp80) REVERT: i 1 MET cc_start: 0.5091 (tpt) cc_final: 0.3884 (mtt) REVERT: i 8 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6661 (ttmt) REVERT: i 12 GLN cc_start: 0.7906 (pt0) cc_final: 0.7516 (mt0) REVERT: i 15 SER cc_start: 0.7891 (t) cc_final: 0.7682 (p) REVERT: i 42 ASP cc_start: 0.8669 (p0) cc_final: 0.8442 (p0) REVERT: i 71 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8028 (tttp) REVERT: i 114 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8249 (mtmt) REVERT: i 122 GLN cc_start: 0.8592 (mp10) cc_final: 0.8364 (mt0) REVERT: j 18 VAL cc_start: 0.7551 (t) cc_final: 0.7283 (m) REVERT: j 24 LYS cc_start: 0.7170 (ttmp) cc_final: 0.6554 (tptp) REVERT: j 54 MET cc_start: 0.7111 (mmt) cc_final: 0.6892 (mmt) REVERT: j 56 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: j 77 VAL cc_start: 0.7258 (p) cc_final: 0.7017 (m) REVERT: k 16 LYS cc_start: 0.6511 (mmtt) cc_final: 0.6292 (mmpt) REVERT: k 92 ASN cc_start: 0.8078 (t0) cc_final: 0.7853 (t0) REVERT: k 138 MET cc_start: 0.8465 (mtm) cc_final: 0.7971 (mtp) REVERT: k 143 PHE cc_start: 0.7702 (m-10) cc_final: 0.7487 (m-80) REVERT: k 185 LYS cc_start: 0.7284 (mtpt) cc_final: 0.6726 (mmtp) REVERT: k 293 PHE cc_start: 0.8564 (t80) cc_final: 0.8253 (t80) REVERT: k 315 LYS cc_start: 0.7594 (mptt) cc_final: 0.7329 (tptp) REVERT: k 318 TRP cc_start: 0.7489 (p-90) cc_final: 0.7126 (p-90) REVERT: l 12 ASP cc_start: 0.8266 (t0) cc_final: 0.7971 (t70) REVERT: l 69 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: l 73 LYS cc_start: 0.7930 (tttm) cc_final: 0.7697 (ttpt) REVERT: m 10 ASN cc_start: 0.7640 (t0) cc_final: 0.7040 (m-40) REVERT: m 14 LYS cc_start: 0.7431 (mtmt) cc_final: 0.7123 (tppt) REVERT: n 13 MET cc_start: 0.4448 (ttt) cc_final: 0.3910 (mpp) REVERT: n 62 PHE cc_start: 0.6441 (t80) cc_final: 0.6174 (t80) REVERT: o 16 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6250 (t70) REVERT: o 55 SER cc_start: 0.7830 (m) cc_final: 0.7576 (t) REVERT: o 97 HIS cc_start: 0.7505 (m90) cc_final: 0.7249 (m-70) REVERT: q 89 ASN cc_start: 0.8552 (m-40) cc_final: 0.8236 (m110) REVERT: q 120 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6569 (tpt) REVERT: q 122 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7985 (mt-10) REVERT: r 10 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6640 (ttt90) REVERT: r 27 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7069 (mt) REVERT: r 71 PHE cc_start: 0.7968 (t80) cc_final: 0.7542 (t80) REVERT: r 98 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: r 102 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6577 (ttp80) REVERT: s 6 ARG cc_start: 0.4925 (mtm110) cc_final: 0.4388 (mtt90) REVERT: s 20 ARG cc_start: 0.6093 (ptm-80) cc_final: 0.5634 (mpp-170) REVERT: s 100 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: s 108 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6048 (tp) REVERT: s 121 MET cc_start: 0.3798 (tpt) cc_final: 0.3275 (mtp) REVERT: t 50 HIS cc_start: 0.5542 (m-70) cc_final: 0.5134 (m-70) REVERT: t 56 MET cc_start: 0.3344 (mmm) cc_final: 0.2831 (ttt) REVERT: t 83 GLU cc_start: 0.8187 (mp0) cc_final: 0.7756 (mt-10) REVERT: t 134 ARG cc_start: 0.6484 (mtm180) cc_final: 0.5967 (tpt170) REVERT: t 137 LYS cc_start: 0.5935 (pttp) cc_final: 0.5655 (ttpt) REVERT: u 7 ILE cc_start: 0.5951 (OUTLIER) cc_final: 0.5522 (mp) REVERT: u 41 TRP cc_start: 0.6632 (t-100) cc_final: 0.6132 (t-100) REVERT: v 59 ASP cc_start: 0.6901 (t0) cc_final: 0.6627 (t0) REVERT: v 70 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5686 (mmt90) REVERT: v 77 MET cc_start: 0.8194 (mtt) cc_final: 0.7898 (mtp) REVERT: v 80 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: v 108 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5721 (m-80) REVERT: v 141 GLU cc_start: 0.7297 (mp0) cc_final: 0.6976 (mp0) REVERT: v 149 GLU cc_start: 0.6101 (tt0) cc_final: 0.5885 (tm-30) REVERT: w 109 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7161 (tp30) REVERT: x 30 TYR cc_start: 0.8035 (t80) cc_final: 0.7759 (t80) REVERT: x 34 GLN cc_start: 0.7958 (tp40) cc_final: 0.7732 (tp40) REVERT: y 32 GLU cc_start: 0.7800 (tp30) cc_final: 0.7592 (tt0) REVERT: y 40 LYS cc_start: 0.8235 (mttt) cc_final: 0.7958 (mtpp) REVERT: z 23 THR cc_start: 0.8850 (t) cc_final: 0.8490 (m) REVERT: z 25 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7444 (mtt180) REVERT: z 59 ARG cc_start: 0.8577 (mmt-90) cc_final: 0.8205 (mtm180) outliers start: 269 outliers final: 98 residues processed: 1421 average time/residue: 1.5211 time to fit residues: 2814.1385 Evaluate side-chains 1330 residues out of total 7062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1198 time to evaluate : 5.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 253 THR Chi-restraints excluded: chain 1 residue 292 ASP Chi-restraints excluded: chain 1 residue 437 HIS Chi-restraints excluded: chain 2 residue 170 GLU Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 201 ASP Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 341 ASP Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 605 GLU Chi-restraints excluded: chain 3 residue 673 MET Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 227 GLU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 5 residue 186 GLU Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 32 ARG Chi-restraints excluded: chain 9 residue 86 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 307 SER Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 374 ILE Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain L residue 439 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 321 LYS Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 65 CYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 99 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 117 VAL 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 a residue 45 ASP Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 98 GLU Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 281 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 39 LYS Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain g residue 95 VAL Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain i residue 32 ASP Chi-restraints excluded: chain i residue 111 THR Chi-restraints excluded: chain i residue 123 GLN Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 56 ASP Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 78 SER Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 289 SER Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 36 GLU Chi-restraints excluded: chain l residue 69 GLN Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain o residue 16 ASP Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain p residue 43 LYS Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain r residue 10 ARG Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 98 GLU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 95 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain s residue 108 LEU Chi-restraints excluded: chain t residue 89 SER Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 108 PHE Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 32 ILE Chi-restraints excluded: chain y residue 29 LYS Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 6.9990 chunk 537 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 341 optimal weight: 0.0870 chunk 480 optimal weight: 20.0000 chunk 717 optimal weight: 20.0000 chunk 759 optimal weight: 6.9990 chunk 374 optimal weight: 10.0000 chunk 680 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: