Starting phenix.real_space_refine on Fri Feb 16 19:14:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkg_11248/02_2024/6zkg_11248_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.026 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 44 5.49 5 S 468 5.16 5 C 43968 2.51 5 N 11233 2.21 5 O 12178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" 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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 142": "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 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "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 "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "d ARG 325": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 58": "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 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 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 149": "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" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67921 Number of models: 1 Model: "" Number of chains: 68 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: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3457 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} 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: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2748 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 361 Unusual residues: {'3PE': 3, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "M" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 288 Unusual residues: {'3PE': 1, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 158 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 46 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: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "o" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 102.399 53.611 239.340 1.00 17.05 S ATOM 4116 SG CYS 2 103 100.195 47.964 258.047 1.00 64.99 S ATOM 4150 SG CYS 2 108 97.968 45.498 259.765 1.00 73.77 S ATOM 4430 SG CYS 2 144 101.923 44.501 254.197 1.00 56.66 S ATOM 4453 SG CYS 2 148 99.878 41.614 255.651 1.00 73.35 S ATOM 5793 SG CYS 3 114 104.561 72.255 225.276 1.00 29.58 S ATOM 5732 SG CYS 3 105 99.090 75.457 227.109 1.00 50.45 S ATOM 5753 SG CYS 3 108 105.088 77.274 229.070 1.00 55.68 S ATOM 6125 SG CYS 3 156 111.815 64.768 229.849 1.00 36.28 S ATOM 6102 SG CYS 3 153 109.813 67.672 235.476 1.00 50.85 S ATOM 6149 SG CYS 3 159 115.824 68.766 233.615 1.00 72.33 S ATOM 6479 SG CYS 3 203 111.466 71.045 229.996 1.00 43.08 S ATOM 5238 SG CYS 3 41 110.959 58.328 227.738 1.00 55.93 S ATOM 5324 SG CYS 3 52 107.287 59.317 226.949 1.00 30.66 S ATOM 5349 SG CYS 3 55 107.884 54.541 223.144 1.00 59.68 S ATOM 5450 SG CYS 3 69 111.463 54.505 224.845 1.00 23.91 S ATOM 15674 SG CYS 6 54 82.468 95.554 202.403 1.00 62.78 S ATOM 17600 SG CYS 9 116 89.901 96.555 214.901 1.00 41.01 S ATOM 17647 SG CYS 9 122 90.472 91.971 219.387 1.00 9.79 S ATOM 17374 SG CYS 9 87 94.427 91.940 214.113 1.00 39.68 S ATOM 17676 SG CYS 9 126 92.728 88.459 226.490 1.00 58.79 S ATOM 17347 SG CYS 9 83 96.311 90.341 221.503 1.00 29.92 S ATOM 17305 SG CYS 9 77 98.395 91.955 227.276 1.00 32.99 S ATOM 17324 SG CYS 9 80 97.845 85.407 225.591 1.00 52.14 S ATOM 41371 SG CYS b 59 94.362 83.590 241.726 1.00 34.00 S ATOM 41549 SG CYS b 84 97.399 83.679 239.528 1.00 18.27 S ATOM 41571 SG CYS b 87 95.663 86.546 240.464 1.00 40.18 S Time building chain proxies: 26.42, per 1000 atoms: 0.39 Number of scatterers: 67921 At special positions: 0 Unit cell: (175.065, 196.285, 290.714, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 468 16.00 P 44 15.00 O 12178 8.00 N 11233 7.00 C 43968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.01 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb="FE2 SF4 9 402 " - pdb=" NE2 HIS 9 65 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 334 helices and 29 sheets defined 50.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.554A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 62 removed outlier: 3.774A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.737A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.899A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 237 removed outlier: 4.420A pdb=" N SER 1 231 " --> pdb=" O THR 1 227 " (cutoff:3.500A) Proline residue: 1 232 - end of helix 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 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.484A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 397 removed outlier: 4.041A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 436 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.818A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.508A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 4.346A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.753A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 31 Processing helix chain '3' and resid 84 through 97 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 198 through 202 removed outlier: 3.941A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 296 through 308 removed outlier: 4.154A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 432 removed outlier: 3.825A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 440 through 445 Processing helix chain '3' and resid 463 through 480 removed outlier: 3.764A pdb=" N SER 3 480 " --> pdb=" O LYS 3 476 " (cutoff:3.500A) Processing helix chain '3' and resid 497 through 504 removed outlier: 4.786A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 607 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 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 691 Processing helix chain '4' and resid 8 through 14 removed outlier: 4.181A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.108A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix removed outlier: 4.030A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 165 through 184 removed outlier: 4.075A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 215 Processing helix chain '4' and resid 218 through 229 Processing helix chain '4' and resid 233 through 239 Processing helix chain '4' and resid 247 through 251 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.601A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.419A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.561A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.422A 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: 3.949A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 4.323A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU 5 64 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 4.046A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 42 Processing helix chain '6' and resid 54 through 62 removed outlier: 3.664A pdb=" N GLU 6 58 " --> pdb=" O CYS 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' 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 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 6.020A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.918A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.913A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 4.048A pdb=" N LEU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.449A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 12 through 32 removed outlier: 3.919A pdb=" N VAL H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 55 removed outlier: 3.909A pdb=" N LEU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.937A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 4.126A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 removed outlier: 4.092A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.928A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 289 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 43 removed outlier: 3.750A pdb=" N CYS J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 4.123A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 108 removed outlier: 4.020A pdb=" N THR J 92 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 107 " --> pdb=" O MET J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.766A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 148 removed outlier: 3.936A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 removed outlier: 3.923A pdb=" N ARG J 173 " --> pdb=" O MET J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.948A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 51 removed outlier: 3.554A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 84 removed outlier: 3.885A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 5.068A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET K 80 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR K 84 " --> pdb=" O VAL K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 4 through 24 removed outlier: 3.610A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.550A pdb=" N PHE L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 56 removed outlier: 4.066A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.915A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.611A pdb=" N THR L 133 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.985A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.060A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.323A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.639A 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: 3.759A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 4.685A 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: 4.392A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.809A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU L 394 " --> pdb=" O SER L 391 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.591A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 4.013A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 removed outlier: 4.159A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 5.115A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.507A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.225A 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: 3.627A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.963A 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 81 removed outlier: 3.684A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.827A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 107 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.782A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 170 removed outlier: 3.837A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix 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: 4.973A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.754A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.555A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.270A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.230A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 334 Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.532A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 3.940A 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 132 Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.793A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 4.023A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 232 removed outlier: 4.000A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.521A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.819A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.942A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.779A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.973A 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 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 20 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 76 removed outlier: 3.535A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 89 Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 115 removed outlier: 3.850A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 141 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 43 through 45 No H-bonds generated for 'chain 'a' and resid 43 through 45' Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.804A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.802A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 removed outlier: 3.589A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 28 through 31 No H-bonds generated for 'chain 'c' and resid 28 through 31' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.425A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 99 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 29 through 39 removed outlier: 4.013A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 62 removed outlier: 5.326A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 87 removed outlier: 3.769A pdb=" N GLU d 86 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS d 87 " --> pdb=" O ARG d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 195 through 197 No H-bonds generated for 'chain 'd' and resid 195 through 197' Processing helix chain 'd' and resid 207 through 218 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 260 through 263 No H-bonds generated for 'chain 'd' and resid 260 through 263' Processing helix chain 'd' and resid 265 through 269 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 312 No H-bonds generated for 'chain 'd' and resid 310 through 312' Processing helix chain 'd' and resid 314 through 321 removed outlier: 5.545A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'd' and resid 331 through 333 No H-bonds generated for 'chain 'd' and resid 331 through 333' Processing helix chain 'e' and resid 27 through 39 removed outlier: 5.215A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU e 37 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS e 38 " --> pdb=" O PHE e 35 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG e 39 " --> pdb=" O ILE e 36 " (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: 4.271A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.995A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.381A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 103 Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'i' and resid 3 through 16 Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.914A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 83 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.903A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 4.115A 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 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.431A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 215 Processing helix chain 'k' and resid 231 through 240 removed outlier: 4.340A pdb=" N TYR k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 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 66 Processing helix chain 'l' and resid 69 through 87 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.640A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 38 removed outlier: 4.238A pdb=" N ARG n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 45 through 48 No H-bonds generated for 'chain 'n' and resid 45 through 48' 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: 3.860A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.623A pdb=" N SER o 20 " --> pdb=" O GLU o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 4.096A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.923A pdb=" N ALA p 31 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN p 32 " --> pdb=" O THR p 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 71 Processing helix chain 'p' and resid 83 through 92 removed outlier: 4.030A pdb=" N LEU p 91 " --> pdb=" O LEU p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 98 Proline residue: q 72 - end of helix removed outlier: 3.693A pdb=" N GLU q 92 " --> pdb=" O GLU q 88 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR q 95 " --> pdb=" O GLU q 91 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS q 98 " --> pdb=" O ALA q 94 " (cutoff:3.500A) 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 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 50 removed outlier: 4.385A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 115 through 139 removed outlier: 4.271A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.805A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA w 89 " --> pdb=" O GLN w 86 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 removed outlier: 3.602A pdb=" N ASN x 46 " --> pdb=" O TYR x 42 " (cutoff:3.500A) Processing helix chain 'y' and resid 16 through 32 removed outlier: 3.938A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 Proline residue: z 7 - end of helix removed outlier: 4.401A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.958A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.069A 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: 6.624A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 282 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.746A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.446A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 571 through 574 removed outlier: 3.541A pdb=" N ALA 3 571 " --> pdb=" O THR 3 583 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 removed outlier: 3.642A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.631A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 85 through 89 removed outlier: 6.688A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 5.909A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.517A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.263A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.911A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.609A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.531A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP k 173 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR k 223 " --> pdb=" O ASP k 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC 2722 hydrogen bonds defined for protein. 7653 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: 24.46 Time building geometry restraints manager: 23.14 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: 28750 1.43 - 1.66: 40017 1.66 - 1.90: 761 1.90 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69608 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.598 0.235 3.80e-02 6.93e+02 3.82e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" OA3 CDL z 101 " pdb=" PA1 CDL z 101 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.15e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.340 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 69603 not shown) Histogram of bond angle deviations from ideal: 62.20 - 77.67: 74 77.67 - 93.13: 8 93.13 - 108.60: 5180 108.60 - 124.06: 86778 124.06 - 139.53: 2068 Bond angle restraints: 94108 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 71.42 49.18 3.00e+00 1.11e-01 2.69e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 69.91 39.39 3.00e+00 1.11e-01 1.72e+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 90.07 14.26 1.14e+00 7.69e-01 1.56e+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 89.98 14.35 1.20e+00 6.94e-01 1.43e+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 91.57 12.76 1.14e+00 7.69e-01 1.25e+02 ... (remaining 94103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 41562 35.24 - 70.47: 707 70.47 - 105.71: 46 105.71 - 140.94: 2 140.94 - 176.18: 3 Dihedral angle restraints: 42320 sinusoidal: 18345 harmonic: 23975 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual -180.00 -110.69 -69.31 0 5.00e+00 4.00e-02 1.92e+02 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 -129.79 -50.21 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -133.47 -46.53 0 5.00e+00 4.00e-02 8.66e+01 ... (remaining 42317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.230: 10161 4.230 - 8.460: 5 8.460 - 12.690: 0 12.690 - 16.920: 0 16.920 - 21.151: 24 Chirality restraints: 10190 Sorted by residual: chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.15 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S3 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.57 -21.13 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10187 not shown) Planarity restraints: 11747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.020 2.00e-02 2.50e+03 2.78e-02 1.54e+01 pdb=" CG TYR 9 40 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.032 2.00e-02 2.50e+03 2.68e-02 1.44e+01 pdb=" CG TYR 6 125 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.026 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP 1 371 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.003 2.00e-02 2.50e+03 ... (remaining 11744 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 17647 2.80 - 3.38: 73079 3.38 - 3.97: 139115 3.97 - 4.55: 195642 4.55 - 5.14: 288472 Nonbonded interactions: 713955 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.234 2.440 nonbonded pdb=" O PHE A 56 " pdb=" OH TYR J 70 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP 5 77 " pdb=" OG1 THR 5 79 " model vdw 2.246 2.440 nonbonded pdb=" OE1 GLN 4 54 " pdb=" OH TYR A 37 " model vdw 2.257 2.440 ... (remaining 713950 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 4.820 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 158.920 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.250 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.007 0.235 69608 Z= 0.460 Angle : 1.013 49.179 94108 Z= 0.532 Chirality : 1.023 21.151 10190 Planarity : 0.008 0.067 11747 Dihedral : 12.486 176.175 26840 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.07), residues: 8122 helix: -2.15 (0.06), residues: 4216 sheet: -1.85 (0.24), residues: 376 loop : -2.14 (0.09), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP 1 371 HIS 0.016 0.002 HIS t 25 PHE 0.044 0.003 PHE o 68 TYR 0.064 0.003 TYR 6 125 ARG 0.024 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2146 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2142 time to evaluate : 5.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 167 CYS cc_start: 0.8046 (m) cc_final: 0.7717 (t) REVERT: 3 19 MET cc_start: 0.8263 (mmm) cc_final: 0.8023 (mmm) REVERT: 3 121 MET cc_start: 0.8275 (mmm) cc_final: 0.7952 (mmm) REVERT: 3 287 GLU cc_start: 0.7796 (pm20) cc_final: 0.7579 (tt0) REVERT: 3 311 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6972 (tm-30) REVERT: 3 347 GLU cc_start: 0.7562 (tt0) cc_final: 0.7061 (tp30) REVERT: 3 445 GLU cc_start: 0.7938 (pt0) cc_final: 0.7694 (mm-30) REVERT: 3 520 LYS cc_start: 0.8691 (pttt) cc_final: 0.8100 (mmtm) REVERT: 3 655 GLN cc_start: 0.7521 (mm-40) cc_final: 0.6334 (tt0) REVERT: 4 152 MET cc_start: 0.8778 (tpp) cc_final: 0.8540 (tpt) REVERT: 4 182 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8639 (tm-30) REVERT: 4 334 LYS cc_start: 0.8737 (mttm) cc_final: 0.8493 (mtmt) REVERT: 4 430 ARG cc_start: 0.7974 (mpp80) cc_final: 0.7324 (mpp80) REVERT: 6 25 ARG cc_start: 0.6107 (ttt180) cc_final: 0.5260 (ttp-170) REVERT: 9 14 MET cc_start: 0.7757 (tpt) cc_final: 0.7309 (tmm) REVERT: 9 15 LYS cc_start: 0.7570 (tptp) cc_final: 0.6625 (mmtt) REVERT: 9 40 TYR cc_start: 0.8592 (m-10) cc_final: 0.8333 (m-80) REVERT: 9 153 LYS cc_start: 0.8930 (tptt) cc_final: 0.8445 (tptm) REVERT: 9 157 ASN cc_start: 0.8983 (m-40) cc_final: 0.8727 (m-40) REVERT: A 4 MET cc_start: 0.8474 (mtm) cc_final: 0.7994 (mpp) REVERT: A 28 ASN cc_start: 0.7184 (t0) cc_final: 0.6973 (t0) REVERT: A 101 SER cc_start: 0.8135 (t) cc_final: 0.7701 (p) REVERT: H 1 MET cc_start: 0.7581 (ttp) cc_final: 0.7360 (ttp) REVERT: H 202 GLU cc_start: 0.8123 (tt0) cc_final: 0.7766 (tm-30) REVERT: H 225 MET cc_start: 0.8459 (ptp) cc_final: 0.8223 (ptp) REVERT: H 233 MET cc_start: 0.9041 (tmm) cc_final: 0.8744 (tmm) REVERT: H 234 MET cc_start: 0.7893 (tpp) cc_final: 0.7466 (mmt) REVERT: J 2 MET cc_start: 0.8074 (tpt) cc_final: 0.7768 (tpt) REVERT: J 101 PHE cc_start: 0.7055 (m-80) cc_final: 0.6816 (m-80) REVERT: J 103 MET cc_start: 0.7210 (ptp) cc_final: 0.6782 (mmt) REVERT: J 167 VAL cc_start: 0.8821 (t) cc_final: 0.8407 (t) REVERT: K 40 LEU cc_start: 0.9078 (mt) cc_final: 0.8874 (mt) REVERT: L 52 MET cc_start: 0.7667 (mtm) cc_final: 0.7427 (mtt) REVERT: L 53 MET cc_start: 0.7810 (ptm) cc_final: 0.7380 (ptm) REVERT: L 88 MET cc_start: 0.8260 (mmp) cc_final: 0.7797 (mmm) REVERT: L 105 MET cc_start: 0.8063 (mtp) cc_final: 0.7780 (mtp) REVERT: L 261 ILE cc_start: 0.8361 (mt) cc_final: 0.8071 (mt) REVERT: L 277 MET cc_start: 0.7642 (mtm) cc_final: 0.7287 (mtm) REVERT: L 478 PRO cc_start: 0.6986 (Cg_endo) cc_final: 0.6769 (Cg_exo) REVERT: L 511 LEU cc_start: 0.7189 (mt) cc_final: 0.6883 (pt) REVERT: L 528 TYR cc_start: 0.7316 (m-10) cc_final: 0.7059 (m-80) REVERT: L 544 MET cc_start: 0.5475 (tmm) cc_final: 0.4927 (mmt) REVERT: M 3 LYS cc_start: 0.8264 (ptpp) cc_final: 0.8012 (pttm) REVERT: M 43 ASN cc_start: 0.8858 (t0) cc_final: 0.8550 (t0) REVERT: M 114 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8075 (tt0) REVERT: M 200 MET cc_start: 0.8077 (mmm) cc_final: 0.7846 (mmm) REVERT: M 378 GLU cc_start: 0.8483 (tp30) cc_final: 0.8087 (tt0) REVERT: M 400 MET cc_start: 0.8387 (mtm) cc_final: 0.8158 (ttp) REVERT: N 11 MET cc_start: 0.7679 (mmp) cc_final: 0.7135 (mtp) REVERT: N 44 MET cc_start: 0.9419 (mtt) cc_final: 0.9135 (mtm) REVERT: N 104 MET cc_start: 0.8256 (mtp) cc_final: 0.8045 (mtt) REVERT: N 190 MET cc_start: 0.8933 (mtt) cc_final: 0.8717 (mtm) REVERT: N 220 MET cc_start: 0.8079 (mtm) cc_final: 0.7811 (mtp) REVERT: N 251 MET cc_start: 0.8964 (mtp) cc_final: 0.8684 (mtp) REVERT: N 281 LEU cc_start: 0.8367 (mp) cc_final: 0.8105 (mp) REVERT: N 298 TYR cc_start: 0.8138 (m-10) cc_final: 0.7879 (m-10) REVERT: V 9 TRP cc_start: 0.7604 (m100) cc_final: 0.7148 (m100) REVERT: V 103 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7855 (tpt170) REVERT: V 128 GLN cc_start: 0.6850 (tm-30) cc_final: 0.6131 (tm-30) REVERT: W 19 LYS cc_start: 0.8858 (mtpm) cc_final: 0.8656 (mtmm) REVERT: W 23 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8740 (mttt) REVERT: X 33 ASN cc_start: 0.7569 (m110) cc_final: 0.6753 (t0) REVERT: X 57 GLU cc_start: 0.7041 (tp30) cc_final: 0.6789 (tp30) REVERT: Y 10 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7209 (mp0) REVERT: Y 36 ASP cc_start: 0.8175 (t0) cc_final: 0.7878 (t0) REVERT: Y 37 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8041 (mmtt) REVERT: Y 40 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7606 (mtpt) REVERT: Y 63 ASN cc_start: 0.8958 (t160) cc_final: 0.8646 (t0) REVERT: Y 86 THR cc_start: 0.8666 (m) cc_final: 0.8416 (p) REVERT: Y 158 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8421 (mmmt) REVERT: Z 22 GLN cc_start: 0.5882 (tm-30) cc_final: 0.5544 (mt0) REVERT: Z 77 HIS cc_start: 0.7546 (m-70) cc_final: 0.7163 (m-70) REVERT: Z 115 ARG cc_start: 0.8398 (ptp-110) cc_final: 0.7878 (ptp-110) REVERT: Z 136 LYS cc_start: 0.7462 (tptp) cc_final: 0.7102 (ttmm) REVERT: Z 169 THR cc_start: 0.7017 (m) cc_final: 0.6787 (p) REVERT: b 41 ILE cc_start: 0.9091 (tt) cc_final: 0.8887 (tt) REVERT: b 54 SER cc_start: 0.7889 (t) cc_final: 0.7507 (m) REVERT: d 52 GLU cc_start: 0.8590 (tp30) cc_final: 0.8037 (mp0) REVERT: d 102 LYS cc_start: 0.7652 (ttpm) cc_final: 0.6888 (tppt) REVERT: d 285 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8213 (mm-30) REVERT: d 308 THR cc_start: 0.8129 (m) cc_final: 0.7816 (p) REVERT: d 325 ARG cc_start: 0.6416 (ptt180) cc_final: 0.4734 (tmt-80) REVERT: f 91 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7604 (mtt90) REVERT: h 17 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7276 (mtt90) REVERT: h 63 MET cc_start: 0.8457 (mmm) cc_final: 0.7689 (ttt) REVERT: i 26 VAL cc_start: 0.8671 (p) cc_final: 0.8428 (t) REVERT: i 82 VAL cc_start: 0.9129 (t) cc_final: 0.8872 (m) REVERT: i 144 TYR cc_start: 0.5990 (p90) cc_final: 0.5377 (p90) REVERT: j 20 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7635 (mmmm) REVERT: j 23 ASP cc_start: 0.7156 (p0) cc_final: 0.6856 (t0) REVERT: j 37 MET cc_start: 0.7662 (mmt) cc_final: 0.6599 (tpt) REVERT: j 66 ASP cc_start: 0.6006 (p0) cc_final: 0.5561 (t0) REVERT: k 89 ASN cc_start: 0.6999 (t0) cc_final: 0.6606 (t0) REVERT: k 240 TYR cc_start: 0.7847 (m-80) cc_final: 0.7381 (m-10) REVERT: k 262 LEU cc_start: 0.7583 (tp) cc_final: 0.7355 (tp) REVERT: k 284 ILE cc_start: 0.8730 (mm) cc_final: 0.8455 (pt) REVERT: l 7 LYS cc_start: 0.8699 (tttm) cc_final: 0.8325 (mmtt) REVERT: l 37 LYS cc_start: 0.8578 (tmmm) cc_final: 0.8285 (tmtt) REVERT: m 15 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8201 (mm-30) REVERT: m 46 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7826 (ptp-170) REVERT: n 13 MET cc_start: 0.5066 (ttt) cc_final: 0.4702 (tmm) REVERT: n 67 LEU cc_start: 0.7901 (mt) cc_final: 0.7654 (tp) REVERT: o 16 ASP cc_start: 0.7495 (t70) cc_final: 0.7104 (t70) REVERT: o 60 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7672 (ttm170) REVERT: o 74 TYR cc_start: 0.8272 (m-80) cc_final: 0.7785 (m-80) REVERT: p 52 ASP cc_start: 0.8590 (t0) cc_final: 0.8224 (t0) REVERT: p 60 GLU cc_start: 0.7579 (pt0) cc_final: 0.7116 (tt0) REVERT: p 107 ASP cc_start: 0.8746 (t70) cc_final: 0.8256 (t0) REVERT: p 110 ARG cc_start: 0.6868 (tmm160) cc_final: 0.6441 (ttp-110) REVERT: q 20 TYR cc_start: 0.7965 (p90) cc_final: 0.7722 (p90) REVERT: q 34 MET cc_start: 0.7792 (mtm) cc_final: 0.7010 (mmm) REVERT: q 44 PHE cc_start: 0.8325 (t80) cc_final: 0.7982 (t80) REVERT: q 75 GLN cc_start: 0.8771 (tp40) cc_final: 0.8222 (tp-100) REVERT: q 79 ASP cc_start: 0.8375 (m-30) cc_final: 0.7754 (m-30) REVERT: q 92 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7341 (mp0) REVERT: r 24 ASP cc_start: 0.7336 (m-30) cc_final: 0.7125 (t0) REVERT: r 33 VAL cc_start: 0.8596 (t) cc_final: 0.8347 (p) REVERT: r 78 VAL cc_start: 0.8961 (t) cc_final: 0.8758 (p) REVERT: r 87 TYR cc_start: 0.7864 (m-80) cc_final: 0.7064 (m-80) REVERT: s 4 LEU cc_start: 0.6592 (mm) cc_final: 0.6251 (tp) REVERT: t 58 LYS cc_start: 0.6653 (tptp) cc_final: 0.6241 (ttmm) REVERT: t 89 SER cc_start: 0.8656 (t) cc_final: 0.8256 (t) REVERT: t 127 LEU cc_start: 0.8334 (tp) cc_final: 0.7915 (mt) REVERT: u 32 MET cc_start: 0.7832 (ttp) cc_final: 0.7407 (tmm) REVERT: v 7 ASP cc_start: 0.7420 (p0) cc_final: 0.7182 (p0) REVERT: v 91 THR cc_start: 0.8508 (p) cc_final: 0.8215 (p) REVERT: v 141 GLU cc_start: 0.6686 (mp0) cc_final: 0.6194 (mm-30) REVERT: v 154 VAL cc_start: 0.5244 (t) cc_final: 0.4961 (t) REVERT: v 157 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6303 (tt0) REVERT: w 41 ASN cc_start: 0.8016 (t0) cc_final: 0.7659 (t0) REVERT: w 54 ASP cc_start: 0.8598 (t70) cc_final: 0.8365 (t0) REVERT: w 56 TRP cc_start: 0.7519 (t60) cc_final: 0.6416 (m100) REVERT: x 3 TYR cc_start: 0.7568 (m-80) cc_final: 0.7149 (m-80) REVERT: y 33 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7964 (mtmm) REVERT: y 53 GLU cc_start: 0.6472 (pm20) cc_final: 0.5996 (pm20) REVERT: z 53 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7777 (mtt180) outliers start: 4 outliers final: 1 residues processed: 2146 average time/residue: 0.7160 time to fit residues: 2520.1318 Evaluate side-chains 1244 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1243 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 20.0000 chunk 607 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 chunk 207 optimal weight: 0.0010 chunk 410 optimal weight: 5.9990 chunk 324 optimal weight: 30.0000 chunk 628 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 467 optimal weight: 9.9990 chunk 728 optimal weight: 40.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 24 ASN 1 148 ASN 1 356 HIS 1 373 ASN ** 1 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 99 HIS ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 459 GLN 3 581 GLN 4 252 ASN 4 313 GLN 6 82 GLN J 86 ASN K 83 ASN K 92 ASN L 199 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 546 GLN M 44 GLN M 81 GLN M 168 GLN M 184 GLN M 434 ASN N 144 GLN N 232 HIS ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 GLN Y 64 GLN Y 105 GLN Y 162 HIS Z 55 HIS Z 58 ASN Z 90 GLN Z 130 GLN b 51 GLN c 46 GLN d 67 GLN d 87 HIS d 89 ASN d 184 ASN f 49 GLN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 47 HIS g 125 HIS i 69 ASN k 50 HIS ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 141 GLN k 180 GLN k 204 ASN k 294 GLN l 20 GLN m 70 GLN n 32 GLN o 12 GLN o 61 GLN p 32 GLN s 53 GLN ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 138 GLN u 21 GLN v 55 GLN v 87 ASN v 137 ASN y 13 HIS Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.285 69608 Z= 0.575 Angle : 1.584 50.986 94108 Z= 1.018 Chirality : 0.309 6.540 10190 Planarity : 0.005 0.064 11747 Dihedral : 12.865 179.458 10578 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 2.11 % Allowed : 9.38 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.09), residues: 8122 helix: -0.56 (0.07), residues: 4246 sheet: -1.50 (0.25), residues: 383 loop : -1.61 (0.10), residues: 3493 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 0.039 0.002 PHE N 292 TYR 0.035 0.002 TYR 9 118 ARG 0.009 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1324 time to evaluate : 5.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 425 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7778 (tp30) REVERT: 2 52 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: 3 19 MET cc_start: 0.8326 (mmm) cc_final: 0.7970 (mmm) REVERT: 3 121 MET cc_start: 0.8225 (mmm) cc_final: 0.7840 (mmm) REVERT: 3 248 MET cc_start: 0.8875 (mmm) cc_final: 0.8541 (mmt) REVERT: 3 287 GLU cc_start: 0.7758 (pm20) cc_final: 0.7479 (tt0) REVERT: 3 293 HIS cc_start: 0.8994 (m-70) cc_final: 0.8611 (m-70) REVERT: 3 297 GLU cc_start: 0.7854 (mp0) cc_final: 0.7515 (tt0) REVERT: 3 445 GLU cc_start: 0.7975 (pt0) cc_final: 0.7676 (mm-30) REVERT: 3 476 LYS cc_start: 0.8704 (tttm) cc_final: 0.7931 (mmtp) REVERT: 3 520 LYS cc_start: 0.8660 (pttt) cc_final: 0.8107 (mmtm) REVERT: 3 613 TYR cc_start: 0.7869 (p90) cc_final: 0.7394 (p90) REVERT: 3 641 TYR cc_start: 0.8051 (m-10) cc_final: 0.7684 (m-80) REVERT: 3 655 GLN cc_start: 0.7523 (mm-40) cc_final: 0.6317 (tt0) REVERT: 3 666 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7855 (mt) REVERT: 4 170 MET cc_start: 0.9233 (mmm) cc_final: 0.8851 (mmm) REVERT: 4 182 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8694 (tm-30) REVERT: 4 334 LYS cc_start: 0.8730 (mttm) cc_final: 0.8497 (mtmt) REVERT: 5 176 TYR cc_start: 0.8910 (t80) cc_final: 0.8670 (t80) REVERT: 6 25 ARG cc_start: 0.6248 (ttt180) cc_final: 0.5179 (tmm160) REVERT: 6 62 MET cc_start: 0.9008 (tmm) cc_final: 0.8682 (ttt) REVERT: 9 15 LYS cc_start: 0.7494 (tptp) cc_final: 0.6582 (mmtp) REVERT: 9 157 ASN cc_start: 0.8968 (m-40) cc_final: 0.8707 (m-40) REVERT: A 4 MET cc_start: 0.8575 (mtm) cc_final: 0.8076 (mpp) REVERT: A 28 ASN cc_start: 0.7312 (t0) cc_final: 0.6955 (t0) REVERT: A 101 SER cc_start: 0.8022 (t) cc_final: 0.7791 (p) REVERT: H 59 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: H 192 GLU cc_start: 0.8733 (tt0) cc_final: 0.8459 (tt0) REVERT: H 202 GLU cc_start: 0.8214 (tt0) cc_final: 0.7785 (tm-30) REVERT: J 2 MET cc_start: 0.8050 (tpt) cc_final: 0.7828 (tpt) REVERT: J 103 MET cc_start: 0.7032 (ptp) cc_final: 0.6143 (mmt) REVERT: J 106 TYR cc_start: 0.7521 (m-80) cc_final: 0.7266 (m-80) REVERT: J 167 VAL cc_start: 0.8800 (t) cc_final: 0.8419 (t) REVERT: L 52 MET cc_start: 0.7570 (mtm) cc_final: 0.7259 (mtt) REVERT: L 277 MET cc_start: 0.7336 (mtm) cc_final: 0.7112 (mtm) REVERT: L 478 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6962 (Cg_exo) REVERT: L 511 LEU cc_start: 0.7366 (mt) cc_final: 0.6929 (pt) REVERT: L 528 TYR cc_start: 0.7469 (m-10) cc_final: 0.7149 (m-80) REVERT: L 544 MET cc_start: 0.5932 (tmm) cc_final: 0.5151 (mmt) REVERT: M 43 ASN cc_start: 0.8956 (t0) cc_final: 0.8724 (t0) REVERT: M 114 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8063 (tt0) REVERT: M 144 ASN cc_start: 0.8474 (t0) cc_final: 0.8142 (t0) REVERT: M 186 MET cc_start: 0.8242 (ttm) cc_final: 0.7973 (ttp) REVERT: M 340 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.7885 (mtm-85) REVERT: M 378 GLU cc_start: 0.8445 (tp30) cc_final: 0.8159 (tt0) REVERT: N 11 MET cc_start: 0.7860 (mmp) cc_final: 0.7379 (mtp) REVERT: N 79 MET cc_start: 0.9026 (mtt) cc_final: 0.8747 (mtt) REVERT: N 220 MET cc_start: 0.8104 (mtm) cc_final: 0.7818 (mtp) REVERT: N 265 MET cc_start: 0.8737 (mmm) cc_final: 0.8510 (mmm) REVERT: N 298 TYR cc_start: 0.8202 (m-10) cc_final: 0.7850 (m-10) REVERT: W 19 LYS cc_start: 0.8884 (mtpm) cc_final: 0.8679 (mtmm) REVERT: W 107 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9071 (tt0) REVERT: X 33 ASN cc_start: 0.7555 (m110) cc_final: 0.6912 (t0) REVERT: X 75 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: Y 37 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7986 (mmtt) REVERT: Y 40 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7692 (mtmt) REVERT: Y 63 ASN cc_start: 0.8823 (t160) cc_final: 0.8556 (t0) REVERT: Y 86 THR cc_start: 0.8744 (m) cc_final: 0.8495 (p) REVERT: Y 158 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8457 (mmmt) REVERT: Z 22 GLN cc_start: 0.5931 (tm-30) cc_final: 0.5608 (mt0) REVERT: Z 136 LYS cc_start: 0.7535 (tptp) cc_final: 0.7102 (ttmm) REVERT: Z 169 THR cc_start: 0.7146 (m) cc_final: 0.6904 (p) REVERT: c 45 MET cc_start: 0.8792 (mmm) cc_final: 0.8544 (mmt) REVERT: d 52 GLU cc_start: 0.8432 (tp30) cc_final: 0.8020 (mp0) REVERT: d 102 LYS cc_start: 0.7534 (ttpm) cc_final: 0.6783 (tppt) REVERT: d 285 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8215 (mm-30) REVERT: d 308 THR cc_start: 0.8151 (m) cc_final: 0.7858 (p) REVERT: d 325 ARG cc_start: 0.6446 (ptt180) cc_final: 0.4699 (tmt-80) REVERT: f 91 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7617 (mtt90) REVERT: g 35 TYR cc_start: 0.8952 (t80) cc_final: 0.8649 (t80) REVERT: h 17 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7295 (mtt90) REVERT: h 63 MET cc_start: 0.8452 (mmm) cc_final: 0.7772 (ttt) REVERT: i 144 TYR cc_start: 0.5980 (p90) cc_final: 0.5375 (p90) REVERT: j 20 LYS cc_start: 0.7901 (ptpt) cc_final: 0.7690 (mmmm) REVERT: j 23 ASP cc_start: 0.7116 (p0) cc_final: 0.6793 (t0) REVERT: j 75 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7335 (mt-10) REVERT: k 12 GLU cc_start: 0.7815 (tt0) cc_final: 0.7067 (tp30) REVERT: k 89 ASN cc_start: 0.7035 (t0) cc_final: 0.6651 (t0) REVERT: k 240 TYR cc_start: 0.7724 (m-80) cc_final: 0.7331 (m-10) REVERT: k 242 LYS cc_start: 0.6797 (mptt) cc_final: 0.6438 (mppt) REVERT: k 284 ILE cc_start: 0.8802 (mm) cc_final: 0.8470 (pt) REVERT: l 37 LYS cc_start: 0.8536 (tmmm) cc_final: 0.8334 (tmtt) REVERT: l 64 GLU cc_start: 0.8474 (tp30) cc_final: 0.8010 (tp30) REVERT: l 88 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6485 (mt-10) REVERT: n 13 MET cc_start: 0.5061 (ttt) cc_final: 0.4776 (tmm) REVERT: n 67 LEU cc_start: 0.7890 (mt) cc_final: 0.7644 (tt) REVERT: o 16 ASP cc_start: 0.7589 (t70) cc_final: 0.7215 (t70) REVERT: o 74 TYR cc_start: 0.8384 (m-80) cc_final: 0.7908 (m-80) REVERT: p 60 GLU cc_start: 0.7724 (pt0) cc_final: 0.7342 (tt0) REVERT: p 107 ASP cc_start: 0.8733 (t70) cc_final: 0.8259 (t0) REVERT: p 110 ARG cc_start: 0.6833 (tmm160) cc_final: 0.6517 (ttm-80) REVERT: q 34 MET cc_start: 0.7746 (mtm) cc_final: 0.6946 (mmm) REVERT: q 75 GLN cc_start: 0.8671 (tp40) cc_final: 0.8133 (tp-100) REVERT: q 79 ASP cc_start: 0.8411 (m-30) cc_final: 0.7861 (m-30) REVERT: q 92 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7228 (mp0) REVERT: r 24 ASP cc_start: 0.7417 (m-30) cc_final: 0.7068 (t0) REVERT: r 87 TYR cc_start: 0.7830 (m-80) cc_final: 0.7531 (m-80) REVERT: s 38 MET cc_start: 0.7422 (tpt) cc_final: 0.6525 (tpt) REVERT: t 58 LYS cc_start: 0.6590 (tptp) cc_final: 0.6197 (ttmm) REVERT: t 89 SER cc_start: 0.8649 (t) cc_final: 0.8395 (t) REVERT: t 127 LEU cc_start: 0.8387 (tp) cc_final: 0.7929 (mt) REVERT: u 32 MET cc_start: 0.7891 (ttp) cc_final: 0.7437 (tmm) REVERT: v 7 ASP cc_start: 0.7543 (p0) cc_final: 0.7342 (p0) REVERT: v 46 ASP cc_start: 0.7279 (p0) cc_final: 0.7030 (p0) REVERT: v 91 THR cc_start: 0.8431 (p) cc_final: 0.8129 (p) REVERT: v 157 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6180 (tt0) REVERT: w 41 ASN cc_start: 0.7971 (t0) cc_final: 0.7626 (t0) REVERT: w 50 ASP cc_start: 0.8313 (t0) cc_final: 0.8043 (t0) REVERT: w 56 TRP cc_start: 0.7513 (t60) cc_final: 0.6426 (m100) REVERT: x 3 TYR cc_start: 0.7590 (m-80) cc_final: 0.7218 (m-80) REVERT: y 53 GLU cc_start: 0.6275 (pm20) cc_final: 0.6066 (pm20) outliers start: 152 outliers final: 81 residues processed: 1417 average time/residue: 0.6659 time to fit residues: 1615.9216 Evaluate side-chains 1249 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1164 time to evaluate : 5.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 32 ARG Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 666 LEU Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 191 ILE Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 75 GLU Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain r residue 81 ILE Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 606 optimal weight: 2.9990 chunk 495 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 729 optimal weight: 40.0000 chunk 788 optimal weight: 5.9990 chunk 649 optimal weight: 30.0000 chunk 723 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 585 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 24 ASN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 237 ASN ** 3 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN J 86 ASN K 83 ASN L 25 ASN L 27 HIS L 116 GLN L 248 HIS M 138 ASN M 169 ASN N 144 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Z 54 GLN Z 58 ASN Z 106 GLN b 36 ASN d 89 ASN d 180 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 91 HIS ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 200 GLN l 6 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 97 HIS s 53 GLN ** s 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 84 HIS ** t 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 GLN v 55 GLN v 87 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.282 69608 Z= 0.591 Angle : 1.585 51.051 94108 Z= 1.018 Chirality : 0.310 6.615 10190 Planarity : 0.005 0.055 11747 Dihedral : 12.462 172.965 10577 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.30 % Favored : 95.69 % Rotamer: Outliers : 2.75 % Allowed : 10.67 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.09), residues: 8122 helix: 0.09 (0.08), residues: 4255 sheet: -1.37 (0.25), residues: 388 loop : -1.30 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 106 HIS 0.023 0.001 HIS 9 65 PHE 0.038 0.002 PHE N 292 TYR 0.027 0.002 TYR 9 118 ARG 0.009 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1225 time to evaluate : 5.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: 3 19 MET cc_start: 0.8336 (mmm) cc_final: 0.7741 (mmm) REVERT: 3 74 MET cc_start: 0.8436 (mmt) cc_final: 0.7294 (mtp) REVERT: 3 121 MET cc_start: 0.8263 (mmm) cc_final: 0.7908 (mmm) REVERT: 3 171 ASP cc_start: 0.7817 (m-30) cc_final: 0.7421 (m-30) REVERT: 3 248 MET cc_start: 0.8792 (mmm) cc_final: 0.8456 (mmt) REVERT: 3 287 GLU cc_start: 0.7763 (pm20) cc_final: 0.7478 (tt0) REVERT: 3 293 HIS cc_start: 0.8969 (m-70) cc_final: 0.8728 (m-70) REVERT: 3 445 GLU cc_start: 0.7973 (pt0) cc_final: 0.7674 (mm-30) REVERT: 3 476 LYS cc_start: 0.8698 (tttm) cc_final: 0.7884 (mmtp) REVERT: 3 520 LYS cc_start: 0.8709 (pttt) cc_final: 0.8138 (mmtm) REVERT: 3 613 TYR cc_start: 0.7968 (p90) cc_final: 0.7552 (p90) REVERT: 3 641 TYR cc_start: 0.8073 (m-10) cc_final: 0.7672 (m-80) REVERT: 3 655 GLN cc_start: 0.7499 (mm-40) cc_final: 0.6263 (tt0) REVERT: 4 182 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8694 (tm-30) REVERT: 4 290 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8299 (mtp85) REVERT: 4 334 LYS cc_start: 0.8669 (mttm) cc_final: 0.8432 (mtmt) REVERT: 6 25 ARG cc_start: 0.6428 (ttt180) cc_final: 0.4966 (tmm160) REVERT: 6 62 MET cc_start: 0.9008 (tmm) cc_final: 0.8788 (ttt) REVERT: 9 15 LYS cc_start: 0.7558 (tptp) cc_final: 0.6588 (mmtp) REVERT: 9 157 ASN cc_start: 0.8952 (m-40) cc_final: 0.8693 (m-40) REVERT: A 4 MET cc_start: 0.8669 (mtm) cc_final: 0.8159 (mpp) REVERT: A 28 ASN cc_start: 0.7506 (t0) cc_final: 0.7241 (t0) REVERT: A 101 SER cc_start: 0.8095 (t) cc_final: 0.7881 (p) REVERT: H 202 GLU cc_start: 0.8493 (tt0) cc_final: 0.7994 (tm-30) REVERT: J 2 MET cc_start: 0.7894 (tpt) cc_final: 0.7571 (tpt) REVERT: J 103 MET cc_start: 0.7042 (ptp) cc_final: 0.6154 (mmt) REVERT: J 167 VAL cc_start: 0.8851 (t) cc_final: 0.8493 (t) REVERT: L 8 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8468 (m) REVERT: L 52 MET cc_start: 0.7616 (mtm) cc_final: 0.7252 (mtt) REVERT: L 277 MET cc_start: 0.7346 (mtm) cc_final: 0.7105 (mtm) REVERT: L 331 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8571 (p) REVERT: L 478 PRO cc_start: 0.7120 (Cg_endo) cc_final: 0.6817 (Cg_exo) REVERT: L 528 TYR cc_start: 0.7501 (m-10) cc_final: 0.7168 (m-80) REVERT: L 544 MET cc_start: 0.6001 (tmm) cc_final: 0.5230 (mmt) REVERT: M 43 ASN cc_start: 0.8995 (t0) cc_final: 0.8742 (t0) REVERT: M 114 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8097 (tt0) REVERT: M 123 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8183 (mm-30) REVERT: M 144 ASN cc_start: 0.8516 (t0) cc_final: 0.8245 (t0) REVERT: M 302 LEU cc_start: 0.9101 (mt) cc_final: 0.8870 (mt) REVERT: N 11 MET cc_start: 0.7957 (mmp) cc_final: 0.7425 (mtp) REVERT: N 176 ARG cc_start: 0.8466 (mtm180) cc_final: 0.8190 (mtm180) REVERT: N 190 MET cc_start: 0.9030 (mtt) cc_final: 0.8821 (mtp) REVERT: N 220 MET cc_start: 0.8155 (mtm) cc_final: 0.7844 (mtp) REVERT: N 298 TYR cc_start: 0.8275 (m-10) cc_final: 0.7899 (m-10) REVERT: V 78 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7515 (mm-40) REVERT: W 107 GLU cc_start: 0.9375 (tm-30) cc_final: 0.9101 (tt0) REVERT: X 33 ASN cc_start: 0.7631 (m110) cc_final: 0.6969 (t0) REVERT: Y 37 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7996 (mmtt) REVERT: Y 63 ASN cc_start: 0.8833 (t160) cc_final: 0.8614 (t0) REVERT: Y 86 THR cc_start: 0.8815 (m) cc_final: 0.8560 (p) REVERT: Y 158 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8368 (mttm) REVERT: Z 22 GLN cc_start: 0.5814 (tm-30) cc_final: 0.5466 (mt0) REVERT: Z 136 LYS cc_start: 0.7702 (tptp) cc_final: 0.7212 (ttmm) REVERT: Z 169 THR cc_start: 0.7243 (m) cc_final: 0.7001 (p) REVERT: c 28 GLU cc_start: 0.8522 (pt0) cc_final: 0.8276 (tt0) REVERT: d 52 GLU cc_start: 0.8320 (tp30) cc_final: 0.7937 (mp0) REVERT: d 102 LYS cc_start: 0.7537 (ttpm) cc_final: 0.6599 (tppp) REVERT: d 308 THR cc_start: 0.8171 (m) cc_final: 0.7875 (p) REVERT: f 91 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7788 (mtt90) REVERT: h 17 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7356 (mtt90) REVERT: h 63 MET cc_start: 0.8437 (mmm) cc_final: 0.7818 (ttt) REVERT: i 78 ASP cc_start: 0.8814 (t0) cc_final: 0.8438 (t70) REVERT: i 144 TYR cc_start: 0.6019 (p90) cc_final: 0.5311 (p90) REVERT: j 20 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7640 (mmmm) REVERT: j 23 ASP cc_start: 0.7085 (p0) cc_final: 0.6732 (t0) REVERT: j 57 GLU cc_start: 0.7777 (tt0) cc_final: 0.7277 (tt0) REVERT: j 71 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.4679 (ptp) REVERT: j 75 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7259 (mt-10) REVERT: k 12 GLU cc_start: 0.7887 (tt0) cc_final: 0.7135 (tp30) REVERT: k 89 ASN cc_start: 0.7077 (t0) cc_final: 0.6693 (t0) REVERT: k 240 TYR cc_start: 0.7779 (m-80) cc_final: 0.7393 (m-80) REVERT: l 64 GLU cc_start: 0.8601 (tp30) cc_final: 0.8057 (tp30) REVERT: n 67 LEU cc_start: 0.7915 (mt) cc_final: 0.7518 (tt) REVERT: n 70 PHE cc_start: 0.8258 (t80) cc_final: 0.7931 (t80) REVERT: o 16 ASP cc_start: 0.7470 (t70) cc_final: 0.7109 (t70) REVERT: p 60 GLU cc_start: 0.7676 (pt0) cc_final: 0.7344 (tt0) REVERT: p 107 ASP cc_start: 0.8825 (t70) cc_final: 0.8347 (t0) REVERT: p 110 ARG cc_start: 0.6792 (tmm160) cc_final: 0.6491 (ttm-80) REVERT: q 22 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8102 (ttm170) REVERT: q 34 MET cc_start: 0.7898 (mtm) cc_final: 0.7085 (mmm) REVERT: q 75 GLN cc_start: 0.8697 (tp40) cc_final: 0.8173 (tp-100) REVERT: q 79 ASP cc_start: 0.8390 (m-30) cc_final: 0.7935 (m-30) REVERT: q 130 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8316 (tm-30) REVERT: r 24 ASP cc_start: 0.7332 (m-30) cc_final: 0.7118 (t0) REVERT: s 4 LEU cc_start: 0.6836 (mm) cc_final: 0.6511 (tt) REVERT: s 34 LYS cc_start: 0.7533 (ptpt) cc_final: 0.6499 (tptp) REVERT: s 38 MET cc_start: 0.7449 (tpt) cc_final: 0.6679 (tpt) REVERT: s 83 GLN cc_start: 0.8502 (tt0) cc_final: 0.7890 (tt0) REVERT: t 58 LYS cc_start: 0.6702 (tptp) cc_final: 0.6284 (ttmm) REVERT: t 65 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: t 69 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: t 89 SER cc_start: 0.8690 (t) cc_final: 0.8475 (t) REVERT: t 161 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6710 (t0) REVERT: v 8 MET cc_start: 0.8973 (mmm) cc_final: 0.8632 (mmp) REVERT: v 91 THR cc_start: 0.8457 (p) cc_final: 0.8164 (p) REVERT: v 136 ASN cc_start: 0.7175 (m-40) cc_final: 0.6732 (t0) REVERT: v 148 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7410 (mmtm) REVERT: v 157 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6229 (tt0) REVERT: w 41 ASN cc_start: 0.7961 (t0) cc_final: 0.7567 (t0) REVERT: w 50 ASP cc_start: 0.8238 (t0) cc_final: 0.7980 (t0) REVERT: w 56 TRP cc_start: 0.7480 (t60) cc_final: 0.6392 (m100) REVERT: x 3 TYR cc_start: 0.7627 (m-80) cc_final: 0.7349 (m-80) REVERT: y 53 GLU cc_start: 0.6202 (pm20) cc_final: 0.5979 (pm20) outliers start: 198 outliers final: 120 residues processed: 1346 average time/residue: 0.6448 time to fit residues: 1487.7327 Evaluate side-chains 1266 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1139 time to evaluate : 5.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 3 residue 281 GLU Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 88 SER Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 71 MET Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 99 ASN Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 20.0000 chunk 548 optimal weight: 7.9990 chunk 378 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 489 optimal weight: 20.0000 chunk 732 optimal weight: 20.0000 chunk 775 optimal weight: 0.8980 chunk 382 optimal weight: 7.9990 chunk 693 optimal weight: 40.0000 chunk 208 optimal weight: 10.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 398 GLN 1 402 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 110 GLN 3 437 HIS 5 87 GLN J 86 ASN L 194 ASN L 580 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Z 106 GLN d 89 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 GLN j 47 GLN l 6 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 87 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.278 69608 Z= 0.586 Angle : 1.578 51.089 94108 Z= 1.016 Chirality : 0.309 6.586 10190 Planarity : 0.004 0.054 11747 Dihedral : 12.254 168.341 10577 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.36 % Favored : 95.63 % Rotamer: Outliers : 3.17 % Allowed : 11.85 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 8122 helix: 0.37 (0.08), residues: 4274 sheet: -1.21 (0.25), residues: 374 loop : -1.15 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 106 HIS 0.017 0.001 HIS 9 65 PHE 0.036 0.002 PHE N 292 TYR 0.026 0.002 TYR 9 118 ARG 0.007 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1190 time to evaluate : 5.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: 3 19 MET cc_start: 0.8329 (mmm) cc_final: 0.7728 (mmm) REVERT: 3 74 MET cc_start: 0.8447 (mmt) cc_final: 0.7294 (mtp) REVERT: 3 121 MET cc_start: 0.8213 (mmm) cc_final: 0.7855 (mmm) REVERT: 3 248 MET cc_start: 0.8748 (mmm) cc_final: 0.8374 (mmt) REVERT: 3 287 GLU cc_start: 0.7782 (pm20) cc_final: 0.7398 (tt0) REVERT: 3 293 HIS cc_start: 0.8957 (m-70) cc_final: 0.8581 (m-70) REVERT: 3 445 GLU cc_start: 0.7995 (pt0) cc_final: 0.7710 (mm-30) REVERT: 3 476 LYS cc_start: 0.8696 (tttm) cc_final: 0.7854 (mmtp) REVERT: 3 520 LYS cc_start: 0.8596 (pttt) cc_final: 0.8084 (mmtm) REVERT: 3 613 TYR cc_start: 0.8067 (p90) cc_final: 0.7395 (p90) REVERT: 3 634 ASP cc_start: 0.7323 (t0) cc_final: 0.7117 (t0) REVERT: 3 641 TYR cc_start: 0.8071 (m-80) cc_final: 0.7689 (m-80) REVERT: 3 655 GLN cc_start: 0.7521 (mm-40) cc_final: 0.6280 (tt0) REVERT: 3 689 LYS cc_start: 0.8626 (tttm) cc_final: 0.8385 (tptt) REVERT: 4 182 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8716 (tm-30) REVERT: 4 290 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8306 (mtp85) REVERT: 6 25 ARG cc_start: 0.6277 (ttt180) cc_final: 0.4741 (tmm160) REVERT: 6 178 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7926 (mtt90) REVERT: 9 15 LYS cc_start: 0.7674 (tptp) cc_final: 0.6610 (mmtp) REVERT: 9 115 LYS cc_start: 0.9013 (mttt) cc_final: 0.8637 (mttt) REVERT: 9 157 ASN cc_start: 0.8962 (m-40) cc_final: 0.8708 (m-40) REVERT: A 4 MET cc_start: 0.8655 (mtm) cc_final: 0.8146 (mpp) REVERT: A 77 TRP cc_start: 0.8925 (m-10) cc_final: 0.8629 (m-10) REVERT: H 202 GLU cc_start: 0.8547 (tt0) cc_final: 0.8045 (tm-30) REVERT: H 206 GLU cc_start: 0.8319 (mp0) cc_final: 0.7802 (mp0) REVERT: J 2 MET cc_start: 0.7925 (tpt) cc_final: 0.7637 (tpt) REVERT: J 86 ASN cc_start: 0.7665 (t0) cc_final: 0.7172 (t0) REVERT: J 103 MET cc_start: 0.7022 (ptp) cc_final: 0.6101 (mmt) REVERT: J 167 VAL cc_start: 0.8896 (t) cc_final: 0.8559 (t) REVERT: L 8 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8453 (m) REVERT: L 17 MET cc_start: 0.7301 (mtm) cc_final: 0.7065 (mtm) REVERT: L 52 MET cc_start: 0.7548 (mtm) cc_final: 0.7206 (mtt) REVERT: L 140 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8981 (tt) REVERT: L 246 LEU cc_start: 0.9023 (tp) cc_final: 0.8805 (tp) REVERT: L 277 MET cc_start: 0.7225 (mtm) cc_final: 0.7024 (mtm) REVERT: L 353 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7470 (tm-30) REVERT: L 488 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6251 (mmt) REVERT: L 528 TYR cc_start: 0.7502 (m-10) cc_final: 0.7130 (m-80) REVERT: L 544 MET cc_start: 0.6023 (tmm) cc_final: 0.5314 (mmt) REVERT: L 558 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7801 (mm) REVERT: M 43 ASN cc_start: 0.8992 (t0) cc_final: 0.8722 (t0) REVERT: M 114 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8215 (mt-10) REVERT: N 11 MET cc_start: 0.7916 (mmp) cc_final: 0.7383 (mtt) REVERT: N 208 TYR cc_start: 0.9062 (t80) cc_final: 0.8848 (t80) REVERT: N 220 MET cc_start: 0.8194 (mtm) cc_final: 0.7900 (mtp) REVERT: N 298 TYR cc_start: 0.8250 (m-10) cc_final: 0.7793 (m-10) REVERT: V 78 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7522 (mm-40) REVERT: W 97 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8019 (mm-30) REVERT: X 33 ASN cc_start: 0.7697 (m110) cc_final: 0.7000 (t0) REVERT: Y 37 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7958 (mmtt) REVERT: Y 63 ASN cc_start: 0.8882 (t160) cc_final: 0.8651 (t0) REVERT: Y 86 THR cc_start: 0.8798 (m) cc_final: 0.8543 (p) REVERT: Y 158 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8345 (mttm) REVERT: Z 136 LYS cc_start: 0.7692 (tptp) cc_final: 0.7190 (ttmm) REVERT: Z 169 THR cc_start: 0.7148 (m) cc_final: 0.6920 (p) REVERT: c 28 GLU cc_start: 0.8557 (pt0) cc_final: 0.8347 (tt0) REVERT: d 52 GLU cc_start: 0.8250 (tp30) cc_final: 0.7962 (mp0) REVERT: d 102 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6683 (tppt) REVERT: d 177 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7636 (tpp-160) REVERT: d 308 THR cc_start: 0.8183 (m) cc_final: 0.7868 (p) REVERT: f 91 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7644 (mtt90) REVERT: h 17 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7351 (mtt90) REVERT: i 78 ASP cc_start: 0.8780 (t0) cc_final: 0.8348 (t70) REVERT: i 144 TYR cc_start: 0.6053 (p90) cc_final: 0.5335 (p90) REVERT: j 20 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7656 (mmmm) REVERT: j 23 ASP cc_start: 0.7082 (p0) cc_final: 0.6817 (t0) REVERT: j 57 GLU cc_start: 0.7774 (tt0) cc_final: 0.7362 (tt0) REVERT: k 12 GLU cc_start: 0.7898 (tt0) cc_final: 0.7206 (tp30) REVERT: k 89 ASN cc_start: 0.7101 (t0) cc_final: 0.6726 (t0) REVERT: k 240 TYR cc_start: 0.7742 (m-80) cc_final: 0.7307 (m-80) REVERT: l 64 GLU cc_start: 0.8697 (tp30) cc_final: 0.8219 (tp30) REVERT: l 69 GLN cc_start: 0.8664 (mt0) cc_final: 0.8310 (mm-40) REVERT: l 83 ASP cc_start: 0.8390 (t0) cc_final: 0.8140 (t0) REVERT: l 88 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6244 (mm-30) REVERT: n 13 MET cc_start: 0.5528 (tmm) cc_final: 0.5264 (tmm) REVERT: n 67 LEU cc_start: 0.7953 (mt) cc_final: 0.7536 (tt) REVERT: n 70 PHE cc_start: 0.8298 (t80) cc_final: 0.7846 (t80) REVERT: o 16 ASP cc_start: 0.7430 (t70) cc_final: 0.7106 (t70) REVERT: p 60 GLU cc_start: 0.7755 (pt0) cc_final: 0.7462 (tt0) REVERT: p 107 ASP cc_start: 0.8898 (t70) cc_final: 0.8451 (t0) REVERT: p 110 ARG cc_start: 0.6941 (tmm160) cc_final: 0.6536 (ttm-80) REVERT: q 34 MET cc_start: 0.7922 (mtm) cc_final: 0.7067 (mmm) REVERT: q 71 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8569 (ttp) REVERT: q 75 GLN cc_start: 0.8578 (tp40) cc_final: 0.8071 (tp-100) REVERT: q 79 ASP cc_start: 0.8372 (m-30) cc_final: 0.7777 (m-30) REVERT: q 130 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8152 (tm-30) REVERT: r 24 ASP cc_start: 0.7423 (m-30) cc_final: 0.7135 (t0) REVERT: r 87 TYR cc_start: 0.7986 (m-80) cc_final: 0.7228 (m-80) REVERT: s 4 LEU cc_start: 0.6930 (mm) cc_final: 0.6421 (tp) REVERT: s 34 LYS cc_start: 0.7533 (ptpt) cc_final: 0.6486 (tptp) REVERT: s 38 MET cc_start: 0.7418 (tpt) cc_final: 0.6713 (tpt) REVERT: t 58 LYS cc_start: 0.6734 (tptp) cc_final: 0.6320 (ttmm) REVERT: t 65 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: t 69 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: t 89 SER cc_start: 0.8737 (t) cc_final: 0.8516 (t) REVERT: v 7 ASP cc_start: 0.7396 (p0) cc_final: 0.7062 (p0) REVERT: v 8 MET cc_start: 0.8859 (mmm) cc_final: 0.8641 (mmm) REVERT: v 91 THR cc_start: 0.8462 (p) cc_final: 0.8183 (p) REVERT: v 136 ASN cc_start: 0.7131 (m-40) cc_final: 0.6688 (t0) REVERT: v 148 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7497 (mmtm) REVERT: v 157 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6161 (tt0) REVERT: w 41 ASN cc_start: 0.7991 (t0) cc_final: 0.7578 (t0) REVERT: w 56 TRP cc_start: 0.7234 (t60) cc_final: 0.6647 (t-100) REVERT: w 70 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8192 (mp) REVERT: x 3 TYR cc_start: 0.7610 (m-80) cc_final: 0.7346 (m-80) REVERT: x 6 GLU cc_start: 0.8457 (tp30) cc_final: 0.8218 (tp30) REVERT: y 8 ARG cc_start: 0.4339 (tpm170) cc_final: 0.3774 (tpp80) outliers start: 228 outliers final: 153 residues processed: 1328 average time/residue: 0.6422 time to fit residues: 1464.7614 Evaluate side-chains 1285 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1121 time to evaluate : 5.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 431 GLN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 82 GLN Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain L residue 488 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 88 SER Chi-restraints excluded: chain d residue 89 ASN Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 177 ARG Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 4 ASP Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain m residue 73 GLN Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 71 MET Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 113 THR Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 50 HIS Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 9.9990 chunk 440 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 577 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 661 optimal weight: 10.0000 chunk 535 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 395 optimal weight: 10.0000 chunk 695 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 436 GLN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 150 ASN ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 43 HIS 3 308 GLN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 471 ASN M 333 ASN N 235 ASN W 143 ASN X 33 ASN Y 64 GLN ** Z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 87 HIS d 89 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 294 GLN l 20 GLN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN ** q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 GLN s 54 GLN ** t 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 52 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.278 69608 Z= 0.638 Angle : 1.603 51.142 94108 Z= 1.026 Chirality : 0.310 6.610 10190 Planarity : 0.005 0.059 11747 Dihedral : 12.293 168.674 10577 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.10 % Favored : 94.89 % Rotamer: Outliers : 3.60 % Allowed : 12.48 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 8122 helix: 0.35 (0.08), residues: 4278 sheet: -1.21 (0.26), residues: 367 loop : -1.12 (0.10), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 106 HIS 0.016 0.002 HIS 9 65 PHE 0.037 0.002 PHE N 292 TYR 0.034 0.002 TYR J 60 ARG 0.008 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1159 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: 3 74 MET cc_start: 0.8532 (mmt) cc_final: 0.7351 (mtp) REVERT: 3 181 MET cc_start: 0.8556 (ttp) cc_final: 0.8061 (ttp) REVERT: 3 248 MET cc_start: 0.8753 (mmm) cc_final: 0.8405 (mmt) REVERT: 3 254 MET cc_start: 0.9067 (ttp) cc_final: 0.8797 (ttp) REVERT: 3 287 GLU cc_start: 0.7986 (pm20) cc_final: 0.7576 (tt0) REVERT: 3 293 HIS cc_start: 0.8988 (m-70) cc_final: 0.8566 (m-70) REVERT: 3 445 GLU cc_start: 0.8027 (pt0) cc_final: 0.7699 (mm-30) REVERT: 3 476 LYS cc_start: 0.8689 (tttm) cc_final: 0.7874 (mmtp) REVERT: 3 613 TYR cc_start: 0.8149 (p90) cc_final: 0.7412 (p90) REVERT: 3 634 ASP cc_start: 0.7529 (t0) cc_final: 0.7294 (t0) REVERT: 3 641 TYR cc_start: 0.8056 (m-80) cc_final: 0.7737 (m-80) REVERT: 3 655 GLN cc_start: 0.7547 (mm-40) cc_final: 0.6295 (tt0) REVERT: 3 689 LYS cc_start: 0.8639 (tttm) cc_final: 0.8409 (tptt) REVERT: 4 182 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8969 (tm-30) REVERT: 6 25 ARG cc_start: 0.6430 (ttt180) cc_final: 0.4403 (ttp-110) REVERT: 6 178 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7902 (mtt90) REVERT: 9 14 MET cc_start: 0.7453 (mmm) cc_final: 0.7106 (tmm) REVERT: 9 15 LYS cc_start: 0.7784 (tptp) cc_final: 0.6678 (mmtp) REVERT: 9 157 ASN cc_start: 0.8921 (m-40) cc_final: 0.8610 (m-40) REVERT: A 4 MET cc_start: 0.8469 (mtm) cc_final: 0.8049 (mpp) REVERT: A 98 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8312 (tp) REVERT: H 43 TYR cc_start: 0.8522 (m-80) cc_final: 0.8276 (m-80) REVERT: H 206 GLU cc_start: 0.8592 (mp0) cc_final: 0.8200 (mp0) REVERT: J 2 MET cc_start: 0.7884 (tpt) cc_final: 0.7624 (tpt) REVERT: J 103 MET cc_start: 0.7218 (ptp) cc_final: 0.6390 (mmt) REVERT: J 167 VAL cc_start: 0.8948 (t) cc_final: 0.8581 (t) REVERT: K 25 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6771 (t-170) REVERT: L 8 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8481 (m) REVERT: L 52 MET cc_start: 0.7572 (mtm) cc_final: 0.7162 (mtt) REVERT: L 140 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8991 (tt) REVERT: L 246 LEU cc_start: 0.9100 (tp) cc_final: 0.8864 (tp) REVERT: L 277 MET cc_start: 0.7244 (mtm) cc_final: 0.7012 (mtm) REVERT: L 331 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8667 (p) REVERT: L 528 TYR cc_start: 0.7603 (m-10) cc_final: 0.7190 (m-80) REVERT: L 544 MET cc_start: 0.6098 (tmm) cc_final: 0.5373 (mmt) REVERT: L 558 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7906 (mm) REVERT: M 19 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8098 (mmtm) REVERT: M 43 ASN cc_start: 0.8951 (t0) cc_final: 0.8652 (t0) REVERT: M 98 MET cc_start: 0.8724 (mmm) cc_final: 0.8491 (mmm) REVERT: M 114 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8187 (mt-10) REVERT: N 11 MET cc_start: 0.7959 (mmp) cc_final: 0.7423 (mtp) REVERT: N 176 ARG cc_start: 0.8466 (mtm180) cc_final: 0.8148 (mtm180) REVERT: N 220 MET cc_start: 0.8205 (mtm) cc_final: 0.7907 (mtp) REVERT: N 298 TYR cc_start: 0.8322 (m-10) cc_final: 0.7889 (m-10) REVERT: V 78 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7527 (mm-40) REVERT: X 33 ASN cc_start: 0.7492 (m-40) cc_final: 0.7096 (t0) REVERT: Y 3 ILE cc_start: 0.8050 (mm) cc_final: 0.7658 (tt) REVERT: Y 37 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7855 (mmtt) REVERT: Y 63 ASN cc_start: 0.8879 (t160) cc_final: 0.8627 (t0) REVERT: Y 77 CYS cc_start: 0.8872 (m) cc_final: 0.8667 (m) REVERT: Y 86 THR cc_start: 0.8883 (m) cc_final: 0.8626 (p) REVERT: Y 158 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8417 (mmmt) REVERT: Z 169 THR cc_start: 0.7186 (m) cc_final: 0.6940 (p) REVERT: c 45 MET cc_start: 0.8687 (mmm) cc_final: 0.8443 (mmm) REVERT: d 52 GLU cc_start: 0.8279 (tp30) cc_final: 0.7974 (mp0) REVERT: d 102 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6724 (tppt) REVERT: d 177 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7780 (mtp180) REVERT: d 254 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7750 (pt) REVERT: d 308 THR cc_start: 0.8137 (m) cc_final: 0.7807 (p) REVERT: f 91 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7655 (mtt90) REVERT: h 63 MET cc_start: 0.8452 (mmm) cc_final: 0.7816 (ptm) REVERT: h 111 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: i 78 ASP cc_start: 0.8827 (t0) cc_final: 0.8398 (t70) REVERT: j 20 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7613 (mmmm) REVERT: j 23 ASP cc_start: 0.7242 (p0) cc_final: 0.6999 (t0) REVERT: k 12 GLU cc_start: 0.7895 (tt0) cc_final: 0.7239 (tp30) REVERT: k 18 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6459 (mmm) REVERT: k 89 ASN cc_start: 0.7335 (t0) cc_final: 0.6982 (t0) REVERT: k 240 TYR cc_start: 0.7784 (m-80) cc_final: 0.7378 (m-80) REVERT: k 284 ILE cc_start: 0.8696 (mm) cc_final: 0.8298 (pt) REVERT: l 64 GLU cc_start: 0.8770 (tp30) cc_final: 0.8425 (tp30) REVERT: l 69 GLN cc_start: 0.8641 (mt0) cc_final: 0.8264 (mm-40) REVERT: m 71 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: n 13 MET cc_start: 0.5327 (tmm) cc_final: 0.4949 (tmm) REVERT: n 67 LEU cc_start: 0.7921 (mt) cc_final: 0.7546 (tt) REVERT: n 70 PHE cc_start: 0.8306 (t80) cc_final: 0.7945 (t80) REVERT: p 60 GLU cc_start: 0.7736 (pt0) cc_final: 0.7379 (tt0) REVERT: p 107 ASP cc_start: 0.8921 (t70) cc_final: 0.8516 (t0) REVERT: p 110 ARG cc_start: 0.6868 (tmm160) cc_final: 0.6551 (ttm-80) REVERT: q 34 MET cc_start: 0.7999 (mtm) cc_final: 0.7156 (mmm) REVERT: q 75 GLN cc_start: 0.8642 (tp40) cc_final: 0.8090 (tp40) REVERT: q 79 ASP cc_start: 0.8436 (m-30) cc_final: 0.7975 (m-30) REVERT: q 130 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8406 (tm-30) REVERT: r 87 TYR cc_start: 0.8091 (m-80) cc_final: 0.7415 (m-80) REVERT: s 34 LYS cc_start: 0.7352 (ptpt) cc_final: 0.6380 (tptp) REVERT: s 38 MET cc_start: 0.7441 (tpt) cc_final: 0.6660 (tpt) REVERT: s 62 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (mt) REVERT: t 58 LYS cc_start: 0.6535 (tptp) cc_final: 0.6219 (ttmm) REVERT: t 65 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: t 69 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: v 91 THR cc_start: 0.8522 (p) cc_final: 0.8260 (p) REVERT: v 136 ASN cc_start: 0.7624 (m-40) cc_final: 0.6585 (t0) REVERT: v 148 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7503 (mmtm) REVERT: w 41 ASN cc_start: 0.7996 (t0) cc_final: 0.7578 (t0) REVERT: w 56 TRP cc_start: 0.7071 (t60) cc_final: 0.6760 (t-100) REVERT: w 70 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8273 (mp) REVERT: x 3 TYR cc_start: 0.7558 (m-80) cc_final: 0.7326 (m-80) outliers start: 259 outliers final: 178 residues processed: 1331 average time/residue: 0.6670 time to fit residues: 1532.4100 Evaluate side-chains 1293 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1098 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 431 GLN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 373 GLU Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 11 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain L residue 431 LEU Chi-restraints excluded: chain L residue 492 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 89 MET Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 112 LYS Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 177 ARG Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 108 ASP Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain k residue 135 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 4 ASP Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain m residue 71 ASP Chi-restraints excluded: chain m residue 73 GLN Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain p residue 27 GLU Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain u residue 50 HIS Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 43 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 3.9990 chunk 698 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 455 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 775 optimal weight: 30.0000 chunk 644 optimal weight: 30.0000 chunk 359 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 407 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 214 GLN 3 517 ASN L 194 ASN ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 235 ASN d 87 HIS d 180 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 50 HIS m 51 ASN m 61 ASN q 53 ASN ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 GLN t 32 HIS t 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.273 69608 Z= 0.560 Angle : 1.570 51.031 94108 Z= 1.012 Chirality : 0.309 6.544 10190 Planarity : 0.004 0.058 11747 Dihedral : 11.958 167.913 10577 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.10 % Favored : 95.89 % Rotamer: Outliers : 3.07 % Allowed : 13.78 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 8122 helix: 0.60 (0.08), residues: 4260 sheet: -1.06 (0.26), residues: 361 loop : -0.95 (0.11), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 106 HIS 0.015 0.001 HIS 9 65 PHE 0.036 0.002 PHE N 292 TYR 0.024 0.002 TYR d 244 ARG 0.005 0.000 ARG M 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1196 time to evaluate : 5.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: 3 74 MET cc_start: 0.8512 (mmt) cc_final: 0.7307 (mtp) REVERT: 3 181 MET cc_start: 0.8517 (ttp) cc_final: 0.8077 (ttp) REVERT: 3 248 MET cc_start: 0.8705 (mmm) cc_final: 0.8341 (mmt) REVERT: 3 254 MET cc_start: 0.9020 (ttp) cc_final: 0.8792 (ttp) REVERT: 3 287 GLU cc_start: 0.7953 (pm20) cc_final: 0.7543 (tt0) REVERT: 3 293 HIS cc_start: 0.8931 (m-70) cc_final: 0.8640 (m-70) REVERT: 3 445 GLU cc_start: 0.8003 (pt0) cc_final: 0.7705 (mm-30) REVERT: 3 476 LYS cc_start: 0.8669 (tttm) cc_final: 0.7874 (mmtp) REVERT: 3 613 TYR cc_start: 0.8125 (p90) cc_final: 0.7343 (p90) REVERT: 3 634 ASP cc_start: 0.7497 (t0) cc_final: 0.7252 (t0) REVERT: 3 641 TYR cc_start: 0.8026 (m-80) cc_final: 0.7824 (m-80) REVERT: 3 655 GLN cc_start: 0.7498 (mm-40) cc_final: 0.6231 (tt0) REVERT: 3 689 LYS cc_start: 0.8612 (tttm) cc_final: 0.8396 (tptt) REVERT: 4 182 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8725 (tm-30) REVERT: 4 290 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8298 (mtp85) REVERT: 6 25 ARG cc_start: 0.6392 (ttt180) cc_final: 0.4535 (tmm160) REVERT: 6 178 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7858 (mtt90) REVERT: 9 15 LYS cc_start: 0.7745 (tptp) cc_final: 0.6642 (mmtp) REVERT: 9 65 HIS cc_start: 0.7659 (m-70) cc_final: 0.7371 (m-70) REVERT: 9 143 THR cc_start: 0.8879 (m) cc_final: 0.8547 (p) REVERT: 9 157 ASN cc_start: 0.8945 (m-40) cc_final: 0.8642 (m-40) REVERT: A 4 MET cc_start: 0.8489 (mtm) cc_final: 0.8130 (mpp) REVERT: A 98 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8301 (tp) REVERT: H 93 TYR cc_start: 0.8476 (m-80) cc_final: 0.7653 (m-80) REVERT: H 206 GLU cc_start: 0.8581 (mp0) cc_final: 0.8174 (mp0) REVERT: J 2 MET cc_start: 0.7776 (tpt) cc_final: 0.7524 (tpt) REVERT: J 103 MET cc_start: 0.7095 (ptp) cc_final: 0.6179 (mmt) REVERT: J 167 VAL cc_start: 0.8957 (t) cc_final: 0.8627 (t) REVERT: J 170 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8466 (mm-30) REVERT: L 8 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8501 (m) REVERT: L 52 MET cc_start: 0.7537 (mtm) cc_final: 0.7099 (mtt) REVERT: L 140 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8977 (tt) REVERT: L 277 MET cc_start: 0.7237 (mtm) cc_final: 0.7018 (mtm) REVERT: L 331 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8610 (p) REVERT: L 528 TYR cc_start: 0.7543 (m-10) cc_final: 0.7117 (m-80) REVERT: L 544 MET cc_start: 0.5966 (tmm) cc_final: 0.5243 (mmt) REVERT: M 43 ASN cc_start: 0.8921 (t0) cc_final: 0.8620 (t0) REVERT: M 59 ASP cc_start: 0.8046 (p0) cc_final: 0.7808 (p0) REVERT: M 114 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8177 (mt-10) REVERT: N 11 MET cc_start: 0.7950 (mmp) cc_final: 0.7417 (mtt) REVERT: N 220 MET cc_start: 0.8168 (mtm) cc_final: 0.7727 (mtp) REVERT: N 298 TYR cc_start: 0.8198 (m-10) cc_final: 0.7739 (m-10) REVERT: V 6 HIS cc_start: 0.6790 (m90) cc_final: 0.6571 (m-70) REVERT: V 78 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7501 (mm-40) REVERT: W 40 ILE cc_start: 0.8371 (mm) cc_final: 0.8105 (mp) REVERT: W 97 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7522 (tp30) REVERT: X 33 ASN cc_start: 0.7653 (m-40) cc_final: 0.7206 (t0) REVERT: Y 3 ILE cc_start: 0.8119 (mm) cc_final: 0.7691 (tt) REVERT: Y 37 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7859 (mmtt) REVERT: Y 63 ASN cc_start: 0.8918 (t160) cc_final: 0.8658 (t0) REVERT: Y 86 THR cc_start: 0.8857 (m) cc_final: 0.8611 (p) REVERT: Y 158 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8299 (mttm) REVERT: Z 169 THR cc_start: 0.7059 (m) cc_final: 0.6847 (p) REVERT: c 45 MET cc_start: 0.8724 (mmm) cc_final: 0.8492 (mmt) REVERT: d 52 GLU cc_start: 0.8238 (tp30) cc_final: 0.7980 (mp0) REVERT: d 102 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6590 (tppp) REVERT: d 308 THR cc_start: 0.8128 (m) cc_final: 0.7733 (p) REVERT: f 91 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7600 (mtt90) REVERT: f 93 MET cc_start: 0.7181 (tpp) cc_final: 0.6949 (mpp) REVERT: h 17 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7271 (mtt90) REVERT: h 63 MET cc_start: 0.8429 (mmm) cc_final: 0.7828 (ptm) REVERT: h 111 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: i 78 ASP cc_start: 0.8758 (t0) cc_final: 0.8334 (t70) REVERT: j 20 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7666 (mmmm) REVERT: k 12 GLU cc_start: 0.7917 (tt0) cc_final: 0.7245 (tp30) REVERT: k 18 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6531 (mmm) REVERT: k 89 ASN cc_start: 0.7326 (t0) cc_final: 0.6974 (t0) REVERT: k 240 TYR cc_start: 0.7717 (m-80) cc_final: 0.7270 (m-80) REVERT: k 284 ILE cc_start: 0.8551 (mm) cc_final: 0.8155 (pt) REVERT: l 64 GLU cc_start: 0.8736 (tp30) cc_final: 0.8314 (tp30) REVERT: l 69 GLN cc_start: 0.8638 (mt0) cc_final: 0.8199 (mm-40) REVERT: l 83 ASP cc_start: 0.8374 (t0) cc_final: 0.8116 (t0) REVERT: l 87 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7582 (mmmt) REVERT: m 71 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: n 13 MET cc_start: 0.5358 (tmm) cc_final: 0.5008 (tmm) REVERT: n 67 LEU cc_start: 0.7886 (mt) cc_final: 0.7525 (tt) REVERT: n 70 PHE cc_start: 0.8248 (t80) cc_final: 0.7901 (t80) REVERT: o 16 ASP cc_start: 0.7512 (t70) cc_final: 0.7209 (t70) REVERT: p 60 GLU cc_start: 0.7580 (pt0) cc_final: 0.7278 (tt0) REVERT: p 107 ASP cc_start: 0.8936 (t70) cc_final: 0.8565 (t0) REVERT: p 110 ARG cc_start: 0.6921 (tmm160) cc_final: 0.6527 (ttm-80) REVERT: q 34 MET cc_start: 0.8029 (mtm) cc_final: 0.7141 (mmm) REVERT: q 75 GLN cc_start: 0.8529 (tp40) cc_final: 0.8072 (tp-100) REVERT: q 79 ASP cc_start: 0.8344 (m-30) cc_final: 0.7694 (m-30) REVERT: q 130 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8140 (tm-30) REVERT: r 87 TYR cc_start: 0.8100 (m-80) cc_final: 0.7503 (m-80) REVERT: s 38 MET cc_start: 0.7331 (tpt) cc_final: 0.6676 (tpt) REVERT: s 62 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7815 (mt) REVERT: t 58 LYS cc_start: 0.6522 (tptp) cc_final: 0.6136 (ttmm) REVERT: t 65 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: t 69 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: v 91 THR cc_start: 0.8507 (p) cc_final: 0.8242 (p) REVERT: v 136 ASN cc_start: 0.7579 (m-40) cc_final: 0.6535 (t0) REVERT: v 148 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7470 (mmtm) REVERT: w 41 ASN cc_start: 0.8029 (t0) cc_final: 0.7609 (t0) REVERT: w 56 TRP cc_start: 0.7023 (t60) cc_final: 0.6688 (t-100) REVERT: x 3 TYR cc_start: 0.7569 (m-80) cc_final: 0.7367 (m-80) outliers start: 221 outliers final: 163 residues processed: 1343 average time/residue: 0.6770 time to fit residues: 1571.4922 Evaluate side-chains 1306 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1131 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 32 ARG Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 431 GLN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 373 GLU Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 4 residue 7 ASP Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 236 ARG Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 96 MET Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 431 LEU Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 89 MET Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 112 LYS Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 263 TYR Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 135 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 4 ASP Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain m residue 71 ASP Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 23 ASP Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 442 optimal weight: 9.9990 chunk 566 optimal weight: 10.0000 chunk 439 optimal weight: 20.0000 chunk 653 optimal weight: 20.0000 chunk 433 optimal weight: 6.9990 chunk 772 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 chunk 471 optimal weight: 3.9990 chunk 356 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN N 235 ASN Y 64 GLN ** Z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 87 HIS ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 33 ASN k 50 HIS l 20 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN q 89 ASN ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 GLN t 52 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.279 69608 Z= 0.603 Angle : 1.588 51.052 94108 Z= 1.019 Chirality : 0.309 6.551 10190 Planarity : 0.004 0.059 11747 Dihedral : 11.934 168.122 10577 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.89 % Favored : 95.10 % Rotamer: Outliers : 3.32 % Allowed : 14.23 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 8122 helix: 0.56 (0.08), residues: 4286 sheet: -1.10 (0.26), residues: 364 loop : -0.95 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 106 HIS 0.014 0.001 HIS 9 65 PHE 0.035 0.002 PHE N 292 TYR 0.029 0.002 TYR J 60 ARG 0.005 0.001 ARG d 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1146 time to evaluate : 6.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: 3 74 MET cc_start: 0.8516 (mmt) cc_final: 0.7316 (mtp) REVERT: 3 181 MET cc_start: 0.8528 (ttp) cc_final: 0.8057 (ttp) REVERT: 3 248 MET cc_start: 0.8715 (mmm) cc_final: 0.8352 (mmt) REVERT: 3 254 MET cc_start: 0.9045 (ttp) cc_final: 0.8785 (ttp) REVERT: 3 287 GLU cc_start: 0.7923 (pm20) cc_final: 0.7531 (tt0) REVERT: 3 293 HIS cc_start: 0.8949 (m-70) cc_final: 0.8644 (m-70) REVERT: 3 445 GLU cc_start: 0.8002 (pt0) cc_final: 0.7665 (mm-30) REVERT: 3 476 LYS cc_start: 0.8681 (tttm) cc_final: 0.7893 (mmtp) REVERT: 3 613 TYR cc_start: 0.8269 (p90) cc_final: 0.7575 (p90) REVERT: 3 629 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8841 (p0) REVERT: 3 634 ASP cc_start: 0.7524 (t0) cc_final: 0.7270 (t0) REVERT: 3 641 TYR cc_start: 0.8041 (m-80) cc_final: 0.7714 (m-80) REVERT: 3 655 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6093 (tt0) REVERT: 3 689 LYS cc_start: 0.8646 (tttm) cc_final: 0.8422 (tptt) REVERT: 4 182 GLU cc_start: 0.9234 (tm-30) cc_final: 0.9000 (tm-30) REVERT: 4 334 LYS cc_start: 0.8592 (mttm) cc_final: 0.8368 (mtmt) REVERT: 6 178 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7880 (mtt90) REVERT: 9 15 LYS cc_start: 0.7776 (tptp) cc_final: 0.6663 (mmtp) REVERT: 9 157 ASN cc_start: 0.8938 (m-40) cc_final: 0.8645 (m-40) REVERT: A 4 MET cc_start: 0.8552 (mtm) cc_final: 0.8077 (mpp) REVERT: A 98 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8322 (tp) REVERT: H 93 TYR cc_start: 0.8497 (m-80) cc_final: 0.7708 (m-80) REVERT: J 2 MET cc_start: 0.7790 (tpt) cc_final: 0.7524 (tpt) REVERT: J 103 MET cc_start: 0.7135 (ptp) cc_final: 0.6293 (mmt) REVERT: J 167 VAL cc_start: 0.8938 (t) cc_final: 0.8591 (t) REVERT: L 8 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8503 (m) REVERT: L 52 MET cc_start: 0.7573 (mtm) cc_final: 0.7177 (mtt) REVERT: L 140 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8982 (tt) REVERT: L 277 MET cc_start: 0.7263 (mtm) cc_final: 0.7022 (mtm) REVERT: L 331 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8615 (p) REVERT: L 528 TYR cc_start: 0.7572 (m-10) cc_final: 0.7106 (m-80) REVERT: L 544 MET cc_start: 0.6022 (tmm) cc_final: 0.5290 (mmt) REVERT: M 43 ASN cc_start: 0.8942 (t0) cc_final: 0.8639 (t0) REVERT: M 59 ASP cc_start: 0.8031 (p0) cc_final: 0.7788 (p0) REVERT: M 98 MET cc_start: 0.8670 (mmm) cc_final: 0.8459 (mmm) REVERT: M 114 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8149 (mt-10) REVERT: N 11 MET cc_start: 0.7906 (mmp) cc_final: 0.7395 (mtt) REVERT: N 220 MET cc_start: 0.8181 (mtm) cc_final: 0.7739 (mtp) REVERT: N 298 TYR cc_start: 0.8245 (m-10) cc_final: 0.7762 (m-10) REVERT: V 6 HIS cc_start: 0.6778 (m90) cc_final: 0.6543 (m-70) REVERT: V 78 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7479 (mm-40) REVERT: W 40 ILE cc_start: 0.8367 (mm) cc_final: 0.8039 (mp) REVERT: X 33 ASN cc_start: 0.7790 (m-40) cc_final: 0.7124 (t0) REVERT: Y 3 ILE cc_start: 0.8186 (mm) cc_final: 0.7762 (tt) REVERT: Y 37 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7873 (mmtt) REVERT: Y 63 ASN cc_start: 0.8906 (t160) cc_final: 0.8631 (t0) REVERT: Y 77 CYS cc_start: 0.8847 (m) cc_final: 0.8629 (m) REVERT: Y 86 THR cc_start: 0.8874 (m) cc_final: 0.8640 (p) REVERT: Y 158 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8315 (mttm) REVERT: Z 9 TYR cc_start: 0.7194 (m-80) cc_final: 0.6826 (m-80) REVERT: Z 169 THR cc_start: 0.7106 (m) cc_final: 0.6889 (p) REVERT: b 90 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: d 52 GLU cc_start: 0.8261 (tp30) cc_final: 0.7981 (mp0) REVERT: d 102 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6717 (tppt) REVERT: d 254 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7714 (pt) REVERT: d 308 THR cc_start: 0.8156 (m) cc_final: 0.7727 (p) REVERT: f 91 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7628 (mtt90) REVERT: f 93 MET cc_start: 0.7237 (tpp) cc_final: 0.7014 (mpp) REVERT: h 17 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7313 (mtt90) REVERT: h 63 MET cc_start: 0.8456 (mmm) cc_final: 0.7841 (ptm) REVERT: h 111 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: i 78 ASP cc_start: 0.8829 (t0) cc_final: 0.8343 (t70) REVERT: j 20 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7636 (mmmm) REVERT: k 12 GLU cc_start: 0.7905 (tt0) cc_final: 0.7276 (tp30) REVERT: k 18 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6630 (mmm) REVERT: k 89 ASN cc_start: 0.7337 (t0) cc_final: 0.6980 (t0) REVERT: k 240 TYR cc_start: 0.7744 (m-80) cc_final: 0.7304 (m-80) REVERT: k 284 ILE cc_start: 0.8556 (mm) cc_final: 0.8150 (pt) REVERT: l 64 GLU cc_start: 0.8753 (tp30) cc_final: 0.8410 (tp30) REVERT: m 71 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: n 13 MET cc_start: 0.5322 (tmm) cc_final: 0.4913 (tmm) REVERT: n 70 PHE cc_start: 0.8276 (t80) cc_final: 0.7997 (t80) REVERT: p 34 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: p 60 GLU cc_start: 0.7594 (pt0) cc_final: 0.7327 (tt0) REVERT: p 84 LYS cc_start: 0.6555 (tttm) cc_final: 0.6190 (tppt) REVERT: p 107 ASP cc_start: 0.8938 (t70) cc_final: 0.8557 (t0) REVERT: p 110 ARG cc_start: 0.6915 (tmm160) cc_final: 0.6525 (ttm-80) REVERT: q 34 MET cc_start: 0.7919 (mtm) cc_final: 0.7011 (mmm) REVERT: q 75 GLN cc_start: 0.8516 (tp40) cc_final: 0.8043 (tp-100) REVERT: q 79 ASP cc_start: 0.8370 (m-30) cc_final: 0.7749 (m-30) REVERT: q 130 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8142 (tm-30) REVERT: r 87 TYR cc_start: 0.8134 (m-80) cc_final: 0.7521 (m-80) REVERT: s 38 MET cc_start: 0.7364 (tpt) cc_final: 0.6657 (tpt) REVERT: s 62 LEU cc_start: 0.8048 (mt) cc_final: 0.7771 (mt) REVERT: t 58 LYS cc_start: 0.6526 (tptp) cc_final: 0.6161 (ttmm) REVERT: t 65 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: t 69 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: v 30 ARG cc_start: 0.6415 (mtp85) cc_final: 0.5871 (mtp85) REVERT: v 91 THR cc_start: 0.8521 (p) cc_final: 0.8260 (p) REVERT: v 136 ASN cc_start: 0.7600 (m-40) cc_final: 0.6510 (t0) REVERT: v 148 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7591 (mmtm) REVERT: w 41 ASN cc_start: 0.8028 (t0) cc_final: 0.7602 (t0) REVERT: w 56 TRP cc_start: 0.7012 (t60) cc_final: 0.6693 (t-100) REVERT: w 70 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8263 (mp) REVERT: w 94 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8327 (mt-10) REVERT: x 3 TYR cc_start: 0.7436 (m-80) cc_final: 0.7227 (m-80) outliers start: 239 outliers final: 185 residues processed: 1305 average time/residue: 0.6369 time to fit residues: 1434.7266 Evaluate side-chains 1313 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1112 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 431 GLN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 373 GLU Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 3 residue 629 ASN Chi-restraints excluded: chain 3 residue 666 LEU Chi-restraints excluded: chain 4 residue 7 ASP Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 236 ARG Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 96 MET Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 11 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 217 ILE Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain L residue 431 LEU Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 89 MET Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 112 LYS Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 263 TYR Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 135 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 245 LYS Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 4 ASP Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain m residue 71 ASP Chi-restraints excluded: chain m residue 73 GLN Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 99 ASN Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 43 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 461 optimal weight: 0.0050 chunk 232 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 491 optimal weight: 7.9990 chunk 526 optimal weight: 3.9990 chunk 382 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 607 optimal weight: 5.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 331 ASN d 87 HIS ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 GLN k 50 HIS l 20 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN p 32 GLN ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 GLN t 52 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.273 69608 Z= 0.555 Angle : 1.568 51.039 94108 Z= 1.011 Chirality : 0.309 6.512 10190 Planarity : 0.004 0.055 11747 Dihedral : 11.643 167.889 10577 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.25 % Favored : 95.74 % Rotamer: Outliers : 3.00 % Allowed : 14.93 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % 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: -0.06 (0.09), residues: 8122 helix: 0.73 (0.08), residues: 4270 sheet: -1.08 (0.26), residues: 366 loop : -0.82 (0.11), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 106 HIS 0.014 0.001 HIS 9 65 PHE 0.036 0.001 PHE N 292 TYR 0.024 0.002 TYR y 25 ARG 0.006 0.000 ARG w 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1183 time to evaluate : 5.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 52 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: 3 74 MET cc_start: 0.8508 (mmt) cc_final: 0.7299 (mtp) REVERT: 3 181 MET cc_start: 0.8454 (ttp) cc_final: 0.8056 (ttp) REVERT: 3 248 MET cc_start: 0.8685 (mmm) cc_final: 0.8355 (mmt) REVERT: 3 254 MET cc_start: 0.8996 (ttp) cc_final: 0.8748 (ttp) REVERT: 3 287 GLU cc_start: 0.7917 (pm20) cc_final: 0.7525 (tt0) REVERT: 3 293 HIS cc_start: 0.8943 (m-70) cc_final: 0.8663 (m-70) REVERT: 3 445 GLU cc_start: 0.7963 (pt0) cc_final: 0.7664 (mm-30) REVERT: 3 476 LYS cc_start: 0.8692 (tttm) cc_final: 0.7902 (mmtp) REVERT: 3 495 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8121 (ptt180) REVERT: 3 613 TYR cc_start: 0.8191 (p90) cc_final: 0.7505 (p90) REVERT: 3 629 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8787 (p0) REVERT: 3 634 ASP cc_start: 0.7498 (t0) cc_final: 0.7265 (t0) REVERT: 3 641 TYR cc_start: 0.8012 (m-80) cc_final: 0.7730 (m-80) REVERT: 3 655 GLN cc_start: 0.7297 (mm-40) cc_final: 0.6031 (tt0) REVERT: 3 689 LYS cc_start: 0.8628 (tttm) cc_final: 0.8406 (tptt) REVERT: 4 20 TYR cc_start: 0.8357 (m-80) cc_final: 0.7803 (m-10) REVERT: 4 182 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8998 (tm-30) REVERT: 4 259 MET cc_start: 0.9203 (mmm) cc_final: 0.8983 (mmm) REVERT: 4 334 LYS cc_start: 0.8600 (mttm) cc_final: 0.8373 (mtmt) REVERT: 6 74 VAL cc_start: 0.8744 (t) cc_final: 0.8522 (t) REVERT: 6 178 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7860 (mtt90) REVERT: 9 15 LYS cc_start: 0.7654 (tptp) cc_final: 0.6571 (mmtp) REVERT: 9 157 ASN cc_start: 0.8903 (m-40) cc_final: 0.8616 (m-40) REVERT: A 4 MET cc_start: 0.8588 (mtm) cc_final: 0.8199 (mpp) REVERT: A 98 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8313 (tp) REVERT: H 93 TYR cc_start: 0.8483 (m-80) cc_final: 0.7690 (m-80) REVERT: H 233 MET cc_start: 0.8635 (tmm) cc_final: 0.8369 (tmm) REVERT: J 65 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8524 (ttt) REVERT: J 103 MET cc_start: 0.7154 (ptp) cc_final: 0.6310 (mmt) REVERT: J 167 VAL cc_start: 0.8894 (t) cc_final: 0.8524 (t) REVERT: L 8 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8500 (m) REVERT: L 29 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.5112 (t80) REVERT: L 140 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8988 (tt) REVERT: L 277 MET cc_start: 0.7237 (mtm) cc_final: 0.6979 (mtm) REVERT: L 331 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8600 (p) REVERT: L 410 LEU cc_start: 0.8380 (tp) cc_final: 0.7898 (mm) REVERT: L 528 TYR cc_start: 0.7576 (m-10) cc_final: 0.7112 (m-80) REVERT: L 544 MET cc_start: 0.5981 (tmm) cc_final: 0.5259 (mmt) REVERT: M 43 ASN cc_start: 0.8918 (t0) cc_final: 0.8618 (t0) REVERT: M 114 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8144 (mt-10) REVERT: N 11 MET cc_start: 0.7812 (mmp) cc_final: 0.7301 (mtt) REVERT: N 220 MET cc_start: 0.8152 (mtm) cc_final: 0.7716 (mtp) REVERT: N 270 MET cc_start: 0.8521 (mtm) cc_final: 0.8258 (mtp) REVERT: N 298 TYR cc_start: 0.8189 (m-10) cc_final: 0.7578 (m-10) REVERT: V 6 HIS cc_start: 0.6670 (m90) cc_final: 0.6439 (m-70) REVERT: W 97 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7511 (tp30) REVERT: X 33 ASN cc_start: 0.7812 (m-40) cc_final: 0.7036 (t0) REVERT: Y 3 ILE cc_start: 0.8092 (mm) cc_final: 0.7678 (tt) REVERT: Y 37 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7861 (mmtt) REVERT: Y 63 ASN cc_start: 0.8877 (t160) cc_final: 0.8675 (t0) REVERT: Y 77 CYS cc_start: 0.8848 (m) cc_final: 0.8639 (m) REVERT: Y 86 THR cc_start: 0.8857 (m) cc_final: 0.8626 (p) REVERT: Y 158 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8299 (mttm) REVERT: Y 169 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.7256 (m-90) REVERT: b 90 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: c 45 MET cc_start: 0.8721 (mmm) cc_final: 0.8435 (mmm) REVERT: d 52 GLU cc_start: 0.8234 (tp30) cc_final: 0.7995 (mp0) REVERT: d 102 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6606 (tppp) REVERT: d 171 ILE cc_start: 0.8795 (mt) cc_final: 0.8440 (mm) REVERT: d 199 LYS cc_start: 0.8573 (mptm) cc_final: 0.8214 (mtpp) REVERT: d 254 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7689 (pt) REVERT: d 308 THR cc_start: 0.8107 (m) cc_final: 0.7659 (p) REVERT: f 91 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7583 (mtt90) REVERT: f 93 MET cc_start: 0.7152 (tpp) cc_final: 0.6924 (mpp) REVERT: h 17 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7240 (mtt90) REVERT: h 63 MET cc_start: 0.8440 (mmm) cc_final: 0.7853 (ptm) REVERT: h 111 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: i 78 ASP cc_start: 0.8782 (t0) cc_final: 0.8312 (t70) REVERT: j 20 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7638 (mmmm) REVERT: k 12 GLU cc_start: 0.7907 (tt0) cc_final: 0.7298 (tp30) REVERT: k 18 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6464 (mmm) REVERT: k 89 ASN cc_start: 0.7322 (t0) cc_final: 0.6961 (t0) REVERT: k 240 TYR cc_start: 0.7758 (m-80) cc_final: 0.7325 (m-80) REVERT: l 64 GLU cc_start: 0.8739 (tp30) cc_final: 0.8395 (tp30) REVERT: l 87 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7640 (mmmt) REVERT: m 71 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: n 13 MET cc_start: 0.5328 (tmm) cc_final: 0.4972 (tmm) REVERT: n 70 PHE cc_start: 0.8243 (t80) cc_final: 0.8032 (t80) REVERT: p 34 GLU cc_start: 0.8183 (tp30) cc_final: 0.7861 (tm-30) REVERT: p 46 TYR cc_start: 0.7741 (t80) cc_final: 0.7499 (t80) REVERT: p 60 GLU cc_start: 0.7646 (pt0) cc_final: 0.7389 (tt0) REVERT: p 107 ASP cc_start: 0.8937 (t70) cc_final: 0.8572 (t0) REVERT: p 110 ARG cc_start: 0.6925 (tmm160) cc_final: 0.6527 (ttm-80) REVERT: q 34 MET cc_start: 0.7902 (mtm) cc_final: 0.6997 (mmm) REVERT: q 75 GLN cc_start: 0.8452 (tp40) cc_final: 0.8061 (tp-100) REVERT: q 79 ASP cc_start: 0.8240 (m-30) cc_final: 0.7662 (m-30) REVERT: q 130 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8178 (tm-30) REVERT: r 87 TYR cc_start: 0.8096 (m-80) cc_final: 0.7502 (m-80) REVERT: s 38 MET cc_start: 0.7265 (tpt) cc_final: 0.6751 (tpt) REVERT: s 62 LEU cc_start: 0.7893 (mt) cc_final: 0.7642 (mt) REVERT: t 58 LYS cc_start: 0.6517 (tptp) cc_final: 0.6154 (ttmm) REVERT: t 65 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: t 69 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: t 90 TYR cc_start: 0.8731 (t80) cc_final: 0.8437 (t80) REVERT: t 94 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7743 (mm-30) REVERT: t 127 LEU cc_start: 0.8680 (tp) cc_final: 0.8165 (mt) REVERT: v 30 ARG cc_start: 0.6444 (mtp85) cc_final: 0.5987 (mtp85) REVERT: v 91 THR cc_start: 0.8510 (p) cc_final: 0.8239 (p) REVERT: v 136 ASN cc_start: 0.7575 (m-40) cc_final: 0.6496 (t0) REVERT: v 148 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7538 (mmtm) REVERT: w 27 GLN cc_start: 0.6755 (mm110) cc_final: 0.5645 (tt0) REVERT: w 41 ASN cc_start: 0.8034 (t0) cc_final: 0.7651 (t0) REVERT: w 56 TRP cc_start: 0.7036 (t60) cc_final: 0.6706 (t-100) REVERT: y 25 TYR cc_start: 0.8501 (t80) cc_final: 0.8147 (t80) outliers start: 216 outliers final: 165 residues processed: 1329 average time/residue: 0.6343 time to fit residues: 1453.3465 Evaluate side-chains 1315 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1132 time to evaluate : 7.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 431 GLN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 373 GLU Chi-restraints excluded: chain 3 residue 495 ARG Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 3 residue 629 ASN Chi-restraints excluded: chain 3 residue 666 LEU Chi-restraints excluded: chain 4 residue 7 ASP Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 69 SER Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 236 ARG Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 6 residue 27 GLU Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 96 MET Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 431 LEU Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 169 TRP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 89 MET Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 112 LYS Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 263 TYR Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 135 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain m residue 71 ASP Chi-restraints excluded: chain m residue 73 GLN Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 89 SER Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 47 VAL Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 99 ASN Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 43 ASP Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 8.9990 chunk 740 optimal weight: 30.0000 chunk 675 optimal weight: 7.9990 chunk 720 optimal weight: 40.0000 chunk 433 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 chunk 565 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 650 optimal weight: 10.0000 chunk 681 optimal weight: 6.9990 chunk 717 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 197 ASN V 18 HIS X 74 GLN d 87 HIS ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 GLN l 20 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN p 47 GLN ** r 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 GLN t 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.274 69608 Z= 0.579 Angle : 1.581 50.991 94108 Z= 1.016 Chirality : 0.309 6.527 10190 Planarity : 0.004 0.057 11747 Dihedral : 11.585 168.157 10577 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.64 % Favored : 95.35 % Rotamer: Outliers : 2.98 % Allowed : 15.40 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.09), residues: 8122 helix: 0.72 (0.08), residues: 4273 sheet: -1.04 (0.27), residues: 364 loop : -0.80 (0.11), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 106 HIS 0.014 0.001 HIS 9 65 PHE 0.035 0.002 PHE N 292 TYR 0.025 0.002 TYR J 60 ARG 0.006 0.000 ARG w 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1141 time to evaluate : 5.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 167 CYS cc_start: 0.8002 (m) cc_final: 0.7774 (t) REVERT: 2 52 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: 3 74 MET cc_start: 0.8522 (mmt) cc_final: 0.7324 (mtp) REVERT: 3 181 MET cc_start: 0.8507 (ttp) cc_final: 0.8102 (ttp) REVERT: 3 248 MET cc_start: 0.8695 (mmm) cc_final: 0.8394 (mmt) REVERT: 3 254 MET cc_start: 0.9022 (ttp) cc_final: 0.8771 (ttp) REVERT: 3 287 GLU cc_start: 0.7931 (pm20) cc_final: 0.7532 (tt0) REVERT: 3 293 HIS cc_start: 0.8969 (m-70) cc_final: 0.8674 (m-70) REVERT: 3 445 GLU cc_start: 0.7976 (pt0) cc_final: 0.7694 (mm-30) REVERT: 3 476 LYS cc_start: 0.8681 (tttm) cc_final: 0.7902 (mmtp) REVERT: 3 495 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8136 (ptt180) REVERT: 3 613 TYR cc_start: 0.8229 (p90) cc_final: 0.7500 (p90) REVERT: 3 629 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8790 (p0) REVERT: 3 634 ASP cc_start: 0.7515 (t0) cc_final: 0.7280 (t0) REVERT: 3 641 TYR cc_start: 0.8024 (m-80) cc_final: 0.7815 (m-80) REVERT: 3 655 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6006 (tt0) REVERT: 3 689 LYS cc_start: 0.8623 (tttm) cc_final: 0.8413 (tptt) REVERT: 4 20 TYR cc_start: 0.8454 (m-80) cc_final: 0.8125 (m-10) REVERT: 4 182 GLU cc_start: 0.9248 (tm-30) cc_final: 0.9023 (tm-30) REVERT: 4 276 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: 4 334 LYS cc_start: 0.8614 (mttm) cc_final: 0.8391 (mtmt) REVERT: 5 14 ARG cc_start: 0.7484 (tpt-90) cc_final: 0.7146 (tpp-160) REVERT: 6 178 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7866 (mtt90) REVERT: 9 15 LYS cc_start: 0.7686 (tptp) cc_final: 0.6557 (mmtp) REVERT: 9 157 ASN cc_start: 0.8917 (m-40) cc_final: 0.8621 (m-40) REVERT: A 4 MET cc_start: 0.8561 (mtm) cc_final: 0.8087 (mpp) REVERT: A 98 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8310 (tp) REVERT: H 93 TYR cc_start: 0.8506 (m-80) cc_final: 0.7712 (m-80) REVERT: J 65 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8529 (ttt) REVERT: J 103 MET cc_start: 0.7193 (ptp) cc_final: 0.6382 (mmt) REVERT: J 167 VAL cc_start: 0.8923 (t) cc_final: 0.8573 (t) REVERT: L 8 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8584 (m) REVERT: L 29 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5249 (t80) REVERT: L 140 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8993 (tt) REVERT: L 277 MET cc_start: 0.7262 (mtm) cc_final: 0.7013 (mtm) REVERT: L 331 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8605 (p) REVERT: L 410 LEU cc_start: 0.8354 (tp) cc_final: 0.7902 (mm) REVERT: L 528 TYR cc_start: 0.7634 (m-10) cc_final: 0.7178 (m-80) REVERT: L 544 MET cc_start: 0.6005 (tmm) cc_final: 0.5278 (mmt) REVERT: M 43 ASN cc_start: 0.8938 (t0) cc_final: 0.8631 (t0) REVERT: M 114 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8137 (mt-10) REVERT: N 11 MET cc_start: 0.7894 (mmp) cc_final: 0.7361 (mtt) REVERT: N 220 MET cc_start: 0.8179 (mtm) cc_final: 0.7715 (mtp) REVERT: N 298 TYR cc_start: 0.8216 (m-10) cc_final: 0.7612 (m-10) REVERT: V 6 HIS cc_start: 0.6680 (m90) cc_final: 0.6442 (m-70) REVERT: W 40 ILE cc_start: 0.8401 (mm) cc_final: 0.8150 (mp) REVERT: W 97 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7520 (tp30) REVERT: X 33 ASN cc_start: 0.7798 (m-40) cc_final: 0.6971 (t0) REVERT: Y 3 ILE cc_start: 0.8118 (mm) cc_final: 0.7754 (tt) REVERT: Y 37 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7876 (mmtt) REVERT: Y 63 ASN cc_start: 0.8925 (t160) cc_final: 0.8711 (t0) REVERT: Y 77 CYS cc_start: 0.8869 (m) cc_final: 0.8644 (m) REVERT: Y 86 THR cc_start: 0.8920 (m) cc_final: 0.8645 (p) REVERT: Y 158 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8307 (mttm) REVERT: Y 169 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.7274 (m-90) REVERT: Z 9 TYR cc_start: 0.7350 (m-80) cc_final: 0.6912 (m-80) REVERT: a 45 ASP cc_start: 0.7334 (m-30) cc_final: 0.7023 (p0) REVERT: b 90 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: c 45 MET cc_start: 0.8730 (mmm) cc_final: 0.8450 (mmm) REVERT: d 52 GLU cc_start: 0.8248 (tp30) cc_final: 0.7991 (mp0) REVERT: d 102 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6644 (tppp) REVERT: d 171 ILE cc_start: 0.8823 (mt) cc_final: 0.8423 (mm) REVERT: d 199 LYS cc_start: 0.8582 (mptm) cc_final: 0.8219 (mtpp) REVERT: d 254 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7744 (pt) REVERT: d 308 THR cc_start: 0.8084 (m) cc_final: 0.7594 (p) REVERT: f 91 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7606 (mtt90) REVERT: f 93 MET cc_start: 0.7196 (tpp) cc_final: 0.6979 (tpp) REVERT: h 17 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7262 (mtt90) REVERT: h 57 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.7582 (p0) REVERT: h 63 MET cc_start: 0.8464 (mmm) cc_final: 0.7866 (ptm) REVERT: h 111 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: i 78 ASP cc_start: 0.8803 (t0) cc_final: 0.8331 (t70) REVERT: j 20 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7647 (mmmm) REVERT: k 12 GLU cc_start: 0.7961 (tt0) cc_final: 0.7319 (tp30) REVERT: k 18 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6485 (mmm) REVERT: k 89 ASN cc_start: 0.7397 (t0) cc_final: 0.7051 (t0) REVERT: k 240 TYR cc_start: 0.7777 (m-80) cc_final: 0.7341 (m-80) REVERT: l 64 GLU cc_start: 0.8742 (tp30) cc_final: 0.8390 (tp30) REVERT: m 71 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: n 13 MET cc_start: 0.5242 (tmm) cc_final: 0.4860 (tmm) REVERT: n 70 PHE cc_start: 0.8257 (t80) cc_final: 0.8014 (t80) REVERT: p 60 GLU cc_start: 0.7637 (pt0) cc_final: 0.7380 (tt0) REVERT: p 84 LYS cc_start: 0.6575 (tttm) cc_final: 0.6212 (tppt) REVERT: p 107 ASP cc_start: 0.8938 (t70) cc_final: 0.8568 (t0) REVERT: p 110 ARG cc_start: 0.6903 (tmm160) cc_final: 0.6502 (ttm-80) REVERT: q 34 MET cc_start: 0.7925 (mtm) cc_final: 0.6981 (mmm) REVERT: q 75 GLN cc_start: 0.8488 (tp40) cc_final: 0.8070 (tp-100) REVERT: q 79 ASP cc_start: 0.8285 (m-30) cc_final: 0.7665 (m-30) REVERT: q 130 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8177 (tm-30) REVERT: r 87 TYR cc_start: 0.8146 (m-80) cc_final: 0.7550 (m-80) REVERT: s 38 MET cc_start: 0.7304 (tpt) cc_final: 0.6720 (tpt) REVERT: t 58 LYS cc_start: 0.6541 (tptp) cc_final: 0.6169 (ttmm) REVERT: t 65 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: t 69 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: t 90 TYR cc_start: 0.8795 (t80) cc_final: 0.8478 (t80) REVERT: t 94 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7782 (mm-30) REVERT: t 127 LEU cc_start: 0.8680 (tp) cc_final: 0.8155 (mt) REVERT: v 30 ARG cc_start: 0.6345 (mtp85) cc_final: 0.5992 (mtp85) REVERT: v 91 THR cc_start: 0.8485 (p) cc_final: 0.8225 (p) REVERT: v 136 ASN cc_start: 0.7598 (m-40) cc_final: 0.6481 (t0) REVERT: v 148 LYS cc_start: 0.7753 (mtpp) cc_final: 0.7540 (mmtm) REVERT: w 27 GLN cc_start: 0.6847 (mm110) cc_final: 0.5642 (tt0) REVERT: w 41 ASN cc_start: 0.8044 (t0) cc_final: 0.7637 (t0) REVERT: w 56 TRP cc_start: 0.6990 (t60) cc_final: 0.6772 (t-100) REVERT: w 94 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8321 (mt-10) REVERT: y 25 TYR cc_start: 0.8530 (t80) cc_final: 0.8179 (t80) outliers start: 214 outliers final: 175 residues processed: 1286 average time/residue: 0.6904 time to fit residues: 1540.9791 Evaluate side-chains 1310 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1115 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 431 GLN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 52 ASP Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 373 GLU Chi-restraints excluded: chain 3 residue 495 ARG Chi-restraints excluded: chain 3 residue 498 SER Chi-restraints excluded: chain 3 residue 629 ASN Chi-restraints excluded: chain 3 residue 666 LEU Chi-restraints excluded: chain 4 residue 7 ASP Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 236 ARG Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 281 VAL Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 5 residue 115 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 96 MET Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 431 LEU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 399 ASN Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 296 LEU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 11 ASP Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 169 TRP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 89 MET Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 112 LYS Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 102 LYS Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 263 TYR Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 7 THR Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 50 GLN Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain h residue 30 ILE Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 111 TYR Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain j residue 78 ASP Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 18 MET Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 135 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 168 VAL Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 245 LYS Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain m residue 71 ASP Chi-restraints excluded: chain m residue 73 GLN Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 128 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain t residue 89 SER Chi-restraints excluded: chain t residue 130 GLU Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain v residue 77 MET Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 99 ASN Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain v residue 138 LEU Chi-restraints excluded: chain w residue 43 ASP Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 9.9990 chunk 761 optimal weight: 0.0670 chunk 464 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 529 optimal weight: 20.0000 chunk 798 optimal weight: 0.0370 chunk 735 optimal weight: 0.9980 chunk 636 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 491 optimal weight: 0.6980 chunk 390 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 160 HIS H 230 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 197 ASN Y 64 GLN Z 139 GLN a 40 ASN d 87 HIS ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 70 GLN p 32 GLN p 47 GLN q 75 GLN s 53 GLN t 52 ASN v 87 ASN v 136 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 69608 Z= 0.535 Angle : 1.561 51.006 94108 Z= 1.008 Chirality : 0.308 6.440 10190 Planarity : 0.004 0.054 11747 Dihedral : 11.001 166.517 10577 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.34 % Favored : 96.65 % Rotamer: Outliers : 1.67 % Allowed : 16.69 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 8122 helix: 0.93 (0.08), residues: 4265 sheet: -0.84 (0.26), residues: 389 loop : -0.62 (0.11), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP u 59 HIS 0.012 0.001 HIS 9 65 PHE 0.038 0.001 PHE N 292 TYR 0.024 0.001 TYR 4 275 ARG 0.006 0.000 ARG v 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1297 time to evaluate : 6.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 116 HIS cc_start: 0.7676 (m-70) cc_final: 0.7436 (m-70) REVERT: 2 52 ASP cc_start: 0.8471 (t0) cc_final: 0.7995 (m-30) REVERT: 3 74 MET cc_start: 0.8353 (mmt) cc_final: 0.7096 (mtp) REVERT: 3 192 MET cc_start: 0.7680 (mmm) cc_final: 0.7393 (mmt) REVERT: 3 248 MET cc_start: 0.8583 (mmm) cc_final: 0.8338 (mmt) REVERT: 3 287 GLU cc_start: 0.7782 (pm20) cc_final: 0.7471 (tt0) REVERT: 3 293 HIS cc_start: 0.8933 (m-70) cc_final: 0.8710 (m-70) REVERT: 3 476 LYS cc_start: 0.8712 (tttm) cc_final: 0.7806 (mmtp) REVERT: 3 613 TYR cc_start: 0.8143 (p90) cc_final: 0.7407 (p90) REVERT: 3 634 ASP cc_start: 0.7431 (t0) cc_final: 0.7219 (t0) REVERT: 4 50 ASN cc_start: 0.8566 (t0) cc_final: 0.8101 (t0) REVERT: 4 290 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8036 (mtp85) REVERT: 4 334 LYS cc_start: 0.8642 (mttm) cc_final: 0.8404 (mtmt) REVERT: 6 178 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7833 (mtt90) REVERT: 9 15 LYS cc_start: 0.7496 (tptp) cc_final: 0.6487 (mmtp) REVERT: 9 157 ASN cc_start: 0.8789 (m-40) cc_final: 0.8490 (m-40) REVERT: A 4 MET cc_start: 0.8434 (mtm) cc_final: 0.8102 (mpp) REVERT: A 98 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8310 (tp) REVERT: H 77 LEU cc_start: 0.8821 (tt) cc_final: 0.8474 (tp) REVERT: H 93 TYR cc_start: 0.8457 (m-80) cc_final: 0.7581 (m-80) REVERT: J 81 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7747 (mt-10) REVERT: J 86 ASN cc_start: 0.7574 (t0) cc_final: 0.7211 (t0) REVERT: J 103 MET cc_start: 0.7098 (ptp) cc_final: 0.6190 (mmt) REVERT: J 167 VAL cc_start: 0.8831 (t) cc_final: 0.8450 (t) REVERT: K 38 LEU cc_start: 0.8530 (tp) cc_final: 0.8100 (tt) REVERT: L 8 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (m) REVERT: L 140 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8924 (tt) REVERT: L 277 MET cc_start: 0.7184 (mtm) cc_final: 0.6962 (mtm) REVERT: L 331 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8565 (p) REVERT: L 401 THR cc_start: 0.8005 (p) cc_final: 0.7651 (p) REVERT: L 478 PRO cc_start: 0.6815 (Cg_endo) cc_final: 0.6478 (Cg_exo) REVERT: L 528 TYR cc_start: 0.7517 (m-10) cc_final: 0.7149 (m-80) REVERT: L 544 MET cc_start: 0.6020 (tmm) cc_final: 0.5087 (mmt) REVERT: M 43 ASN cc_start: 0.8813 (t0) cc_final: 0.8532 (t0) REVERT: M 87 GLU cc_start: 0.7668 (tp30) cc_final: 0.7375 (tt0) REVERT: M 114 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8146 (mt-10) REVERT: N 8 ILE cc_start: 0.8050 (mm) cc_final: 0.7841 (tt) REVERT: N 11 MET cc_start: 0.7836 (mmp) cc_final: 0.7270 (mtp) REVERT: N 108 MET cc_start: 0.8964 (mtp) cc_final: 0.8690 (mtp) REVERT: N 171 ASN cc_start: 0.8631 (t0) cc_final: 0.7935 (t0) REVERT: N 220 MET cc_start: 0.8062 (mtm) cc_final: 0.7634 (mtp) REVERT: N 298 TYR cc_start: 0.8127 (m-10) cc_final: 0.7505 (m-10) REVERT: W 40 ILE cc_start: 0.8402 (mm) cc_final: 0.8186 (mp) REVERT: W 91 MET cc_start: 0.8695 (mtp) cc_final: 0.8456 (mmm) REVERT: W 97 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7533 (tp30) REVERT: X 33 ASN cc_start: 0.7710 (m-40) cc_final: 0.6836 (t0) REVERT: Y 3 ILE cc_start: 0.8050 (mm) cc_final: 0.7652 (tt) REVERT: Y 37 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7915 (mmtt) REVERT: Y 86 THR cc_start: 0.8733 (m) cc_final: 0.8478 (p) REVERT: Y 158 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8324 (mttm) REVERT: Y 161 ARG cc_start: 0.7969 (mmp80) cc_final: 0.7649 (tpp80) REVERT: Y 169 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7005 (m-90) REVERT: Z 132 THR cc_start: 0.8987 (m) cc_final: 0.8391 (p) REVERT: c 45 MET cc_start: 0.8604 (mmm) cc_final: 0.8358 (mmm) REVERT: d 52 GLU cc_start: 0.8154 (tp30) cc_final: 0.7850 (mp0) REVERT: d 102 LYS cc_start: 0.7458 (ttpm) cc_final: 0.6596 (tppp) REVERT: d 171 ILE cc_start: 0.8706 (mt) cc_final: 0.8325 (mm) REVERT: d 199 LYS cc_start: 0.8512 (mptm) cc_final: 0.8138 (mtpp) REVERT: d 308 THR cc_start: 0.8011 (m) cc_final: 0.7506 (p) REVERT: d 325 ARG cc_start: 0.6563 (ptt180) cc_final: 0.5077 (tpt90) REVERT: f 91 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7673 (mtt90) REVERT: h 17 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7220 (mtt90) REVERT: h 57 ASP cc_start: 0.8420 (t70) cc_final: 0.7311 (p0) REVERT: h 63 MET cc_start: 0.8407 (mmm) cc_final: 0.7994 (ttt) REVERT: h 101 LYS cc_start: 0.8406 (tppt) cc_final: 0.8172 (mmtm) REVERT: i 5 GLN cc_start: 0.8411 (mm110) cc_final: 0.8107 (mm-40) REVERT: j 20 LYS cc_start: 0.7870 (ptpt) cc_final: 0.7582 (mmmm) REVERT: j 71 MET cc_start: 0.6342 (mmm) cc_final: 0.5179 (ptp) REVERT: k 12 GLU cc_start: 0.7794 (tt0) cc_final: 0.7351 (tp30) REVERT: k 89 ASN cc_start: 0.7342 (t0) cc_final: 0.6984 (t0) REVERT: k 240 TYR cc_start: 0.7676 (m-80) cc_final: 0.7194 (m-80) REVERT: k 265 ASP cc_start: 0.6948 (t0) cc_final: 0.6544 (m-30) REVERT: l 64 GLU cc_start: 0.8688 (tp30) cc_final: 0.8245 (tp30) REVERT: m 71 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: n 13 MET cc_start: 0.5312 (tmm) cc_final: 0.5017 (tmm) REVERT: o 16 ASP cc_start: 0.7458 (t70) cc_final: 0.7185 (t70) REVERT: p 46 TYR cc_start: 0.7462 (t80) cc_final: 0.7240 (t80) REVERT: p 84 LYS cc_start: 0.6534 (tttm) cc_final: 0.6152 (tppt) REVERT: p 107 ASP cc_start: 0.8904 (t70) cc_final: 0.8564 (t0) REVERT: p 110 ARG cc_start: 0.6858 (tmm160) cc_final: 0.6433 (ttm-80) REVERT: q 34 MET cc_start: 0.7858 (mtm) cc_final: 0.6917 (mmm) REVERT: q 75 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7889 (tp-100) REVERT: q 79 ASP cc_start: 0.7966 (m-30) cc_final: 0.6999 (m-30) REVERT: q 130 GLU cc_start: 0.8684 (tm-30) cc_final: 0.7970 (tm-30) REVERT: r 87 TYR cc_start: 0.7864 (m-80) cc_final: 0.7307 (m-80) REVERT: t 58 LYS cc_start: 0.6525 (tptp) cc_final: 0.6158 (ttmm) REVERT: t 65 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: t 69 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: t 127 LEU cc_start: 0.8426 (tp) cc_final: 0.7919 (mt) REVERT: v 81 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8176 (tp) REVERT: v 91 THR cc_start: 0.8415 (p) cc_final: 0.8184 (p) REVERT: v 115 MET cc_start: 0.6276 (mmm) cc_final: 0.5695 (mmm) REVERT: v 136 ASN cc_start: 0.7359 (m-40) cc_final: 0.6368 (t0) REVERT: w 27 GLN cc_start: 0.6579 (mm110) cc_final: 0.5747 (tt0) REVERT: w 41 ASN cc_start: 0.8044 (t0) cc_final: 0.7668 (t0) REVERT: w 56 TRP cc_start: 0.6810 (t60) cc_final: 0.6566 (t-100) REVERT: y 25 TYR cc_start: 0.8587 (t80) cc_final: 0.8167 (t80) REVERT: z 64 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7628 (mmtt) outliers start: 120 outliers final: 80 residues processed: 1368 average time/residue: 0.6493 time to fit residues: 1521.0088 Evaluate side-chains 1251 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1162 time to evaluate : 5.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 2 residue 28 TYR Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 666 LEU Chi-restraints excluded: chain 4 residue 7 ASP Chi-restraints excluded: chain 4 residue 22 THR Chi-restraints excluded: chain 4 residue 164 MET Chi-restraints excluded: chain 4 residue 236 ARG Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 82 GLN Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 97 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain N residue 233 THR Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 140 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 169 TRP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 72 ASP Chi-restraints excluded: chain Z residue 112 CYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 47 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 263 TYR Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain f residue 7 THR Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain i residue 62 VAL Chi-restraints excluded: chain j residue 26 ASP Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 135 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain m residue 71 ASP Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain r residue 119 MET Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 65 GLU Chi-restraints excluded: chain t residue 69 GLU Chi-restraints excluded: chain u residue 8 GLU Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 104 HIS Chi-restraints excluded: chain w residue 43 ASP Chi-restraints excluded: chain w residue 71 VAL Chi-restraints excluded: chain w residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 7.9990 chunk 677 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 637 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 chunk 654 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 398 GLN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN a 40 ASN d 87 HIS ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 ASN h 8 GLN ** j 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 70 GLN ** p 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN t 52 ASN v 136 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106335 restraints weight = 127188.065| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.29 r_work: 0.3288 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.269 69608 Z= 0.557 Angle : 1.571 50.971 94108 Z= 1.012 Chirality : 0.309 6.491 10190 Planarity : 0.004 0.054 11747 Dihedral : 10.961 167.343 10577 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.84 % Favored : 96.15 % Rotamer: Outliers : 1.68 % Allowed : 17.05 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % 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: 0.28 (0.10), residues: 8122 helix: 0.94 (0.08), residues: 4288 sheet: -0.78 (0.27), residues: 373 loop : -0.57 (0.11), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP N 26 HIS 0.014 0.001 HIS 9 65 PHE 0.063 0.001 PHE N 292 TYR 0.045 0.002 TYR v 62 ARG 0.011 0.000 ARG q 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22266.79 seconds wall clock time: 389 minutes 26.40 seconds (23366.40 seconds total)