Starting phenix.real_space_refine on Fri Mar 22 08:18:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/03_2024/6k72_9841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/03_2024/6k72_9841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/03_2024/6k72_9841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/03_2024/6k72_9841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/03_2024/6k72_9841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/03_2024/6k72_9841.pdb" } resolution = 4.6 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 169 5.16 5 C 20759 2.51 5 N 5696 2.21 5 O 6107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 108": "NH1" <-> "NH2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 234": "NH1" <-> "NH2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "F TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 250": "NH1" <-> "NH2" Residue "G ARG 321": "NH1" <-> "NH2" Residue "G ARG 374": "NH1" <-> "NH2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "H ARG 250": "NH1" <-> "NH2" Residue "H ARG 321": "NH1" <-> "NH2" Residue "H ARG 374": "NH1" <-> "NH2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 428": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "K TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 144": "NH1" <-> "NH2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "P PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32731 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2213 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Chain: "B" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2204 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2286 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 11, 'TRANS': 321} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "F" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2255 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 11, 'TRANS': 317} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "G" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2779 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain: "H" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2779 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain: "I" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3312 Classifications: {'peptide': 421} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Chain: "J" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3312 Classifications: {'peptide': 421} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Chain: "K" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1914 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 7, 'TRANS': 231} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1356 Classifications: {'peptide': 165} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 159} Chain breaks: 1 Chain: "M" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 145 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "P" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3204 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 22, 'TRANS': 398} Time building chain proxies: 16.76, per 1000 atoms: 0.51 Number of scatterers: 32731 At special positions: 0 Unit cell: (160.23, 177.87, 202.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 169 16.00 O 6107 8.00 N 5696 7.00 C 20759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 13.58 Conformation dependent library (CDL) restraints added in 7.0 seconds 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8048 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 53 sheets defined 33.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.699A pdb=" N SER A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.632A pdb=" N GLU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.905A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 231 through 235 removed outlier: 4.275A pdb=" N PHE A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.714A pdb=" N ASP A 245 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 246' Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.064A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 42 through 57 removed outlier: 3.651A pdb=" N ARG B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.898A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 116 removed outlier: 5.561A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.556A pdb=" N VAL B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.934A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 53 through 72 removed outlier: 4.523A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.875A pdb=" N HIS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 145 Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.013A pdb=" N VAL C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.502A pdb=" N GLU C 293 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.633A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.516A pdb=" N MET D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 72 removed outlier: 4.011A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 95 removed outlier: 3.737A pdb=" N ARG D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.979A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.302A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.831A pdb=" N GLU D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 207 removed outlier: 3.852A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.637A pdb=" N VAL D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.777A pdb=" N LEU D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 300 through 304 removed outlier: 4.456A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 304' Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.626A pdb=" N LEU E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 removed outlier: 3.836A pdb=" N LYS E 70 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET E 71 " --> pdb=" O LYS E 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 67 through 71' Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.569A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.888A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 removed outlier: 3.522A pdb=" N GLU E 227 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.579A pdb=" N GLY E 287 " --> pdb=" O ASN E 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.516A pdb=" N CYS F 64 " --> pdb=" O LYS F 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA F 65 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU F 66 " --> pdb=" O LEU F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 66' Processing helix chain 'F' and resid 86 through 94 removed outlier: 4.270A pdb=" N LEU F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 124 removed outlier: 3.817A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.623A pdb=" N LEU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.939A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 288 removed outlier: 3.886A pdb=" N ARG F 286 " --> pdb=" O ASN F 283 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP F 288 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.618A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 Processing helix chain 'G' and resid 221 through 240 removed outlier: 3.532A pdb=" N TYR G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.016A pdb=" N ASP G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 252 " --> pdb=" O LEU G 248 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 285 removed outlier: 3.885A pdb=" N HIS G 274 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 324 Processing helix chain 'G' and resid 325 through 327 No H-bonds generated for 'chain 'G' and resid 325 through 327' Processing helix chain 'G' and resid 340 through 351 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.732A pdb=" N HIS G 378 " --> pdb=" O ARG G 374 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY G 380 " --> pdb=" O LEU G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.976A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 429 removed outlier: 3.515A pdb=" N LEU G 423 " --> pdb=" O GLY G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 463 removed outlier: 4.056A pdb=" N ASP G 462 " --> pdb=" O ASP G 459 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 463 " --> pdb=" O PRO G 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 459 through 463' Processing helix chain 'G' and resid 510 through 518 Proline residue: G 513 - end of helix removed outlier: 3.945A pdb=" N ARG G 517 " --> pdb=" O VAL G 514 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 518 " --> pdb=" O VAL G 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 217 removed outlier: 3.606A pdb=" N GLN H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY H 217 " --> pdb=" O GLN H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 240 removed outlier: 4.079A pdb=" N ASP H 239 " --> pdb=" O GLN H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 267 Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 271 through 287 Processing helix chain 'H' and resid 292 through 324 removed outlier: 3.566A pdb=" N ALA H 296 " --> pdb=" O ARG H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 removed outlier: 3.807A pdb=" N SER H 343 " --> pdb=" O SER H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 389 through 391 No H-bonds generated for 'chain 'H' and resid 389 through 391' Processing helix chain 'H' and resid 419 through 429 Processing helix chain 'H' and resid 511 through 518 removed outlier: 4.062A pdb=" N VAL H 514 " --> pdb=" O SER H 511 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL H 515 " --> pdb=" O VAL H 512 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 516 " --> pdb=" O PRO H 513 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG H 517 " --> pdb=" O VAL H 514 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL H 518 " --> pdb=" O VAL H 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 511 through 518' Processing helix chain 'I' and resid 74 through 86 removed outlier: 3.960A pdb=" N TYR I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 109 Processing helix chain 'I' and resid 110 through 113 Processing helix chain 'I' and resid 132 through 141 removed outlier: 3.704A pdb=" N ARG I 136 " --> pdb=" O GLY I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 254 through 263 Processing helix chain 'I' and resid 268 through 277 Processing helix chain 'I' and resid 302 through 313 Processing helix chain 'I' and resid 314 through 316 No H-bonds generated for 'chain 'I' and resid 314 through 316' Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.886A pdb=" N GLN I 333 " --> pdb=" O SER I 330 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER I 334 " --> pdb=" O THR I 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 330 through 334' Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.532A pdb=" N LEU J 68 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.895A pdb=" N GLY J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 106 removed outlier: 3.698A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 142 removed outlier: 3.861A pdb=" N LEU J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 163 removed outlier: 3.722A pdb=" N ARG J 163 " --> pdb=" O ASN J 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 160 through 163' Processing helix chain 'J' and resid 164 through 175 Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.999A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 277 removed outlier: 3.808A pdb=" N LEU J 277 " --> pdb=" O VAL J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 315 Processing helix chain 'J' and resid 338 through 342 removed outlier: 3.929A pdb=" N ASN J 341 " --> pdb=" O SER J 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 40 removed outlier: 3.640A pdb=" N TYR K 39 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 114 removed outlier: 3.996A pdb=" N SER K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 137 through 142 Processing helix chain 'K' and resid 147 through 159 removed outlier: 3.587A pdb=" N ASP K 151 " --> pdb=" O TYR K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 166 Processing helix chain 'K' and resid 169 through 173 Processing helix chain 'K' and resid 201 through 223 removed outlier: 3.535A pdb=" N GLU K 221 " --> pdb=" O ASN K 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN K 222 " --> pdb=" O CYS K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 261 removed outlier: 3.746A pdb=" N VAL K 250 " --> pdb=" O GLU K 246 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS K 261 " --> pdb=" O VAL K 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 107 removed outlier: 3.613A pdb=" N GLU L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 153 removed outlier: 3.663A pdb=" N TYR L 147 " --> pdb=" O LYS L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 180 removed outlier: 4.496A pdb=" N ILE L 180 " --> pdb=" O LEU L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 183 Processing helix chain 'M' and resid 184 through 186 No H-bonds generated for 'chain 'M' and resid 184 through 186' Processing helix chain 'P' and resid 55 through 62 removed outlier: 3.533A pdb=" N ILE P 61 " --> pdb=" O VAL P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 148 Processing helix chain 'P' and resid 196 through 200 removed outlier: 3.839A pdb=" N ALA P 200 " --> pdb=" O GLU P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 211 removed outlier: 3.585A pdb=" N GLN P 206 " --> pdb=" O GLU P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 236 Processing helix chain 'P' and resid 344 through 349 removed outlier: 3.965A pdb=" N ARG P 349 " --> pdb=" O THR P 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.925A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 5.911A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 178 removed outlier: 5.831A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 194 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 283 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 285 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.595A pdb=" N ILE B 207 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.062A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.372A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.483A pdb=" N SER C 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N LEU G 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG G 357 " --> pdb=" O GLY G 330 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL G 332 " --> pdb=" O ARG G 357 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL G 359 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 334 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL G 361 " --> pdb=" O LEU G 334 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS G 400 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU G 334 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 165 through 168 removed outlier: 5.768A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET D 217 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL D 191 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL D 216 " --> pdb=" O LEU H 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 232 through 234 removed outlier: 7.167A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 267 " --> pdb=" O LEU D 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 246 removed outlier: 3.732A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 239 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 54 removed outlier: 7.228A pdb=" N VAL E 53 " --> pdb=" O ILE E 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 103 removed outlier: 3.579A pdb=" N TYR E 205 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.602A pdb=" N ILE E 158 " --> pdb=" O HIS E 196 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 196 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL J 202 " --> pdb=" O GLN J 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AB8, first strand: chain 'E' and resid 397 through 398 removed outlier: 6.841A pdb=" N THR E 397 " --> pdb=" O ILE E 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.950A pdb=" N VAL F 53 " --> pdb=" O ILE F 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AC3, first strand: chain 'F' and resid 167 through 171 removed outlier: 4.635A pdb=" N PHE F 169 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY F 159 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 158 " --> pdb=" O HIS F 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL I 240 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 195 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG I 241 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL I 203 " --> pdb=" O ARG I 241 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 181 through 182 removed outlier: 3.808A pdb=" N ILE F 182 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE I 224 " --> pdb=" O ILE F 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 391 through 392 removed outlier: 6.744A pdb=" N LEU F 391 " --> pdb=" O ILE F 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AC7, first strand: chain 'F' and resid 419 through 420 removed outlier: 3.695A pdb=" N ASP F 420 " --> pdb=" O LYS F 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AC9, first strand: chain 'G' and resid 435 through 437 removed outlier: 6.626A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE G 507 " --> pdb=" O VAL G 500 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 333 through 335 removed outlier: 6.161A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 386 " --> pdb=" O VAL H 360 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 401 through 402 removed outlier: 6.497A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU H 499 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE H 507 " --> pdb=" O VAL H 500 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR H 502 " --> pdb=" O GLY H 505 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 407 through 409 Processing sheet with id=AD4, first strand: chain 'I' and resid 119 through 123 removed outlier: 6.275A pdb=" N THR I 91 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE I 123 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE I 92 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 47 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE I 94 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA I 49 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 251 " --> pdb=" O THR I 182 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR I 182 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 186 through 187 removed outlier: 4.014A pdb=" N LYS I 186 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 342 through 343 Processing sheet with id=AD7, first strand: chain 'I' and resid 366 through 367 Processing sheet with id=AD8, first strand: chain 'I' and resid 378 through 379 removed outlier: 6.383A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 390 through 392 removed outlier: 6.596A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'I' and resid 430 through 431 removed outlier: 7.171A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 46 through 48 removed outlier: 4.050A pdb=" N ILE J 251 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR J 182 " --> pdb=" O ILE J 251 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER J 179 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS J 288 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET J 181 " --> pdb=" O HIS J 288 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS J 290 " --> pdb=" O MET J 181 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET J 183 " --> pdb=" O HIS J 290 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 90 through 93 removed outlier: 6.246A pdb=" N THR J 91 " --> pdb=" O ARG J 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 356 through 358 removed outlier: 3.539A pdb=" N GLU J 357 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR J 375 " --> pdb=" O LEU J 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'J' and resid 366 through 367 Processing sheet with id=AE6, first strand: chain 'J' and resid 378 through 379 removed outlier: 7.618A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 418 through 419 removed outlier: 7.269A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 430 through 431 removed outlier: 7.216A pdb=" N VAL J 430 " --> pdb=" O ILE J 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.911A pdb=" N TYR K 33 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL K 72 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 191 through 194 Processing sheet with id=AF2, first strand: chain 'L' and resid 26 through 27 removed outlier: 3.704A pdb=" N SER L 26 " --> pdb=" O TYR L 33 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 72 through 73 Processing sheet with id=AF4, first strand: chain 'P' and resid 130 through 137 removed outlier: 6.907A pdb=" N ILE P 42 " --> pdb=" O SER P 131 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL P 133 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ILE P 44 " --> pdb=" O VAL P 133 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS P 135 " --> pdb=" O ILE P 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR P 46 " --> pdb=" O CYS P 135 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY P 137 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY P 48 " --> pdb=" O GLY P 137 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HIS P 49 " --> pdb=" O LEU P 158 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 256 through 257 Processing sheet with id=AF6, first strand: chain 'P' and resid 278 through 282 Processing sheet with id=AF7, first strand: chain 'P' and resid 371 through 373 removed outlier: 3.585A pdb=" N LEU P 371 " --> pdb=" O ILE P 427 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY P 425 " --> pdb=" O ILE P 373 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 411 through 414 removed outlier: 3.909A pdb=" N THR P 413 " --> pdb=" O VAL P 406 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL P 406 " --> pdb=" O THR P 413 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET P 405 " --> pdb=" O SER P 444 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2709 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: 9.58 Time building geometry restraints manager: 14.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10412 1.34 - 1.46: 5800 1.46 - 1.58: 16822 1.58 - 1.70: 1 1.70 - 1.82: 258 Bond restraints: 33293 Sorted by residual: bond pdb=" C LEU F 28 " pdb=" N PRO F 29 " ideal model delta sigma weight residual 1.333 1.388 -0.054 1.01e-02 9.80e+03 2.86e+01 bond pdb=" C LEU P 364 " pdb=" N PRO P 365 " ideal model delta sigma weight residual 1.332 1.397 -0.066 1.26e-02 6.30e+03 2.71e+01 bond pdb=" C PRO K 232 " pdb=" N PRO K 233 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.30e-02 5.92e+03 2.55e+01 bond pdb=" CA ILE F 229 " pdb=" CB ILE F 229 " ideal model delta sigma weight residual 1.534 1.565 -0.030 6.80e-03 2.16e+04 1.97e+01 bond pdb=" C LEU B 159 " pdb=" N SER B 160 " ideal model delta sigma weight residual 1.332 1.296 0.037 1.29e-02 6.01e+03 8.05e+00 ... (remaining 33288 not shown) Histogram of bond angle deviations from ideal: 95.20 - 104.35: 529 104.35 - 113.51: 18774 113.51 - 122.66: 21722 122.66 - 131.81: 4040 131.81 - 140.96: 44 Bond angle restraints: 45109 Sorted by residual: angle pdb=" N ASN F 32 " pdb=" CA ASN F 32 " pdb=" C ASN F 32 " ideal model delta sigma weight residual 113.12 103.11 10.01 1.25e+00 6.40e-01 6.41e+01 angle pdb=" N VAL P 447 " pdb=" CA VAL P 447 " pdb=" C VAL P 447 " ideal model delta sigma weight residual 113.71 107.34 6.37 9.50e-01 1.11e+00 4.50e+01 angle pdb=" C SER G 197 " pdb=" N ILE G 198 " pdb=" CA ILE G 198 " ideal model delta sigma weight residual 120.24 124.04 -3.80 6.30e-01 2.52e+00 3.64e+01 angle pdb=" C PHE J 57 " pdb=" N PRO J 58 " pdb=" CA PRO J 58 " ideal model delta sigma weight residual 127.00 140.96 -13.96 2.40e+00 1.74e-01 3.38e+01 angle pdb=" C SER I 189 " pdb=" N PRO I 190 " pdb=" CA PRO I 190 " ideal model delta sigma weight residual 119.05 125.49 -6.44 1.11e+00 8.12e-01 3.37e+01 ... (remaining 45104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 18619 17.49 - 34.98: 1363 34.98 - 52.47: 241 52.47 - 69.96: 16 69.96 - 87.45: 27 Dihedral angle restraints: 20266 sinusoidal: 7868 harmonic: 12398 Sorted by residual: dihedral pdb=" CA HIS L 114 " pdb=" C HIS L 114 " pdb=" N VAL L 115 " pdb=" CA VAL L 115 " ideal model delta harmonic sigma weight residual -180.00 -118.98 -61.02 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" CA GLU L 117 " pdb=" C GLU L 117 " pdb=" N VAL L 118 " pdb=" CA VAL L 118 " ideal model delta harmonic sigma weight residual -180.00 -129.17 -50.83 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA GLN B 156 " pdb=" C GLN B 156 " pdb=" N PRO B 157 " pdb=" CA PRO B 157 " ideal model delta harmonic sigma weight residual 180.00 131.96 48.04 0 5.00e+00 4.00e-02 9.23e+01 ... (remaining 20263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3904 0.073 - 0.145: 1174 0.145 - 0.218: 176 0.218 - 0.290: 36 0.290 - 0.363: 8 Chirality restraints: 5298 Sorted by residual: chirality pdb=" CB ILE I 408 " pdb=" CA ILE I 408 " pdb=" CG1 ILE I 408 " pdb=" CG2 ILE I 408 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU D 39 " pdb=" CB LEU D 39 " pdb=" CD1 LEU D 39 " pdb=" CD2 LEU D 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB ILE F 36 " pdb=" CA ILE F 36 " pdb=" CG1 ILE F 36 " pdb=" CG2 ILE F 36 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 5295 not shown) Planarity restraints: 5784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 156 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO B 157 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 45 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C LEU A 45 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 45 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG A 46 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET K 223 " 0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO K 224 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO K 224 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 224 " 0.046 5.00e-02 4.00e+02 ... (remaining 5781 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1985 2.71 - 3.26: 32023 3.26 - 3.81: 54894 3.81 - 4.35: 63002 4.35 - 4.90: 101553 Nonbonded interactions: 253457 Sorted by model distance: nonbonded pdb=" ND1 HIS I 192 " pdb=" CG2 THR I 194 " model vdw 2.168 3.540 nonbonded pdb=" CE1 HIS I 192 " pdb=" CB THR I 194 " model vdw 2.190 3.690 nonbonded pdb=" O PRO I 193 " pdb=" N ARG I 195 " model vdw 2.206 2.520 nonbonded pdb=" O ARG B 46 " pdb=" OG1 THR B 50 " model vdw 2.259 2.440 nonbonded pdb=" O ALA P 84 " pdb=" OG SER P 131 " model vdw 2.259 2.440 ... (remaining 253452 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 'A' and resid 5 through 305) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 267 or resid 276 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' 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 group one per residue 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: 2.220 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: 0.110 Extract box with map and model: 5.700 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 83.940 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.006 0.091 33293 Z= 0.410 Angle : 1.304 18.472 45109 Z= 0.722 Chirality : 0.069 0.363 5298 Planarity : 0.008 0.107 5784 Dihedral : 12.854 87.445 12218 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.97 % Favored : 85.91 % Rotamer: Outliers : 1.37 % Allowed : 10.79 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 3.49 % Twisted General : 0.69 % 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: -5.39 (0.10), residues: 4188 helix: -3.29 (0.10), residues: 1288 sheet: -3.73 (0.18), residues: 492 loop : -3.87 (0.10), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP I 97 HIS 0.021 0.002 HIS B 128 PHE 0.032 0.004 PHE L 102 TYR 0.044 0.004 TYR G 441 ARG 0.012 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 753 time to evaluate : 3.861 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.5341 (ptp) cc_final: 0.4726 (mtp) REVERT: A 78 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6768 (pp) REVERT: A 187 MET cc_start: 0.7754 (tpt) cc_final: 0.7330 (tpt) REVERT: A 213 ASN cc_start: 0.8615 (p0) cc_final: 0.8331 (p0) REVERT: A 298 ASP cc_start: 0.7604 (t70) cc_final: 0.7136 (t0) REVERT: B 88 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7903 (pmmt) REVERT: B 208 ASN cc_start: 0.8357 (t0) cc_final: 0.7928 (t0) REVERT: B 222 GLN cc_start: 0.8244 (mm110) cc_final: 0.7529 (mm110) REVERT: B 227 TYR cc_start: 0.7826 (m-10) cc_final: 0.7541 (m-10) REVERT: B 242 ASN cc_start: 0.8637 (p0) cc_final: 0.8373 (p0) REVERT: C 18 PHE cc_start: 0.7585 (m-10) cc_final: 0.6704 (m-10) REVERT: C 148 MET cc_start: 0.7445 (mtm) cc_final: 0.6757 (pmm) REVERT: C 203 MET cc_start: 0.8548 (ttt) cc_final: 0.8233 (ttp) REVERT: C 335 TYR cc_start: 0.7599 (t80) cc_final: 0.7290 (t80) REVERT: D 137 ILE cc_start: 0.8995 (pp) cc_final: 0.8790 (pp) REVERT: D 189 VAL cc_start: 0.6089 (p) cc_final: 0.5565 (p) REVERT: D 191 VAL cc_start: 0.6870 (t) cc_final: 0.6343 (p) REVERT: E 64 CYS cc_start: 0.8067 (m) cc_final: 0.7793 (p) REVERT: E 213 ASP cc_start: 0.7762 (p0) cc_final: 0.7268 (p0) REVERT: E 214 PHE cc_start: 0.6711 (t80) cc_final: 0.6487 (t80) REVERT: F 56 THR cc_start: 0.8327 (t) cc_final: 0.8001 (m) REVERT: F 71 MET cc_start: 0.8069 (ppp) cc_final: 0.7715 (ppp) REVERT: F 170 MET cc_start: 0.6869 (tmt) cc_final: 0.6303 (tmm) REVERT: F 188 GLN cc_start: 0.8497 (tt0) cc_final: 0.8010 (pp30) REVERT: G 233 LEU cc_start: 0.8176 (pp) cc_final: 0.7943 (tt) REVERT: G 275 ASN cc_start: 0.8521 (p0) cc_final: 0.8283 (p0) REVERT: G 324 TYR cc_start: 0.7323 (t80) cc_final: 0.7106 (t80) REVERT: G 362 ASP cc_start: 0.7927 (t0) cc_final: 0.7724 (t0) REVERT: G 385 TYR cc_start: 0.7424 (t80) cc_final: 0.7097 (t80) REVERT: G 506 MET cc_start: 0.5689 (tmt) cc_final: 0.5292 (tmt) REVERT: H 196 MET cc_start: 0.7520 (pp-130) cc_final: 0.7219 (ppp) REVERT: H 237 ILE cc_start: 0.9304 (pp) cc_final: 0.9026 (pp) REVERT: H 239 ASP cc_start: 0.8453 (p0) cc_final: 0.8133 (p0) REVERT: H 259 TYR cc_start: 0.8320 (m-10) cc_final: 0.8071 (m-80) REVERT: H 306 ARG cc_start: 0.8248 (ppt170) cc_final: 0.7684 (ttp80) REVERT: H 307 TYR cc_start: 0.8789 (t80) cc_final: 0.8306 (t80) REVERT: H 336 TYR cc_start: 0.8728 (t80) cc_final: 0.8055 (t80) REVERT: H 397 GLU cc_start: 0.8343 (mp0) cc_final: 0.8071 (mp0) REVERT: H 469 GLU cc_start: 0.7692 (pm20) cc_final: 0.6889 (mt-10) REVERT: I 96 CYS cc_start: 0.7519 (t) cc_final: 0.7258 (t) REVERT: I 242 TYR cc_start: 0.7050 (t80) cc_final: 0.6671 (t80) REVERT: I 342 ILE cc_start: 0.8288 (mm) cc_final: 0.7969 (tt) REVERT: I 357 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7776 (mp0) REVERT: J 158 ASN cc_start: 0.8279 (p0) cc_final: 0.7594 (p0) REVERT: J 239 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6359 (mm-30) REVERT: J 251 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7981 (pp) REVERT: J 329 ASP cc_start: 0.8210 (m-30) cc_final: 0.7654 (m-30) REVERT: K 41 ASN cc_start: 0.7860 (m-40) cc_final: 0.6697 (p0) REVERT: K 102 PHE cc_start: 0.8809 (t80) cc_final: 0.8363 (t80) REVERT: L 18 ASP cc_start: 0.7396 (m-30) cc_final: 0.6408 (t0) REVERT: L 21 MET cc_start: 0.7544 (mpm) cc_final: 0.7132 (mtp) REVERT: L 99 GLU cc_start: 0.8426 (mp0) cc_final: 0.8212 (tm-30) REVERT: P 152 MET cc_start: 0.3646 (ptt) cc_final: 0.3420 (mmm) REVERT: P 185 ILE cc_start: 0.5631 (mt) cc_final: 0.5355 (pt) REVERT: P 257 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6486 (tt) outliers start: 48 outliers final: 12 residues processed: 786 average time/residue: 0.4371 time to fit residues: 543.7850 Evaluate side-chains 467 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 451 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 108 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 380 optimal weight: 0.5980 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS C 138 ASN C 242 ASN C 345 HIS D 72 GLN D 138 ASN D 154 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 274 ASN F 41 ASN F 196 HIS G 166 GLN G 182 HIS G 234 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN G 347 GLN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 HIS ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN H 431 ASN ** H 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 HIS I 248 HIS ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS J 72 ASN J 105 HIS ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 HIS ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 452 HIS P 85 ASN P 138 HIS P 231 ASN P 325 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33293 Z= 0.242 Angle : 0.823 13.124 45109 Z= 0.428 Chirality : 0.051 0.249 5298 Planarity : 0.006 0.079 5784 Dihedral : 8.012 52.673 4586 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.87 % Favored : 87.08 % Rotamer: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.35 % 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: -4.45 (0.11), residues: 4188 helix: -2.15 (0.12), residues: 1297 sheet: -3.28 (0.21), residues: 450 loop : -3.51 (0.11), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 111 HIS 0.011 0.001 HIS P 325 PHE 0.034 0.002 PHE J 94 TYR 0.031 0.002 TYR H 489 ARG 0.010 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 608 time to evaluate : 4.201 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: 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: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7231 (pp) REVERT: A 187 MET cc_start: 0.8094 (tpt) cc_final: 0.7802 (tpt) REVERT: A 298 ASP cc_start: 0.7656 (t70) cc_final: 0.7428 (t0) REVERT: B 20 MET cc_start: 0.3280 (tpp) cc_final: 0.2753 (tpt) REVERT: B 49 LEU cc_start: 0.8834 (mt) cc_final: 0.8632 (mt) REVERT: B 88 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7765 (pttm) REVERT: B 130 TYR cc_start: 0.7663 (t80) cc_final: 0.7327 (t80) REVERT: B 222 GLN cc_start: 0.8284 (mm110) cc_final: 0.8069 (mp10) REVERT: B 223 ASN cc_start: 0.7037 (t0) cc_final: 0.6829 (t0) REVERT: B 242 ASN cc_start: 0.8655 (p0) cc_final: 0.8455 (p0) REVERT: C 34 MET cc_start: 0.7819 (mpp) cc_final: 0.7411 (mmt) REVERT: C 166 MET cc_start: 0.7594 (tpt) cc_final: 0.7272 (tpt) REVERT: C 203 MET cc_start: 0.8526 (ttt) cc_final: 0.8077 (ttp) REVERT: C 238 THR cc_start: 0.7894 (p) cc_final: 0.7615 (p) REVERT: C 281 GLU cc_start: 0.7848 (tp30) cc_final: 0.7592 (mp0) REVERT: D 191 VAL cc_start: 0.6775 (t) cc_final: 0.6550 (p) REVERT: E 69 MET cc_start: 0.3614 (ppp) cc_final: 0.2616 (pmm) REVERT: E 132 MET cc_start: 0.6205 (mmp) cc_final: 0.5953 (mmm) REVERT: E 213 ASP cc_start: 0.7647 (p0) cc_final: 0.7039 (p0) REVERT: F 204 LEU cc_start: 0.9092 (tt) cc_final: 0.8828 (mp) REVERT: G 171 LYS cc_start: 0.3948 (pttp) cc_final: 0.3616 (mttt) REVERT: G 197 SER cc_start: 0.8230 (m) cc_final: 0.7549 (p) REVERT: G 325 GLN cc_start: 0.6340 (pt0) cc_final: 0.5789 (tm-30) REVERT: G 452 PHE cc_start: 0.5956 (m-80) cc_final: 0.5645 (m-80) REVERT: H 239 ASP cc_start: 0.8870 (p0) cc_final: 0.8651 (p0) REVERT: H 336 TYR cc_start: 0.8833 (t80) cc_final: 0.8021 (t80) REVERT: H 397 GLU cc_start: 0.8281 (mp0) cc_final: 0.7882 (mp0) REVERT: I 265 ASP cc_start: 0.8423 (p0) cc_final: 0.8124 (p0) REVERT: I 357 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7919 (mp0) REVERT: J 63 GLN cc_start: 0.7253 (tt0) cc_final: 0.6602 (tt0) REVERT: J 75 LEU cc_start: 0.7355 (pt) cc_final: 0.7101 (pt) REVERT: J 158 ASN cc_start: 0.8007 (p0) cc_final: 0.7483 (p0) REVERT: J 183 MET cc_start: 0.6955 (ttm) cc_final: 0.6661 (ttm) REVERT: K 41 ASN cc_start: 0.7866 (m-40) cc_final: 0.6727 (p0) REVERT: K 102 PHE cc_start: 0.8563 (t80) cc_final: 0.8122 (t80) REVERT: K 218 CYS cc_start: 0.7739 (m) cc_final: 0.7141 (t) REVERT: L 18 ASP cc_start: 0.7079 (m-30) cc_final: 0.6241 (t0) REVERT: L 46 ILE cc_start: 0.7864 (mm) cc_final: 0.7549 (mm) REVERT: L 131 PHE cc_start: 0.7327 (m-10) cc_final: 0.6927 (m-10) REVERT: P 180 MET cc_start: 0.2910 (mtm) cc_final: 0.2663 (mtt) REVERT: P 238 TYR cc_start: 0.6576 (m-10) cc_final: 0.6166 (m-80) outliers start: 6 outliers final: 1 residues processed: 612 average time/residue: 0.4156 time to fit residues: 415.6247 Evaluate side-chains 465 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 463 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 316 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 381 optimal weight: 20.0000 chunk 411 optimal weight: 0.0170 chunk 339 optimal weight: 9.9990 chunk 378 optimal weight: 40.0000 chunk 129 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN G 182 HIS ** G 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33293 Z= 0.195 Angle : 0.763 13.311 45109 Z= 0.388 Chirality : 0.050 0.252 5298 Planarity : 0.005 0.076 5784 Dihedral : 7.337 49.833 4586 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.06 % Favored : 87.89 % Rotamer: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.22 % 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: -4.05 (0.12), residues: 4188 helix: -1.60 (0.13), residues: 1303 sheet: -3.03 (0.21), residues: 498 loop : -3.39 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 111 HIS 0.007 0.001 HIS I 452 PHE 0.030 0.002 PHE J 94 TYR 0.032 0.002 TYR H 489 ARG 0.010 0.000 ARG J 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 605 time to evaluate : 4.032 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: 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: A 187 MET cc_start: 0.8023 (tpt) cc_final: 0.7540 (tpt) REVERT: A 238 LEU cc_start: 0.8978 (tp) cc_final: 0.8659 (tp) REVERT: A 298 ASP cc_start: 0.7666 (t70) cc_final: 0.7398 (t0) REVERT: B 20 MET cc_start: 0.3045 (tpp) cc_final: 0.2451 (tpt) REVERT: B 130 TYR cc_start: 0.7546 (t80) cc_final: 0.7340 (t80) REVERT: B 222 GLN cc_start: 0.8305 (mm110) cc_final: 0.8081 (mp10) REVERT: B 223 ASN cc_start: 0.6998 (t0) cc_final: 0.6714 (t0) REVERT: C 34 MET cc_start: 0.7413 (mpp) cc_final: 0.6552 (mpp) REVERT: C 154 GLN cc_start: 0.8964 (mt0) cc_final: 0.8712 (mt0) REVERT: C 166 MET cc_start: 0.7479 (tpt) cc_final: 0.6177 (mtm) REVERT: C 203 MET cc_start: 0.8371 (ttt) cc_final: 0.7675 (ttp) REVERT: C 281 GLU cc_start: 0.8040 (tp30) cc_final: 0.7566 (mp0) REVERT: C 325 ILE cc_start: 0.9129 (tp) cc_final: 0.8701 (mp) REVERT: D 137 ILE cc_start: 0.8862 (pt) cc_final: 0.8650 (pt) REVERT: D 348 ASP cc_start: 0.7059 (m-30) cc_final: 0.6817 (m-30) REVERT: E 69 MET cc_start: 0.3384 (ppp) cc_final: 0.2426 (pmm) REVERT: E 213 ASP cc_start: 0.7803 (p0) cc_final: 0.7249 (p0) REVERT: E 216 MET cc_start: 0.7449 (mmt) cc_final: 0.7162 (mmt) REVERT: G 196 MET cc_start: 0.5441 (tpp) cc_final: 0.5203 (tpp) REVERT: G 197 SER cc_start: 0.8578 (m) cc_final: 0.8053 (p) REVERT: G 325 GLN cc_start: 0.6637 (pt0) cc_final: 0.5736 (tm-30) REVERT: G 506 MET cc_start: 0.5474 (tmm) cc_final: 0.5232 (tmm) REVERT: H 196 MET cc_start: 0.7224 (ppp) cc_final: 0.6794 (ppp) REVERT: H 306 ARG cc_start: 0.7690 (ppt170) cc_final: 0.7317 (ttp80) REVERT: H 329 ASN cc_start: 0.8552 (m110) cc_final: 0.7775 (t0) REVERT: H 336 TYR cc_start: 0.8870 (t80) cc_final: 0.8064 (t80) REVERT: I 169 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7728 (ttm110) REVERT: I 173 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8475 (mmtm) REVERT: I 260 PHE cc_start: 0.8359 (p90) cc_final: 0.7631 (p90) REVERT: I 265 ASP cc_start: 0.8396 (p0) cc_final: 0.8192 (p0) REVERT: I 357 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7743 (mp0) REVERT: J 63 GLN cc_start: 0.6880 (tt0) cc_final: 0.6359 (tt0) REVERT: J 75 LEU cc_start: 0.7294 (pt) cc_final: 0.7089 (pt) REVERT: J 158 ASN cc_start: 0.7938 (p0) cc_final: 0.7424 (p0) REVERT: J 183 MET cc_start: 0.6003 (ttm) cc_final: 0.5648 (ttp) REVERT: K 21 MET cc_start: 0.8753 (mmm) cc_final: 0.7453 (mmm) REVERT: K 41 ASN cc_start: 0.7404 (m-40) cc_final: 0.6363 (p0) REVERT: K 218 CYS cc_start: 0.7658 (m) cc_final: 0.7085 (t) REVERT: L 18 ASP cc_start: 0.7049 (m-30) cc_final: 0.6165 (t0) REVERT: L 46 ILE cc_start: 0.7814 (mm) cc_final: 0.6989 (mp) REVERT: L 131 PHE cc_start: 0.7219 (m-10) cc_final: 0.6770 (m-10) REVERT: P 113 PHE cc_start: 0.3097 (m-10) cc_final: 0.2478 (p90) REVERT: P 180 MET cc_start: 0.2522 (mtm) cc_final: 0.2270 (mtt) REVERT: P 238 TYR cc_start: 0.6606 (m-10) cc_final: 0.6289 (m-80) outliers start: 1 outliers final: 0 residues processed: 606 average time/residue: 0.4064 time to fit residues: 402.8190 Evaluate side-chains 453 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 181 optimal weight: 50.0000 chunk 255 optimal weight: 9.9990 chunk 382 optimal weight: 9.9990 chunk 405 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 362 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 222 GLN D 72 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 HIS J 72 ASN ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 HIS J 304 HIS ** J 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 ASN L 179 ASN ** P 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 33293 Z= 0.449 Angle : 0.952 15.115 45109 Z= 0.500 Chirality : 0.055 0.300 5298 Planarity : 0.006 0.074 5784 Dihedral : 7.914 50.306 4586 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.14 % Favored : 83.79 % Rotamer: Outliers : 0.20 % Allowed : 7.14 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.30 % 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: -4.26 (0.11), residues: 4188 helix: -1.81 (0.12), residues: 1334 sheet: -3.15 (0.22), residues: 422 loop : -3.54 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP J 111 HIS 0.013 0.002 HIS I 105 PHE 0.036 0.003 PHE G 180 TYR 0.039 0.003 TYR C 93 ARG 0.010 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 514 time to evaluate : 3.878 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: A 14 MET cc_start: 0.3915 (ptt) cc_final: 0.3586 (ptt) REVERT: A 48 ASN cc_start: 0.8963 (t0) cc_final: 0.8754 (t0) REVERT: A 222 GLN cc_start: 0.7964 (mp10) cc_final: 0.7736 (mp10) REVERT: A 298 ASP cc_start: 0.7701 (t70) cc_final: 0.7308 (t0) REVERT: B 20 MET cc_start: 0.3604 (tpp) cc_final: 0.3320 (tpt) REVERT: B 24 VAL cc_start: 0.6492 (OUTLIER) cc_final: 0.6011 (p) REVERT: B 223 ASN cc_start: 0.7594 (t0) cc_final: 0.7319 (t0) REVERT: C 154 GLN cc_start: 0.9287 (mt0) cc_final: 0.9059 (mt0) REVERT: C 166 MET cc_start: 0.6708 (tpt) cc_final: 0.5507 (mtm) REVERT: C 325 ILE cc_start: 0.9382 (tp) cc_final: 0.8850 (mp) REVERT: E 70 LYS cc_start: 0.5526 (tppt) cc_final: 0.4923 (tppt) REVERT: E 177 ASP cc_start: 0.7500 (m-30) cc_final: 0.7213 (m-30) REVERT: F 71 MET cc_start: 0.8278 (ppp) cc_final: 0.8048 (ppp) REVERT: F 188 GLN cc_start: 0.8629 (tt0) cc_final: 0.8078 (pp30) REVERT: F 204 LEU cc_start: 0.9165 (tt) cc_final: 0.8896 (mp) REVERT: F 264 TYR cc_start: 0.5959 (t80) cc_final: 0.5149 (t80) REVERT: H 196 MET cc_start: 0.7497 (ppp) cc_final: 0.7006 (ppp) REVERT: H 306 ARG cc_start: 0.7849 (ppt170) cc_final: 0.7528 (ttp80) REVERT: H 397 GLU cc_start: 0.8658 (mp0) cc_final: 0.8280 (mp0) REVERT: H 409 LEU cc_start: 0.8742 (tt) cc_final: 0.8536 (tt) REVERT: H 415 MET cc_start: 0.6694 (mmm) cc_final: 0.5831 (mmm) REVERT: H 469 GLU cc_start: 0.7284 (pm20) cc_final: 0.6898 (pt0) REVERT: I 169 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7774 (ttm110) REVERT: I 173 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8504 (mmtm) REVERT: I 181 MET cc_start: 0.8161 (tpp) cc_final: 0.7673 (tpp) REVERT: I 265 ASP cc_start: 0.8496 (p0) cc_final: 0.8246 (p0) REVERT: I 357 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8129 (mp0) REVERT: J 63 GLN cc_start: 0.7437 (tt0) cc_final: 0.7134 (tt0) REVERT: J 183 MET cc_start: 0.6490 (ttm) cc_final: 0.6277 (ttp) REVERT: J 289 MET cc_start: 0.7370 (tpp) cc_final: 0.7157 (tpp) REVERT: K 21 MET cc_start: 0.8765 (mmm) cc_final: 0.7564 (mmm) REVERT: K 218 CYS cc_start: 0.7520 (m) cc_final: 0.6697 (t) REVERT: L 18 ASP cc_start: 0.7292 (m-30) cc_final: 0.6480 (t0) REVERT: L 21 MET cc_start: 0.7709 (mmp) cc_final: 0.6259 (mtp) REVERT: L 89 ARG cc_start: 0.6910 (pmt170) cc_final: 0.6659 (pmt170) REVERT: L 131 PHE cc_start: 0.7490 (m-10) cc_final: 0.6904 (m-80) REVERT: P 180 MET cc_start: 0.0998 (mtm) cc_final: 0.0747 (mtt) REVERT: P 238 TYR cc_start: 0.6815 (m-10) cc_final: 0.6389 (m-80) outliers start: 7 outliers final: 4 residues processed: 519 average time/residue: 0.4055 time to fit residues: 346.9328 Evaluate side-chains 398 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 393 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 301 optimal weight: 6.9990 chunk 167 optimal weight: 0.0670 chunk 345 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN G 182 HIS ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 HIS I 200 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS J 72 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33293 Z= 0.197 Angle : 0.781 13.123 45109 Z= 0.393 Chirality : 0.051 0.267 5298 Planarity : 0.005 0.079 5784 Dihedral : 7.126 47.495 4586 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.13 % Favored : 88.83 % Rotamer: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.22 % 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: -3.76 (0.12), residues: 4188 helix: -1.21 (0.13), residues: 1300 sheet: -2.82 (0.22), residues: 470 loop : -3.33 (0.11), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 97 HIS 0.007 0.001 HIS B 128 PHE 0.031 0.002 PHE J 94 TYR 0.029 0.002 TYR H 489 ARG 0.006 0.000 ARG C 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 588 time to evaluate : 3.595 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: 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: A 298 ASP cc_start: 0.7896 (t70) cc_final: 0.7512 (t0) REVERT: B 20 MET cc_start: 0.3426 (tpp) cc_final: 0.3132 (tpt) REVERT: B 209 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7406 (mmtt) REVERT: B 222 GLN cc_start: 0.8683 (mm110) cc_final: 0.8375 (mp10) REVERT: B 223 ASN cc_start: 0.7401 (t0) cc_final: 0.7049 (t0) REVERT: C 154 GLN cc_start: 0.9156 (mt0) cc_final: 0.8847 (mt0) REVERT: C 166 MET cc_start: 0.7422 (tpt) cc_final: 0.6241 (mtm) REVERT: C 203 MET cc_start: 0.7294 (ttp) cc_final: 0.7083 (ttp) REVERT: C 238 THR cc_start: 0.7487 (p) cc_final: 0.7178 (p) REVERT: C 325 ILE cc_start: 0.9414 (tp) cc_final: 0.9031 (mp) REVERT: D 191 VAL cc_start: 0.7383 (p) cc_final: 0.7061 (p) REVERT: D 273 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7346 (mtpt) REVERT: D 288 PHE cc_start: 0.6736 (m-80) cc_final: 0.6066 (m-80) REVERT: E 158 ILE cc_start: 0.5713 (tt) cc_final: 0.5451 (tt) REVERT: E 225 ARG cc_start: 0.8155 (ttt-90) cc_final: 0.7422 (mmm160) REVERT: F 71 MET cc_start: 0.8071 (ppp) cc_final: 0.7808 (ppp) REVERT: F 170 MET cc_start: 0.7538 (tmm) cc_final: 0.7313 (tmm) REVERT: F 204 LEU cc_start: 0.8981 (tt) cc_final: 0.8708 (mp) REVERT: G 197 SER cc_start: 0.8206 (m) cc_final: 0.7653 (p) REVERT: G 485 LEU cc_start: 0.8439 (tp) cc_final: 0.8208 (tp) REVERT: H 185 GLN cc_start: 0.6222 (tm-30) cc_final: 0.5865 (tm-30) REVERT: H 196 MET cc_start: 0.7381 (ppp) cc_final: 0.7070 (ppp) REVERT: H 259 TYR cc_start: 0.8385 (m-80) cc_final: 0.7535 (m-80) REVERT: H 306 ARG cc_start: 0.7802 (ppt170) cc_final: 0.7432 (ttp80) REVERT: H 307 TYR cc_start: 0.9206 (t80) cc_final: 0.8468 (t80) REVERT: I 169 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7634 (ttm110) REVERT: I 181 MET cc_start: 0.7914 (tpp) cc_final: 0.7651 (tpp) REVERT: I 189 SER cc_start: 0.9472 (m) cc_final: 0.9268 (m) REVERT: I 260 PHE cc_start: 0.7687 (p90) cc_final: 0.7145 (p90) REVERT: J 63 GLN cc_start: 0.7199 (tt0) cc_final: 0.6794 (tt0) REVERT: J 158 ASN cc_start: 0.7322 (p0) cc_final: 0.6640 (p0) REVERT: J 183 MET cc_start: 0.5962 (ttm) cc_final: 0.5743 (ttm) REVERT: K 21 MET cc_start: 0.8715 (mmm) cc_final: 0.7903 (mmm) REVERT: K 41 ASN cc_start: 0.6951 (m-40) cc_final: 0.5977 (p0) REVERT: K 218 CYS cc_start: 0.7640 (m) cc_final: 0.7070 (t) REVERT: L 18 ASP cc_start: 0.7083 (m-30) cc_final: 0.6221 (t0) REVERT: L 131 PHE cc_start: 0.7204 (m-10) cc_final: 0.6971 (m-10) REVERT: P 238 TYR cc_start: 0.6988 (m-10) cc_final: 0.6489 (m-80) REVERT: P 456 TRP cc_start: 0.4662 (m-90) cc_final: 0.4032 (m-90) outliers start: 2 outliers final: 1 residues processed: 589 average time/residue: 0.4282 time to fit residues: 416.8501 Evaluate side-chains 466 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 9.9990 chunk 364 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 237 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN F 203 HIS G 182 HIS ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33293 Z= 0.198 Angle : 0.758 13.559 45109 Z= 0.381 Chirality : 0.050 0.250 5298 Planarity : 0.005 0.102 5784 Dihedral : 6.822 48.478 4586 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.94 % Favored : 88.01 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.17 % 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: -3.55 (0.12), residues: 4188 helix: -0.96 (0.14), residues: 1304 sheet: -2.76 (0.22), residues: 459 loop : -3.24 (0.11), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 111 HIS 0.007 0.001 HIS B 128 PHE 0.027 0.002 PHE J 94 TYR 0.029 0.002 TYR H 489 ARG 0.010 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 4.249 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.3386 (ptt) cc_final: 0.2413 (ptm) REVERT: A 298 ASP cc_start: 0.7945 (t70) cc_final: 0.7636 (t0) REVERT: B 173 VAL cc_start: 0.8230 (t) cc_final: 0.8000 (t) REVERT: B 222 GLN cc_start: 0.8667 (mm110) cc_final: 0.8416 (mp10) REVERT: B 223 ASN cc_start: 0.7293 (t0) cc_final: 0.6900 (t0) REVERT: C 18 PHE cc_start: 0.8153 (m-10) cc_final: 0.7693 (m-80) REVERT: C 34 MET cc_start: 0.7009 (mpp) cc_final: 0.6438 (mpp) REVERT: C 81 MET cc_start: 0.7211 (ppp) cc_final: 0.6955 (ppp) REVERT: C 154 GLN cc_start: 0.9201 (mt0) cc_final: 0.8914 (mt0) REVERT: C 166 MET cc_start: 0.6966 (tpt) cc_final: 0.6092 (mtm) REVERT: C 238 THR cc_start: 0.7587 (p) cc_final: 0.7314 (p) REVERT: C 325 ILE cc_start: 0.9271 (tp) cc_final: 0.8881 (mp) REVERT: D 191 VAL cc_start: 0.7364 (p) cc_final: 0.7109 (p) REVERT: D 273 LYS cc_start: 0.7951 (mtpt) cc_final: 0.6967 (mtpt) REVERT: D 320 LEU cc_start: 0.8448 (mt) cc_final: 0.8190 (mt) REVERT: D 348 ASP cc_start: 0.7165 (m-30) cc_final: 0.6886 (m-30) REVERT: E 225 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.7557 (mmm-85) REVERT: E 231 TYR cc_start: 0.6622 (p90) cc_final: 0.6232 (p90) REVERT: F 204 LEU cc_start: 0.8997 (tt) cc_final: 0.8693 (mp) REVERT: G 197 SER cc_start: 0.7952 (m) cc_final: 0.7715 (p) REVERT: G 482 LEU cc_start: 0.8676 (tp) cc_final: 0.8474 (tp) REVERT: G 485 LEU cc_start: 0.8538 (tp) cc_final: 0.8326 (tp) REVERT: H 185 GLN cc_start: 0.6115 (tm-30) cc_final: 0.5841 (tm-30) REVERT: H 189 GLN cc_start: 0.6432 (mm110) cc_final: 0.6231 (tp40) REVERT: H 196 MET cc_start: 0.7189 (ppp) cc_final: 0.6749 (ppp) REVERT: H 259 TYR cc_start: 0.8329 (m-80) cc_final: 0.7446 (m-80) REVERT: H 306 ARG cc_start: 0.7589 (ppt170) cc_final: 0.7226 (ttp80) REVERT: H 411 ASN cc_start: 0.8102 (m110) cc_final: 0.7762 (m110) REVERT: I 169 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7936 (ttm110) REVERT: I 260 PHE cc_start: 0.7616 (p90) cc_final: 0.7101 (p90) REVERT: J 63 GLN cc_start: 0.7167 (tt0) cc_final: 0.6768 (tt0) REVERT: J 158 ASN cc_start: 0.7366 (p0) cc_final: 0.6596 (p0) REVERT: K 21 MET cc_start: 0.8594 (mmm) cc_final: 0.7734 (mmm) REVERT: K 41 ASN cc_start: 0.7007 (m-40) cc_final: 0.5971 (p0) REVERT: K 218 CYS cc_start: 0.7633 (m) cc_final: 0.7059 (t) REVERT: L 18 ASP cc_start: 0.7061 (m-30) cc_final: 0.6173 (t0) REVERT: L 21 MET cc_start: 0.6617 (mmp) cc_final: 0.5583 (mtp) REVERT: L 69 GLU cc_start: 0.4986 (tp30) cc_final: 0.4409 (tp30) REVERT: P 185 ILE cc_start: 0.4110 (mm) cc_final: 0.3716 (pt) REVERT: P 238 TYR cc_start: 0.7017 (m-10) cc_final: 0.6486 (m-80) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 0.4088 time to fit residues: 383.4556 Evaluate side-chains 453 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 390 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 341 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 403 optimal weight: 9.9990 chunk 252 optimal weight: 0.3980 chunk 246 optimal weight: 0.0270 chunk 186 optimal weight: 0.0770 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN D 72 GLN G 182 HIS G 265 GLN G 347 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33293 Z= 0.181 Angle : 0.754 13.507 45109 Z= 0.376 Chirality : 0.049 0.230 5298 Planarity : 0.005 0.075 5784 Dihedral : 6.582 48.254 4586 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.82 % Favored : 89.14 % Rotamer: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.10 % 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: -3.41 (0.12), residues: 4188 helix: -0.84 (0.14), residues: 1297 sheet: -2.67 (0.21), residues: 525 loop : -3.14 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 51 HIS 0.007 0.001 HIS D 49 PHE 0.030 0.002 PHE P 113 TYR 0.038 0.002 TYR G 214 ARG 0.009 0.000 ARG G 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 590 time to evaluate : 5.317 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.3700 (ptt) cc_final: 0.3029 (ptm) REVERT: A 104 ILE cc_start: 0.7218 (mm) cc_final: 0.6941 (mm) REVERT: A 238 LEU cc_start: 0.8696 (tp) cc_final: 0.8336 (tt) REVERT: B 173 VAL cc_start: 0.8282 (t) cc_final: 0.8057 (t) REVERT: B 222 GLN cc_start: 0.8659 (mm110) cc_final: 0.8413 (mp10) REVERT: B 223 ASN cc_start: 0.7042 (t0) cc_final: 0.6798 (t0) REVERT: C 23 LYS cc_start: 0.8424 (pttt) cc_final: 0.7959 (tptm) REVERT: C 34 MET cc_start: 0.7009 (mpp) cc_final: 0.6574 (mpp) REVERT: C 154 GLN cc_start: 0.9183 (mt0) cc_final: 0.8887 (mt0) REVERT: C 166 MET cc_start: 0.7464 (tpt) cc_final: 0.6095 (mtm) REVERT: C 238 THR cc_start: 0.7770 (p) cc_final: 0.7381 (p) REVERT: C 325 ILE cc_start: 0.9269 (tp) cc_final: 0.8921 (mp) REVERT: D 191 VAL cc_start: 0.7559 (p) cc_final: 0.7325 (p) REVERT: D 320 LEU cc_start: 0.8448 (mt) cc_final: 0.8175 (mt) REVERT: D 340 MET cc_start: 0.7189 (mmm) cc_final: 0.6931 (mmt) REVERT: D 348 ASP cc_start: 0.7063 (m-30) cc_final: 0.6784 (m-30) REVERT: E 225 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7161 (mmm-85) REVERT: E 231 TYR cc_start: 0.6433 (p90) cc_final: 0.6223 (p90) REVERT: F 204 LEU cc_start: 0.9043 (tt) cc_final: 0.8703 (mp) REVERT: F 205 TYR cc_start: 0.7230 (m-80) cc_final: 0.6908 (m-80) REVERT: G 452 PHE cc_start: 0.6331 (m-80) cc_final: 0.5546 (m-10) REVERT: H 185 GLN cc_start: 0.6211 (tm-30) cc_final: 0.6001 (tm-30) REVERT: H 196 MET cc_start: 0.7052 (ppp) cc_final: 0.6608 (ppp) REVERT: H 259 TYR cc_start: 0.8279 (m-80) cc_final: 0.7502 (m-80) REVERT: H 306 ARG cc_start: 0.7512 (ppt170) cc_final: 0.7150 (ttp80) REVERT: H 395 LEU cc_start: 0.9152 (pp) cc_final: 0.8567 (mt) REVERT: H 432 VAL cc_start: 0.8490 (t) cc_final: 0.8135 (m) REVERT: H 489 TYR cc_start: 0.6769 (t80) cc_final: 0.6033 (t80) REVERT: H 499 LEU cc_start: 0.8228 (pt) cc_final: 0.8023 (pt) REVERT: I 260 PHE cc_start: 0.7672 (p90) cc_final: 0.7082 (p90) REVERT: J 63 GLN cc_start: 0.6870 (tt0) cc_final: 0.6502 (tt0) REVERT: J 158 ASN cc_start: 0.7176 (p0) cc_final: 0.6438 (p0) REVERT: J 300 VAL cc_start: 0.7701 (m) cc_final: 0.7209 (p) REVERT: K 21 MET cc_start: 0.8420 (mmm) cc_final: 0.7764 (mmm) REVERT: K 41 ASN cc_start: 0.6899 (m-40) cc_final: 0.5932 (p0) REVERT: K 218 CYS cc_start: 0.7582 (m) cc_final: 0.7033 (t) REVERT: L 18 ASP cc_start: 0.6952 (m-30) cc_final: 0.6081 (t0) REVERT: P 185 ILE cc_start: 0.4007 (mm) cc_final: 0.3687 (pt) REVERT: P 238 TYR cc_start: 0.6975 (m-10) cc_final: 0.6472 (m-80) REVERT: P 456 TRP cc_start: 0.4690 (m-90) cc_final: 0.4332 (m-90) outliers start: 1 outliers final: 0 residues processed: 591 average time/residue: 0.4098 time to fit residues: 400.9215 Evaluate side-chains 456 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 4.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 249 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 256 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 4 GLN G 182 HIS G 265 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 ASN ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 326 ASN ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33293 Z= 0.187 Angle : 0.757 13.878 45109 Z= 0.376 Chirality : 0.050 0.231 5298 Planarity : 0.005 0.069 5784 Dihedral : 6.443 48.198 4586 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.80 % Rotamer: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.10 % 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: -3.33 (0.12), residues: 4188 helix: -0.73 (0.14), residues: 1299 sheet: -2.74 (0.20), residues: 556 loop : -3.08 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 111 HIS 0.005 0.001 HIS B 116 PHE 0.032 0.002 PHE B 239 TYR 0.027 0.002 TYR B 304 ARG 0.008 0.000 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 575 time to evaluate : 3.670 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.3478 (ptt) cc_final: 0.2885 (ptm) REVERT: A 48 ASN cc_start: 0.8684 (t0) cc_final: 0.8260 (t0) REVERT: A 274 ASP cc_start: 0.8732 (t0) cc_final: 0.8420 (t0) REVERT: A 298 ASP cc_start: 0.8091 (t70) cc_final: 0.7801 (t0) REVERT: B 173 VAL cc_start: 0.8343 (t) cc_final: 0.8080 (t) REVERT: B 222 GLN cc_start: 0.8705 (mm110) cc_final: 0.8438 (mp10) REVERT: B 223 ASN cc_start: 0.7109 (t0) cc_final: 0.6862 (t0) REVERT: C 23 LYS cc_start: 0.8012 (pttt) cc_final: 0.7749 (tptm) REVERT: C 34 MET cc_start: 0.6915 (mpp) cc_final: 0.6418 (mpp) REVERT: C 154 GLN cc_start: 0.9233 (mt0) cc_final: 0.9002 (mt0) REVERT: C 166 MET cc_start: 0.7444 (tpt) cc_final: 0.6117 (mtm) REVERT: C 238 THR cc_start: 0.7994 (p) cc_final: 0.7704 (p) REVERT: C 325 ILE cc_start: 0.9247 (tp) cc_final: 0.8840 (mp) REVERT: D 191 VAL cc_start: 0.7583 (p) cc_final: 0.7334 (p) REVERT: D 288 PHE cc_start: 0.7214 (m-80) cc_final: 0.6729 (m-80) REVERT: D 348 ASP cc_start: 0.7024 (m-30) cc_final: 0.6700 (m-30) REVERT: E 92 TYR cc_start: 0.8108 (t80) cc_final: 0.7635 (t80) REVERT: E 132 MET cc_start: 0.7047 (mmm) cc_final: 0.6712 (mmm) REVERT: E 225 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7521 (mmm-85) REVERT: F 204 LEU cc_start: 0.9041 (tt) cc_final: 0.8834 (tt) REVERT: F 205 TYR cc_start: 0.7296 (m-80) cc_final: 0.6928 (m-80) REVERT: G 384 SER cc_start: 0.8015 (p) cc_final: 0.7580 (t) REVERT: G 485 LEU cc_start: 0.8613 (tp) cc_final: 0.8406 (tt) REVERT: G 490 ASP cc_start: 0.6272 (t0) cc_final: 0.6044 (t0) REVERT: H 185 GLN cc_start: 0.6221 (tm-30) cc_final: 0.6019 (tm-30) REVERT: H 196 MET cc_start: 0.7012 (ppp) cc_final: 0.6564 (ppp) REVERT: H 259 TYR cc_start: 0.8248 (m-80) cc_final: 0.7582 (m-80) REVERT: H 306 ARG cc_start: 0.7478 (ppt170) cc_final: 0.7128 (ttp80) REVERT: H 329 ASN cc_start: 0.8199 (m110) cc_final: 0.7534 (t0) REVERT: H 432 VAL cc_start: 0.8425 (t) cc_final: 0.8042 (m) REVERT: I 260 PHE cc_start: 0.7489 (p90) cc_final: 0.6938 (p90) REVERT: J 63 GLN cc_start: 0.6711 (tt0) cc_final: 0.6331 (tt0) REVERT: J 158 ASN cc_start: 0.7287 (p0) cc_final: 0.6562 (p0) REVERT: J 181 MET cc_start: 0.7997 (tpp) cc_final: 0.6909 (tpt) REVERT: J 300 VAL cc_start: 0.8009 (m) cc_final: 0.7348 (p) REVERT: K 20 VAL cc_start: 0.8546 (m) cc_final: 0.8184 (t) REVERT: K 21 MET cc_start: 0.8460 (mmm) cc_final: 0.7833 (mmm) REVERT: K 41 ASN cc_start: 0.6907 (m-40) cc_final: 0.5961 (p0) REVERT: K 218 CYS cc_start: 0.7599 (m) cc_final: 0.7039 (t) REVERT: L 18 ASP cc_start: 0.7193 (m-30) cc_final: 0.6210 (t0) REVERT: L 21 MET cc_start: 0.6652 (mmp) cc_final: 0.5517 (mtp) REVERT: P 152 MET cc_start: 0.3076 (mmm) cc_final: -0.0137 (ptt) REVERT: P 185 ILE cc_start: 0.4051 (mm) cc_final: 0.3760 (pt) REVERT: P 238 TYR cc_start: 0.6956 (m-10) cc_final: 0.6502 (m-80) outliers start: 1 outliers final: 0 residues processed: 576 average time/residue: 0.4041 time to fit residues: 386.6034 Evaluate side-chains 463 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 367 optimal weight: 2.9990 chunk 386 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 355 optimal weight: 3.9990 chunk 375 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN G 182 HIS ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 ASN ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33293 Z= 0.311 Angle : 0.839 14.766 45109 Z= 0.429 Chirality : 0.052 0.237 5298 Planarity : 0.005 0.076 5784 Dihedral : 6.831 48.456 4586 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.87 % Favored : 86.08 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.15 % 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: -3.42 (0.12), residues: 4188 helix: -0.87 (0.14), residues: 1300 sheet: -2.80 (0.21), residues: 482 loop : -3.11 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 366 HIS 0.010 0.002 HIS C 260 PHE 0.031 0.003 PHE D 288 TYR 0.029 0.003 TYR A 304 ARG 0.024 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 3.993 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6941 (mttt) cc_final: 0.6436 (mtmt) REVERT: A 48 ASN cc_start: 0.8768 (t0) cc_final: 0.8372 (t0) REVERT: A 274 ASP cc_start: 0.8658 (t0) cc_final: 0.8438 (t0) REVERT: A 298 ASP cc_start: 0.7921 (t70) cc_final: 0.7658 (t0) REVERT: B 75 PHE cc_start: 0.7834 (t80) cc_final: 0.7264 (t80) REVERT: B 222 GLN cc_start: 0.8644 (mm110) cc_final: 0.8432 (mp10) REVERT: B 250 PHE cc_start: 0.8622 (m-10) cc_final: 0.8259 (m-80) REVERT: C 23 LYS cc_start: 0.8332 (pttt) cc_final: 0.8032 (tptm) REVERT: C 34 MET cc_start: 0.7225 (mpp) cc_final: 0.6686 (mpp) REVERT: C 154 GLN cc_start: 0.9229 (mt0) cc_final: 0.8948 (mt0) REVERT: C 238 THR cc_start: 0.7749 (p) cc_final: 0.7450 (p) REVERT: D 139 GLU cc_start: 0.8365 (mp0) cc_final: 0.7695 (mp0) REVERT: D 348 ASP cc_start: 0.7228 (m-30) cc_final: 0.6883 (m-30) REVERT: E 225 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.7749 (mmm-85) REVERT: E 231 TYR cc_start: 0.6466 (p90) cc_final: 0.6221 (p90) REVERT: F 170 MET cc_start: 0.6867 (tmm) cc_final: 0.6629 (tmm) REVERT: F 188 GLN cc_start: 0.8597 (tt0) cc_final: 0.8109 (pp30) REVERT: F 264 TYR cc_start: 0.5594 (t80) cc_final: 0.4885 (t80) REVERT: G 384 SER cc_start: 0.8065 (p) cc_final: 0.7688 (t) REVERT: G 482 LEU cc_start: 0.8296 (tp) cc_final: 0.8043 (tp) REVERT: G 506 MET cc_start: 0.5837 (tmm) cc_final: 0.5174 (tmm) REVERT: H 185 GLN cc_start: 0.5936 (tm-30) cc_final: 0.5639 (tm-30) REVERT: H 196 MET cc_start: 0.7235 (ppp) cc_final: 0.6761 (ppp) REVERT: H 259 TYR cc_start: 0.8447 (m-80) cc_final: 0.7786 (m-80) REVERT: H 306 ARG cc_start: 0.7630 (ppt170) cc_final: 0.7159 (ttp80) REVERT: H 432 VAL cc_start: 0.8689 (t) cc_final: 0.8244 (m) REVERT: I 169 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8106 (ttm110) REVERT: I 260 PHE cc_start: 0.7818 (p90) cc_final: 0.7462 (p90) REVERT: J 63 GLN cc_start: 0.7013 (tt0) cc_final: 0.6577 (tt0) REVERT: J 75 LEU cc_start: 0.7635 (pt) cc_final: 0.7423 (pt) REVERT: J 158 ASN cc_start: 0.7536 (p0) cc_final: 0.6951 (p0) REVERT: J 181 MET cc_start: 0.8058 (tpp) cc_final: 0.7237 (tpt) REVERT: J 300 VAL cc_start: 0.8049 (m) cc_final: 0.7441 (p) REVERT: K 21 MET cc_start: 0.8685 (mmm) cc_final: 0.7863 (mmm) REVERT: K 218 CYS cc_start: 0.7713 (m) cc_final: 0.7116 (t) REVERT: L 18 ASP cc_start: 0.7409 (m-30) cc_final: 0.6459 (t0) REVERT: L 21 MET cc_start: 0.6832 (mmp) cc_final: 0.6302 (mtp) REVERT: L 131 PHE cc_start: 0.7147 (m-10) cc_final: 0.6628 (m-10) REVERT: L 136 TRP cc_start: 0.6648 (m-90) cc_final: 0.6375 (m-90) REVERT: P 185 ILE cc_start: 0.4127 (mm) cc_final: 0.3783 (pt) REVERT: P 238 TYR cc_start: 0.6916 (m-10) cc_final: 0.6422 (m-80) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.4017 time to fit residues: 367.1172 Evaluate side-chains 437 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 247 optimal weight: 2.9990 chunk 397 optimal weight: 4.9990 chunk 242 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 417 optimal weight: 20.0000 chunk 384 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 256 optimal weight: 0.4980 chunk 203 optimal weight: 0.0570 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN G 182 HIS G 265 GLN G 431 ASN ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33293 Z= 0.232 Angle : 0.796 15.121 45109 Z= 0.401 Chirality : 0.051 0.225 5298 Planarity : 0.005 0.071 5784 Dihedral : 6.673 48.534 4586 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.37 % Favored : 87.58 % Rotamer: Outliers : 0.06 % Allowed : 0.65 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.10 % 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: -3.33 (0.12), residues: 4188 helix: -0.75 (0.14), residues: 1283 sheet: -2.80 (0.21), residues: 482 loop : -3.05 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 366 HIS 0.008 0.001 HIS B 128 PHE 0.025 0.002 PHE A 72 TYR 0.027 0.002 TYR B 304 ARG 0.013 0.001 ARG A 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 544 time to evaluate : 3.140 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6960 (mttt) cc_final: 0.6481 (mttt) REVERT: A 298 ASP cc_start: 0.8043 (t70) cc_final: 0.7837 (t0) REVERT: B 43 GLN cc_start: 0.8338 (tt0) cc_final: 0.7438 (tt0) REVERT: B 75 PHE cc_start: 0.7847 (t80) cc_final: 0.7221 (t80) REVERT: B 222 GLN cc_start: 0.8647 (mm110) cc_final: 0.8193 (mm-40) REVERT: C 23 LYS cc_start: 0.8239 (pttt) cc_final: 0.7888 (tptm) REVERT: C 34 MET cc_start: 0.7172 (mpp) cc_final: 0.6701 (mpp) REVERT: C 154 GLN cc_start: 0.9191 (mt0) cc_final: 0.8921 (mt0) REVERT: C 217 MET cc_start: 0.8460 (pmm) cc_final: 0.8044 (ptm) REVERT: C 219 ASP cc_start: 0.7932 (m-30) cc_final: 0.7470 (t0) REVERT: C 238 THR cc_start: 0.7886 (p) cc_final: 0.7504 (p) REVERT: D 191 VAL cc_start: 0.7449 (p) cc_final: 0.7222 (p) REVERT: D 348 ASP cc_start: 0.7107 (m-30) cc_final: 0.6784 (m-30) REVERT: E 225 ARG cc_start: 0.8364 (ttt-90) cc_final: 0.7193 (mmm-85) REVERT: E 272 THR cc_start: 0.5458 (p) cc_final: 0.5074 (m) REVERT: F 170 MET cc_start: 0.6646 (tmm) cc_final: 0.6392 (tmm) REVERT: F 188 GLN cc_start: 0.8460 (tt0) cc_final: 0.7876 (pp30) REVERT: G 384 SER cc_start: 0.8021 (p) cc_final: 0.7580 (t) REVERT: G 482 LEU cc_start: 0.8339 (tp) cc_final: 0.8012 (tp) REVERT: G 499 LEU cc_start: 0.8669 (pt) cc_final: 0.8150 (pt) REVERT: G 506 MET cc_start: 0.5814 (tmm) cc_final: 0.5175 (tmm) REVERT: H 185 GLN cc_start: 0.6227 (tm-30) cc_final: 0.5936 (tm-30) REVERT: H 196 MET cc_start: 0.7109 (ppp) cc_final: 0.6686 (ppp) REVERT: H 259 TYR cc_start: 0.8427 (m-80) cc_final: 0.7774 (m-80) REVERT: H 306 ARG cc_start: 0.7692 (ppt170) cc_final: 0.7209 (ttp80) REVERT: H 432 VAL cc_start: 0.8591 (t) cc_final: 0.8168 (m) REVERT: I 169 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8131 (ttm110) REVERT: I 181 MET cc_start: 0.8309 (mmm) cc_final: 0.7711 (tpp) REVERT: I 260 PHE cc_start: 0.7749 (p90) cc_final: 0.7383 (p90) REVERT: J 63 GLN cc_start: 0.6710 (tt0) cc_final: 0.6301 (tt0) REVERT: J 75 LEU cc_start: 0.7689 (pt) cc_final: 0.7485 (pt) REVERT: J 158 ASN cc_start: 0.7611 (p0) cc_final: 0.6907 (p0) REVERT: J 181 MET cc_start: 0.8119 (tpp) cc_final: 0.7276 (tpt) REVERT: J 355 ILE cc_start: 0.8523 (tt) cc_final: 0.8079 (mp) REVERT: K 21 MET cc_start: 0.8719 (mmm) cc_final: 0.7909 (mmm) REVERT: K 41 ASN cc_start: 0.6916 (m-40) cc_final: 0.5783 (p0) REVERT: K 218 CYS cc_start: 0.7638 (m) cc_final: 0.7074 (t) REVERT: L 18 ASP cc_start: 0.7370 (m-30) cc_final: 0.6428 (t0) REVERT: L 102 PHE cc_start: 0.8966 (p90) cc_final: 0.8725 (p90) REVERT: L 131 PHE cc_start: 0.7196 (m-10) cc_final: 0.6696 (m-10) REVERT: L 136 TRP cc_start: 0.6605 (m-90) cc_final: 0.6349 (m-90) REVERT: P 152 MET cc_start: 0.3084 (mmm) cc_final: -0.0272 (ptt) REVERT: P 185 ILE cc_start: 0.4084 (mm) cc_final: 0.3803 (pt) REVERT: P 212 GLN cc_start: 0.5954 (tm-30) cc_final: 0.5636 (tt0) REVERT: P 238 TYR cc_start: 0.6885 (m-10) cc_final: 0.6338 (m-80) outliers start: 2 outliers final: 1 residues processed: 545 average time/residue: 0.4060 time to fit residues: 368.1955 Evaluate side-chains 446 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 264 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 341 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS D 72 GLN G 182 HIS G 265 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.115394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095968 restraints weight = 114755.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096500 restraints weight = 93450.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096953 restraints weight = 71243.352| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33293 Z= 0.253 Angle : 0.801 14.763 45109 Z= 0.404 Chirality : 0.051 0.250 5298 Planarity : 0.005 0.075 5784 Dihedral : 6.671 47.861 4586 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.37 % Favored : 86.58 % Rotamer: Outliers : 0.03 % Allowed : 0.74 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.12 % 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: -3.34 (0.12), residues: 4188 helix: -0.74 (0.14), residues: 1283 sheet: -2.83 (0.21), residues: 483 loop : -3.06 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 111 HIS 0.008 0.001 HIS B 128 PHE 0.025 0.002 PHE J 260 TYR 0.034 0.002 TYR G 489 ARG 0.011 0.001 ARG A 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7408.86 seconds wall clock time: 134 minutes 45.33 seconds (8085.33 seconds total)