Starting phenix.real_space_refine (version: dev) on Fri Dec 16 23:02:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/12_2022/6k72_9841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/12_2022/6k72_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_9841/12_2022/6k72_9841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/12_2022/6k72_9841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/12_2022/6k72_9841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k72_9841/12_2022/6k72_9841.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 17.75, per 1000 atoms: 0.54 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: 13.12 Conformation dependent library (CDL) restraints added in 5.3 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: 1.75 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: 10.08 Time building geometry restraints manager: 14.03 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 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. 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: 0.940 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: 0.020 Extract box with map and model: 6.750 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.260 Process input model: 78.400 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 : 10.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.97 % Favored : 85.91 % Rotamer Outliers : 1.37 % 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 *********************** 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 : 4.091 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 outliers start: 48 outliers final: 12 residues processed: 786 average time/residue: 0.4254 time to fit residues: 532.9970 Evaluate side-chains 446 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 434 time to evaluate : 3.929 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2655 time to fit residues: 11.4368 ------------------------------------------------------------------------------- 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: 0.9990 chunk 169 optimal weight: 0.6980 chunk 328 optimal weight: 9.9990 chunk 127 optimal weight: 0.1980 chunk 199 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 380 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 270 HIS C 138 ASN C 242 ASN C 345 HIS 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** 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 200 ASN 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 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 33293 Z= 0.206 Angle : 0.799 12.423 45109 Z= 0.412 Chirality : 0.050 0.248 5298 Planarity : 0.006 0.080 5784 Dihedral : 7.835 51.923 4586 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.91 % Favored : 88.04 % Rotamer Outliers : 0.31 % 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: -4.38 (0.11), residues: 4188 helix: -2.09 (0.12), residues: 1294 sheet: -3.17 (0.21), residues: 450 loop : -3.48 (0.11), residues: 2444 *********************** 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 634 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 623 time to evaluate : 4.399 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 outliers start: 11 outliers final: 4 residues processed: 630 average time/residue: 0.4181 time to fit residues: 431.1916 Evaluate side-chains 448 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 444 time to evaluate : 4.186 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2881 time to fit residues: 8.0345 ------------------------------------------------------------------------------- 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: 4.9990 chunk 259 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 381 optimal weight: 30.0000 chunk 411 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 378 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 305 optimal weight: 0.0370 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 72 GLN E 4 GLN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN G 182 HIS G 194 GLN 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 406 HIS ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 HIS ** 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** ** I 452 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 33293 Z= 0.277 Angle : 0.802 13.600 45109 Z= 0.415 Chirality : 0.051 0.247 5298 Planarity : 0.005 0.074 5784 Dihedral : 7.511 50.427 4586 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.47 % Favored : 86.49 % Rotamer Outliers : 0.20 % 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: -4.11 (0.11), residues: 4188 helix: -1.65 (0.13), residues: 1304 sheet: -3.22 (0.20), residues: 494 loop : -3.39 (0.11), residues: 2390 *********************** 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 556 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 549 time to evaluate : 4.050 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 outliers start: 7 outliers final: 2 residues processed: 555 average time/residue: 0.4211 time to fit residues: 384.9324 Evaluate side-chains 413 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 411 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2649 time to fit residues: 6.0103 ------------------------------------------------------------------------------- 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: 7.9990 chunk 286 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 181 optimal weight: 50.0000 chunk 255 optimal weight: 2.9990 chunk 382 optimal weight: 0.0470 chunk 405 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN D 72 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS G 325 GLN ** 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 281 ASN ** 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2880 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= 0.206 Angle : 0.752 13.604 45109 Z= 0.383 Chirality : 0.050 0.251 5298 Planarity : 0.005 0.076 5784 Dihedral : 7.119 47.805 4586 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.15 % Favored : 87.80 % Rotamer Outliers : 0.03 % 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: -3.82 (0.12), residues: 4188 helix: -1.32 (0.13), residues: 1305 sheet: -2.96 (0.20), residues: 544 loop : -3.29 (0.12), residues: 2339 *********************** 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 561 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 560 time to evaluate : 3.971 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 outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.4129 time to fit residues: 381.8690 Evaluate side-chains 430 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3677 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.5980 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 363 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 422 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 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** I 337 HIS ** J 63 GLN ** 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** ** J 434 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: 0.7205 moved from start: 0.3141 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= 0.205 Angle : 0.738 13.437 45109 Z= 0.377 Chirality : 0.049 0.262 5298 Planarity : 0.005 0.071 5784 Dihedral : 6.886 46.963 4586 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.25 % Favored : 87.68 % Rotamer Outliers : 0.03 % 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: -3.66 (0.12), residues: 4188 helix: -1.12 (0.13), residues: 1305 sheet: -2.93 (0.20), residues: 535 loop : -3.21 (0.12), residues: 2348 *********************** 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 554 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 3.980 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 outliers start: 1 outliers final: 0 residues processed: 554 average time/residue: 0.4030 time to fit residues: 369.0773 Evaluate side-chains 426 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2235 ------------------------------------------------------------------------------- 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: 7.9990 chunk 364 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 405 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 GLN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN I 210 ASN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** 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 L 187 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.140 33293 Z= 0.399 Angle : 0.908 14.990 45109 Z= 0.470 Chirality : 0.054 0.340 5298 Planarity : 0.006 0.076 5784 Dihedral : 7.432 50.246 4586 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.35 % Favored : 84.55 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.25 % 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: -3.93 (0.12), residues: 4188 helix: -1.39 (0.13), residues: 1334 sheet: -3.16 (0.20), residues: 483 loop : -3.36 (0.12), residues: 2371 *********************** 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 517 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 514 time to evaluate : 4.010 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 outliers start: 3 outliers final: 1 residues processed: 516 average time/residue: 0.4135 time to fit residues: 351.3998 Evaluate side-chains 400 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 399 time to evaluate : 3.997 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2771 time to fit residues: 5.9273 ------------------------------------------------------------------------------- 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: 9.9990 chunk 45 optimal weight: 0.4980 chunk 230 optimal weight: 8.9990 chunk 296 optimal weight: 0.5980 chunk 229 optimal weight: 0.9990 chunk 341 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 403 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 246 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 340 HIS ** J 63 GLN ** 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** ** L 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 33293 Z= 0.201 Angle : 0.774 14.167 45109 Z= 0.390 Chirality : 0.050 0.249 5298 Planarity : 0.005 0.068 5784 Dihedral : 6.926 49.501 4586 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.70 % Favored : 88.25 % Rotamer Outliers : 0.00 % 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: -3.49 (0.12), residues: 4188 helix: -0.93 (0.14), residues: 1288 sheet: -2.82 (0.21), residues: 476 loop : -3.15 (0.12), residues: 2424 *********************** 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 551 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 4.174 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 outliers start: 0 outliers final: 0 residues processed: 551 average time/residue: 0.4076 time to fit residues: 373.9656 Evaluate side-chains 425 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3438 ------------------------------------------------------------------------------- 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: 0.9980 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** 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 63 GLN ** 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 33293 Z= 0.199 Angle : 0.774 14.438 45109 Z= 0.389 Chirality : 0.050 0.243 5298 Planarity : 0.005 0.066 5784 Dihedral : 6.694 48.664 4586 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.11 % Favored : 87.85 % Rotamer Outliers : 0.03 % 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: -3.30 (0.12), residues: 4188 helix: -0.68 (0.14), residues: 1276 sheet: -2.79 (0.21), residues: 496 loop : -3.06 (0.12), residues: 2416 *********************** 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 557 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 556 time to evaluate : 3.918 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 outliers start: 1 outliers final: 0 residues processed: 557 average time/residue: 0.4108 time to fit residues: 379.9533 Evaluate side-chains 434 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 3.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0848 ------------------------------------------------------------------------------- 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: 0.1980 chunk 386 optimal weight: 0.9980 chunk 352 optimal weight: 7.9990 chunk 376 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 295 optimal weight: 5.9990 chunk 115 optimal weight: 0.0370 chunk 340 optimal weight: 0.8980 chunk 355 optimal weight: 7.9990 chunk 375 optimal weight: 9.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 431 ASN ** 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 ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** 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** K 114 HIS ** L 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 33293 Z= 0.192 Angle : 0.768 14.064 45109 Z= 0.384 Chirality : 0.050 0.274 5298 Planarity : 0.005 0.069 5784 Dihedral : 6.546 47.089 4586 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.20 % Favored : 88.75 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -3.25 (0.12), residues: 4188 helix: -0.61 (0.14), residues: 1274 sheet: -2.71 (0.20), residues: 571 loop : -3.04 (0.12), residues: 2343 *********************** 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 571 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 569 time to evaluate : 3.630 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 outliers start: 2 outliers final: 0 residues processed: 571 average time/residue: 0.4115 time to fit residues: 393.1744 Evaluate side-chains 450 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 4.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9413 ------------------------------------------------------------------------------- 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: 0.9980 chunk 397 optimal weight: 5.9990 chunk 242 optimal weight: 0.0470 chunk 188 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 417 optimal weight: 8.9990 chunk 384 optimal weight: 0.2980 chunk 332 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 349 HIS ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 431 ASN ** 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 ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** 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** ** L 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 33293 Z= 0.187 Angle : 0.770 14.350 45109 Z= 0.384 Chirality : 0.050 0.253 5298 Planarity : 0.005 0.066 5784 Dihedral : 6.399 47.576 4586 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.94 % Favored : 89.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.20 % 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: -3.14 (0.12), residues: 4188 helix: -0.49 (0.14), residues: 1264 sheet: -2.69 (0.19), residues: 572 loop : -2.96 (0.12), residues: 2352 ********************** 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 571 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 4.408 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 outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.4315 time to fit residues: 413.3896 Evaluate side-chains 452 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 3.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0416 ------------------------------------------------------------------------------- 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: 0.0000 chunk 354 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 306 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 139 optimal weight: 0.0570 chunk 341 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS E 203 HIS ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN ** 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 63 GLN ** 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 ** L 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.120379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.100931 restraints weight = 111385.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.101781 restraints weight = 85494.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101790 restraints weight = 65014.163| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4301 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= 0.190 Angle : 0.763 14.520 45109 Z= 0.381 Chirality : 0.050 0.237 5298 Planarity : 0.005 0.072 5784 Dihedral : 6.285 46.902 4586 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.84 % Favored : 89.11 % Rotamer Outliers : 0.03 % 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: -3.05 (0.12), residues: 4188 helix: -0.43 (0.15), residues: 1280 sheet: -2.61 (0.19), residues: 593 loop : -2.92 (0.12), residues: 2315 =============================================================================== Job complete usr+sys time: 6971.35 seconds wall clock time: 127 minutes 53.02 seconds (7673.02 seconds total)