Starting phenix.real_space_refine on Fri Mar 6 16:31:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k72_9841/03_2026/6k72_9841.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k72_9841/03_2026/6k72_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 { model { file = "/net/cci-nas-00/data/ceres_data/6k72_9841/03_2026/6k72_9841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k72_9841/03_2026/6k72_9841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k72_9841/03_2026/6k72_9841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k72_9841/03_2026/6k72_9841.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 169 5.16 5 C 20759 2.51 5 N 5696 2.21 5 O 6107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 7, 'ARG:plan': 6, 'GLU:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 1} 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: {'ASP:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 7, 'ARG:plan': 6, 'GLU:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 1} 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: 6.84, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 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: 2.57 Conformation dependent library (CDL) restraints added in 1.4 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: 1.03 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: 8.27 Time building geometry restraints manager: 3.44 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: 0.00 - 3.69: 44185 3.69 - 7.39: 787 7.39 - 11.08: 121 11.08 - 14.78: 14 14.78 - 18.47: 2 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 3.120 nonbonded pdb=" O ARG B 46 " pdb=" OG1 THR B 50 " model vdw 2.259 3.040 nonbonded pdb=" O ALA P 84 " pdb=" OG SER P 131 " model vdw 2.259 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 305) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 267 or resid 276 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.220 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 33293 Z= 0.302 Angle : 1.304 18.472 45109 Z= 0.722 Chirality : 0.069 0.363 5298 Planarity : 0.008 0.107 5784 Dihedral : 12.854 87.445 12218 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.97 % Favored : 85.91 % Rotamer: Outliers : 1.37 % Allowed : 10.79 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 3.49 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.10), residues: 4188 helix: -3.29 (0.10), residues: 1288 sheet: -3.73 (0.18), residues: 492 loop : -3.87 (0.10), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 108 TYR 0.044 0.004 TYR G 441 PHE 0.032 0.004 PHE L 102 TRP 0.025 0.003 TRP I 97 HIS 0.021 0.002 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00623 (33293) covalent geometry : angle 1.30419 (45109) hydrogen bonds : bond 0.18687 ( 957) hydrogen bonds : angle 8.28788 ( 2709) *********************** 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 to be fit. rotamer outliers: 48 poor density : 753 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.5341 (ptp) cc_final: 0.4726 (mtp) REVERT: A 78 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6769 (pp) REVERT: A 187 MET cc_start: 0.7754 (tpt) cc_final: 0.7330 (tpt) REVERT: A 213 ASN cc_start: 0.8614 (p0) cc_final: 0.8331 (p0) REVERT: A 298 ASP cc_start: 0.7604 (t70) cc_final: 0.7137 (t0) REVERT: B 88 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7903 (pmmt) REVERT: B 208 ASN cc_start: 0.8357 (t0) cc_final: 0.7928 (t0) REVERT: B 222 GLN cc_start: 0.8244 (mm110) cc_final: 0.7529 (mm110) REVERT: B 227 TYR cc_start: 0.7826 (m-10) cc_final: 0.7541 (m-10) REVERT: B 242 ASN cc_start: 0.8637 (p0) cc_final: 0.8372 (p0) REVERT: C 18 PHE cc_start: 0.7585 (m-10) cc_final: 0.6704 (m-10) REVERT: C 148 MET cc_start: 0.7445 (mtm) cc_final: 0.6758 (pmm) REVERT: C 203 MET cc_start: 0.8548 (ttt) cc_final: 0.8233 (ttp) REVERT: C 335 TYR cc_start: 0.7599 (t80) cc_final: 0.7291 (t80) REVERT: D 137 ILE cc_start: 0.8995 (pp) cc_final: 0.8789 (pp) REVERT: D 189 VAL cc_start: 0.6089 (p) cc_final: 0.5566 (p) REVERT: D 191 VAL cc_start: 0.6870 (t) cc_final: 0.6345 (p) REVERT: E 64 CYS cc_start: 0.8067 (m) cc_final: 0.7794 (p) REVERT: E 213 ASP cc_start: 0.7762 (p0) cc_final: 0.7268 (p0) REVERT: E 214 PHE cc_start: 0.6711 (t80) cc_final: 0.6488 (t80) REVERT: F 56 THR cc_start: 0.8327 (t) cc_final: 0.8000 (m) REVERT: F 71 MET cc_start: 0.8069 (ppp) cc_final: 0.7716 (ppp) REVERT: F 170 MET cc_start: 0.6869 (tmt) cc_final: 0.6303 (tmm) REVERT: F 188 GLN cc_start: 0.8497 (tt0) cc_final: 0.8010 (pp30) REVERT: G 233 LEU cc_start: 0.8176 (pp) cc_final: 0.7943 (tt) REVERT: G 275 ASN cc_start: 0.8521 (p0) cc_final: 0.8283 (p0) REVERT: G 324 TYR cc_start: 0.7323 (t80) cc_final: 0.7106 (t80) REVERT: G 362 ASP cc_start: 0.7927 (t0) cc_final: 0.7723 (t0) REVERT: G 385 TYR cc_start: 0.7424 (t80) cc_final: 0.7097 (t80) REVERT: G 506 MET cc_start: 0.5689 (tmt) cc_final: 0.5292 (tmt) REVERT: H 196 MET cc_start: 0.7520 (pp-130) cc_final: 0.7219 (ppp) REVERT: H 237 ILE cc_start: 0.9304 (pp) cc_final: 0.9027 (pp) REVERT: H 239 ASP cc_start: 0.8453 (p0) cc_final: 0.8134 (p0) REVERT: H 259 TYR cc_start: 0.8320 (m-10) cc_final: 0.8072 (m-80) REVERT: H 306 ARG cc_start: 0.8248 (ppt170) cc_final: 0.7684 (ttp80) REVERT: H 307 TYR cc_start: 0.8789 (t80) cc_final: 0.8305 (t80) REVERT: H 336 TYR cc_start: 0.8728 (t80) cc_final: 0.8056 (t80) REVERT: H 397 GLU cc_start: 0.8343 (mp0) cc_final: 0.8071 (mp0) REVERT: H 469 GLU cc_start: 0.7692 (pm20) cc_final: 0.6886 (mt-10) REVERT: I 96 CYS cc_start: 0.7519 (t) cc_final: 0.7258 (t) REVERT: I 242 TYR cc_start: 0.7050 (t80) cc_final: 0.6671 (t80) REVERT: I 342 ILE cc_start: 0.8288 (mm) cc_final: 0.7969 (tt) REVERT: I 357 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7776 (mp0) REVERT: J 158 ASN cc_start: 0.8279 (p0) cc_final: 0.7592 (p0) REVERT: J 239 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6361 (mm-30) REVERT: J 251 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7979 (pp) REVERT: J 329 ASP cc_start: 0.8210 (m-30) cc_final: 0.7655 (m-30) REVERT: K 41 ASN cc_start: 0.7860 (m-40) cc_final: 0.6697 (p0) REVERT: K 102 PHE cc_start: 0.8809 (t80) cc_final: 0.8363 (t80) REVERT: L 18 ASP cc_start: 0.7396 (m-30) cc_final: 0.6408 (t0) REVERT: L 21 MET cc_start: 0.7544 (mpm) cc_final: 0.7132 (mtp) REVERT: L 99 GLU cc_start: 0.8426 (mp0) cc_final: 0.8211 (tm-30) REVERT: P 152 MET cc_start: 0.3646 (ptt) cc_final: 0.3419 (mmm) REVERT: P 185 ILE cc_start: 0.5631 (mt) cc_final: 0.5354 (pt) REVERT: P 257 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6487 (tt) outliers start: 48 outliers final: 12 residues processed: 786 average time/residue: 0.1957 time to fit residues: 246.7382 Evaluate side-chains 468 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 452 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 10.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 HIS H 431 ASN H 479 HIS I 168 HIS I 248 HIS ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN J 105 HIS ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 HIS ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 452 HIS P 85 ASN P 138 HIS P 231 ASN P 325 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.119464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099411 restraints weight = 113526.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100432 restraints weight = 88072.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.100965 restraints weight = 67371.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101376 restraints weight = 56618.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101558 restraints weight = 50305.461| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33293 Z= 0.145 Angle : 0.822 12.994 45109 Z= 0.424 Chirality : 0.051 0.257 5298 Planarity : 0.006 0.077 5784 Dihedral : 7.943 52.490 4586 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.70 % Favored : 88.25 % Rotamer: Outliers : 0.23 % Allowed : 5.75 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.91 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.11), residues: 4188 helix: -2.19 (0.12), residues: 1304 sheet: -3.25 (0.20), residues: 517 loop : -3.50 (0.11), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 246 TYR 0.028 0.002 TYR B 304 PHE 0.035 0.002 PHE J 94 TRP 0.021 0.002 TRP J 111 HIS 0.010 0.001 HIS P 325 Details of bonding type rmsd covalent geometry : bond 0.00318 (33293) covalent geometry : angle 0.82240 (45109) hydrogen bonds : bond 0.04933 ( 957) hydrogen bonds : angle 6.53235 ( 2709) *********************** 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 641 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 633 time to evaluate : 1.182 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: A 78 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7207 (pp) REVERT: A 113 ASP cc_start: 0.9422 (m-30) cc_final: 0.9217 (m-30) REVERT: A 187 MET cc_start: 0.7945 (tpt) cc_final: 0.7740 (tpt) REVERT: A 298 ASP cc_start: 0.7828 (t70) cc_final: 0.7594 (t0) REVERT: B 20 MET cc_start: 0.2975 (tpp) cc_final: 0.2397 (tpt) REVERT: B 114 LEU cc_start: 0.8302 (tt) cc_final: 0.7817 (mm) REVERT: B 130 TYR cc_start: 0.7697 (t80) cc_final: 0.7329 (t80) REVERT: B 208 ASN cc_start: 0.8827 (t0) cc_final: 0.8105 (t0) REVERT: B 242 ASN cc_start: 0.8468 (p0) cc_final: 0.8220 (p0) REVERT: C 34 MET cc_start: 0.7895 (mpp) cc_final: 0.7468 (mmt) REVERT: C 203 MET cc_start: 0.8544 (ttt) cc_final: 0.8111 (ttp) REVERT: C 281 GLU cc_start: 0.7908 (tp30) cc_final: 0.7534 (mp0) REVERT: E 69 MET cc_start: 0.3498 (ppp) cc_final: 0.2552 (pmm) REVERT: E 130 MET cc_start: 0.6899 (tpp) cc_final: 0.6238 (tpt) REVERT: E 132 MET cc_start: 0.6166 (mmp) cc_final: 0.5672 (mmm) REVERT: E 213 ASP cc_start: 0.7713 (p0) cc_final: 0.7115 (p0) REVERT: F 91 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.6907 (mtt180) REVERT: G 171 LYS cc_start: 0.3576 (pttp) cc_final: 0.3254 (mttt) REVERT: G 197 SER cc_start: 0.8328 (m) cc_final: 0.7570 (p) REVERT: G 324 TYR cc_start: 0.7011 (t80) cc_final: 0.6589 (t80) REVERT: G 362 ASP cc_start: 0.7822 (t0) cc_final: 0.7567 (t0) REVERT: G 385 TYR cc_start: 0.7225 (t80) cc_final: 0.6794 (t80) REVERT: G 452 PHE cc_start: 0.5788 (m-80) cc_final: 0.5491 (m-80) REVERT: G 507 ILE cc_start: 0.7638 (pt) cc_final: 0.7388 (pt) REVERT: H 239 ASP cc_start: 0.8848 (p0) cc_final: 0.8610 (p0) REVERT: H 259 TYR cc_start: 0.8107 (m-10) cc_final: 0.7856 (m-80) REVERT: H 306 ARG cc_start: 0.8078 (ppt170) cc_final: 0.7530 (ttp80) REVERT: H 329 ASN cc_start: 0.8458 (m110) cc_final: 0.7711 (t0) REVERT: H 376 LEU cc_start: 0.8943 (tt) cc_final: 0.8421 (mm) REVERT: H 439 GLU cc_start: 0.7668 (pp20) cc_final: 0.7426 (mp0) REVERT: H 489 TYR cc_start: 0.7065 (t80) cc_final: 0.6439 (t80) REVERT: I 169 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7799 (ttm110) REVERT: I 265 ASP cc_start: 0.8335 (p0) cc_final: 0.8097 (p0) REVERT: I 342 ILE cc_start: 0.8125 (mm) cc_final: 0.7789 (tt) REVERT: I 357 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7791 (mp0) REVERT: J 63 GLN cc_start: 0.7060 (tt0) cc_final: 0.6472 (tt0) REVERT: J 75 LEU cc_start: 0.7208 (pt) cc_final: 0.6926 (pt) REVERT: J 158 ASN cc_start: 0.7775 (p0) cc_final: 0.7278 (p0) REVERT: J 239 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6503 (mm-30) REVERT: K 41 ASN cc_start: 0.7843 (m-40) cc_final: 0.6698 (p0) REVERT: K 102 PHE cc_start: 0.8512 (t80) cc_final: 0.8062 (t80) REVERT: K 218 CYS cc_start: 0.7736 (m) cc_final: 0.7158 (t) REVERT: L 18 ASP cc_start: 0.7132 (m-30) cc_final: 0.6363 (t0) REVERT: L 99 GLU cc_start: 0.8432 (mp0) cc_final: 0.8178 (tm-30) REVERT: L 131 PHE cc_start: 0.7218 (m-10) cc_final: 0.6866 (m-10) REVERT: P 180 MET cc_start: 0.2923 (mtm) cc_final: 0.2612 (mtt) outliers start: 8 outliers final: 2 residues processed: 638 average time/residue: 0.1866 time to fit residues: 197.0895 Evaluate side-chains 470 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 467 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 38 optimal weight: 0.8980 chunk 409 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 303 optimal weight: 3.9990 chunk 399 optimal weight: 0.9980 chunk 355 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 313 optimal weight: 0.0050 chunk 196 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 274 optimal weight: 5.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 GLN D 154 GLN G 166 GLN G 182 HIS G 194 GLN G 406 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS H 411 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** J 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099989 restraints weight = 111856.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.100514 restraints weight = 87032.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.101289 restraints weight = 67925.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101680 restraints weight = 55928.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101864 restraints weight = 50304.618| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33293 Z= 0.134 Angle : 0.761 13.111 45109 Z= 0.389 Chirality : 0.050 0.245 5298 Planarity : 0.005 0.073 5784 Dihedral : 7.263 50.212 4586 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.12), residues: 4188 helix: -1.60 (0.13), residues: 1300 sheet: -3.09 (0.20), residues: 521 loop : -3.33 (0.11), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 246 TYR 0.028 0.002 TYR B 304 PHE 0.031 0.002 PHE J 94 TRP 0.017 0.001 TRP J 111 HIS 0.006 0.001 HIS I 452 Details of bonding type rmsd covalent geometry : bond 0.00291 (33293) covalent geometry : angle 0.76080 (45109) hydrogen bonds : bond 0.04177 ( 957) hydrogen bonds : angle 5.97005 ( 2709) *********************** 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 608 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.150 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: A 113 ASP cc_start: 0.9505 (m-30) cc_final: 0.9292 (m-30) REVERT: A 187 MET cc_start: 0.8072 (tpt) cc_final: 0.7571 (tpt) REVERT: A 213 ASN cc_start: 0.8432 (p0) cc_final: 0.8211 (p0) REVERT: A 222 GLN cc_start: 0.8045 (mp10) cc_final: 0.7600 (mp10) REVERT: A 298 ASP cc_start: 0.8032 (t70) cc_final: 0.7701 (t0) REVERT: B 20 MET cc_start: 0.3032 (tpp) cc_final: 0.2491 (tpt) REVERT: B 114 LEU cc_start: 0.8433 (tt) cc_final: 0.7907 (mm) REVERT: B 173 VAL cc_start: 0.8471 (t) cc_final: 0.8203 (t) REVERT: B 208 ASN cc_start: 0.8616 (t0) cc_final: 0.8005 (t0) REVERT: B 209 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7862 (mmtt) REVERT: B 222 GLN cc_start: 0.8516 (mm110) cc_final: 0.8195 (mp10) REVERT: C 23 LYS cc_start: 0.8452 (pttt) cc_final: 0.7801 (tptm) REVERT: C 34 MET cc_start: 0.7375 (mpp) cc_final: 0.6944 (mmt) REVERT: C 203 MET cc_start: 0.8455 (ttt) cc_final: 0.7735 (ttp) REVERT: C 238 THR cc_start: 0.8239 (p) cc_final: 0.7966 (p) REVERT: C 271 MET cc_start: 0.8194 (ptm) cc_final: 0.7770 (ppp) REVERT: C 281 GLU cc_start: 0.8090 (tp30) cc_final: 0.7460 (mp0) REVERT: C 325 ILE cc_start: 0.9096 (tp) cc_final: 0.8795 (mp) REVERT: D 301 ASP cc_start: 0.7245 (t0) cc_final: 0.6976 (t0) REVERT: D 348 ASP cc_start: 0.7414 (m-30) cc_final: 0.7185 (m-30) REVERT: E 1 MET cc_start: 0.4786 (tpt) cc_final: 0.4504 (tpp) REVERT: E 69 MET cc_start: 0.3201 (ppp) cc_final: 0.2310 (pmm) REVERT: E 132 MET cc_start: 0.6174 (mmp) cc_final: 0.5873 (mmm) REVERT: E 213 ASP cc_start: 0.7703 (p0) cc_final: 0.7214 (p0) REVERT: E 231 TYR cc_start: 0.6798 (p90) cc_final: 0.6565 (p90) REVERT: F 91 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7131 (mtt180) REVERT: F 170 MET cc_start: 0.7440 (tmm) cc_final: 0.7118 (tmm) REVERT: F 204 LEU cc_start: 0.9032 (tt) cc_final: 0.8718 (mp) REVERT: G 196 MET cc_start: 0.5334 (tpp) cc_final: 0.4995 (tpt) REVERT: G 197 SER cc_start: 0.8428 (m) cc_final: 0.7782 (p) REVERT: G 362 ASP cc_start: 0.7760 (t0) cc_final: 0.7449 (t0) REVERT: G 385 TYR cc_start: 0.7122 (t80) cc_final: 0.6726 (t80) REVERT: G 506 MET cc_start: 0.5274 (tmm) cc_final: 0.4774 (tmm) REVERT: H 196 MET cc_start: 0.7298 (ppp) cc_final: 0.6743 (ppp) REVERT: H 306 ARG cc_start: 0.7935 (ppt170) cc_final: 0.7599 (ttp80) REVERT: H 329 ASN cc_start: 0.8455 (m110) cc_final: 0.7623 (t0) REVERT: H 439 GLU cc_start: 0.7990 (pp20) cc_final: 0.7714 (mp0) REVERT: H 440 THR cc_start: 0.7649 (m) cc_final: 0.7010 (p) REVERT: H 441 TYR cc_start: 0.6712 (p90) cc_final: 0.6422 (p90) REVERT: H 475 ASN cc_start: 0.8410 (p0) cc_final: 0.7902 (p0) REVERT: I 169 ARG cc_start: 0.8253 (ttm110) cc_final: 0.7810 (ttm110) REVERT: I 173 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8477 (mmtm) REVERT: I 181 MET cc_start: 0.8658 (mmm) cc_final: 0.7807 (tpp) REVERT: I 260 PHE cc_start: 0.8262 (p90) cc_final: 0.7721 (p90) REVERT: I 310 CYS cc_start: 0.6475 (p) cc_final: 0.6119 (t) REVERT: I 342 ILE cc_start: 0.8088 (mm) cc_final: 0.7863 (tt) REVERT: J 63 GLN cc_start: 0.6802 (tt0) cc_final: 0.6291 (tt0) REVERT: J 158 ASN cc_start: 0.7775 (p0) cc_final: 0.7292 (p0) REVERT: J 183 MET cc_start: 0.7102 (ttp) cc_final: 0.6605 (ttm) REVERT: J 239 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6663 (mm-30) REVERT: K 21 MET cc_start: 0.8660 (mmm) cc_final: 0.7382 (mmm) REVERT: K 41 ASN cc_start: 0.7872 (m-40) cc_final: 0.6776 (p0) REVERT: K 218 CYS cc_start: 0.7592 (m) cc_final: 0.7048 (t) REVERT: L 18 ASP cc_start: 0.7073 (m-30) cc_final: 0.6268 (t0) REVERT: L 46 ILE cc_start: 0.7751 (mm) cc_final: 0.7529 (tp) REVERT: L 99 GLU cc_start: 0.8559 (mp0) cc_final: 0.8246 (tm-30) REVERT: L 131 PHE cc_start: 0.7325 (m-10) cc_final: 0.6960 (m-10) REVERT: P 113 PHE cc_start: 0.3067 (m-10) cc_final: 0.2555 (p90) REVERT: P 180 MET cc_start: 0.2698 (mtm) cc_final: 0.2494 (mtt) REVERT: P 238 TYR cc_start: 0.6763 (m-10) cc_final: 0.5935 (m-80) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 0.1895 time to fit residues: 190.6022 Evaluate side-chains 457 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 103 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 373 optimal weight: 1.9990 chunk 260 optimal weight: 0.3980 chunk 248 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 400 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN F 41 ASN G 182 HIS ** G 422 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** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS J 72 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.120609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100390 restraints weight = 111313.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.101104 restraints weight = 90924.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.102210 restraints weight = 68465.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.102542 restraints weight = 52601.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102789 restraints weight = 47413.166| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33293 Z= 0.127 Angle : 0.746 13.098 45109 Z= 0.378 Chirality : 0.050 0.269 5298 Planarity : 0.005 0.067 5784 Dihedral : 6.878 47.467 4586 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.96 % Favored : 88.99 % Rotamer: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.12), residues: 4188 helix: -1.26 (0.13), residues: 1296 sheet: -2.86 (0.20), residues: 532 loop : -3.24 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 96 TYR 0.027 0.002 TYR B 304 PHE 0.028 0.002 PHE J 94 TRP 0.015 0.001 TRP J 111 HIS 0.005 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00282 (33293) covalent geometry : angle 0.74553 (45109) hydrogen bonds : bond 0.03840 ( 957) hydrogen bonds : angle 5.69787 ( 2709) *********************** 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 587 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 585 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7900 (tpt) cc_final: 0.7037 (tpt) REVERT: A 213 ASN cc_start: 0.8366 (p0) cc_final: 0.8160 (p0) REVERT: A 222 GLN cc_start: 0.8101 (mp10) cc_final: 0.7626 (mp10) REVERT: A 298 ASP cc_start: 0.8095 (t70) cc_final: 0.7734 (t0) REVERT: B 20 MET cc_start: 0.3132 (tpp) cc_final: 0.2916 (tpt) REVERT: B 114 LEU cc_start: 0.8346 (tt) cc_final: 0.7784 (mm) REVERT: B 173 VAL cc_start: 0.8428 (t) cc_final: 0.8148 (t) REVERT: B 209 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7839 (mmtt) REVERT: B 222 GLN cc_start: 0.8580 (mm110) cc_final: 0.8354 (mp10) REVERT: B 242 ASN cc_start: 0.8265 (p0) cc_final: 0.7986 (p0) REVERT: C 23 LYS cc_start: 0.8391 (pttt) cc_final: 0.7808 (tptm) REVERT: C 34 MET cc_start: 0.6937 (mpp) cc_final: 0.6133 (mpp) REVERT: C 81 MET cc_start: 0.7537 (ppp) cc_final: 0.7307 (ppp) REVERT: C 166 MET cc_start: 0.6850 (tpt) cc_final: 0.6244 (tpt) REVERT: C 203 MET cc_start: 0.8159 (ttt) cc_final: 0.7566 (ttp) REVERT: C 302 ILE cc_start: 0.7831 (mt) cc_final: 0.7481 (mt) REVERT: C 325 ILE cc_start: 0.9181 (tp) cc_final: 0.8812 (mp) REVERT: D 199 GLN cc_start: 0.8808 (pt0) cc_final: 0.8250 (tt0) REVERT: D 301 ASP cc_start: 0.7406 (t0) cc_final: 0.7067 (t0) REVERT: E 1 MET cc_start: 0.4832 (tpt) cc_final: 0.4301 (tpp) REVERT: E 69 MET cc_start: 0.4516 (ppp) cc_final: 0.4157 (pmm) REVERT: E 213 ASP cc_start: 0.7775 (p0) cc_final: 0.7101 (p0) REVERT: F 8 MET cc_start: 0.4730 (ttm) cc_final: 0.4494 (tpp) REVERT: F 91 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7152 (mtt180) REVERT: F 170 MET cc_start: 0.7541 (tmm) cc_final: 0.7288 (tmm) REVERT: F 213 ASP cc_start: 0.7959 (t0) cc_final: 0.7675 (t70) REVERT: G 197 SER cc_start: 0.8311 (m) cc_final: 0.7686 (p) REVERT: G 362 ASP cc_start: 0.7758 (t0) cc_final: 0.7551 (t0) REVERT: G 385 TYR cc_start: 0.7242 (t80) cc_final: 0.6845 (t80) REVERT: G 452 PHE cc_start: 0.6631 (m-80) cc_final: 0.6385 (m-10) REVERT: H 196 MET cc_start: 0.7060 (ppp) cc_final: 0.6367 (ppp) REVERT: H 306 ARG cc_start: 0.7766 (ppt170) cc_final: 0.7292 (ttp80) REVERT: H 329 ASN cc_start: 0.8201 (m110) cc_final: 0.7186 (t0) REVERT: H 336 TYR cc_start: 0.8916 (t80) cc_final: 0.8444 (t80) REVERT: H 432 VAL cc_start: 0.8421 (t) cc_final: 0.8205 (m) REVERT: H 440 THR cc_start: 0.7671 (m) cc_final: 0.7408 (p) REVERT: H 469 GLU cc_start: 0.7520 (pm20) cc_final: 0.7190 (pt0) REVERT: H 475 ASN cc_start: 0.8350 (p0) cc_final: 0.7862 (p0) REVERT: I 169 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7541 (ttm110) REVERT: I 181 MET cc_start: 0.8605 (mmm) cc_final: 0.7891 (tpp) REVERT: I 260 PHE cc_start: 0.8269 (p90) cc_final: 0.7745 (p90) REVERT: J 63 GLN cc_start: 0.6704 (tt0) cc_final: 0.6204 (tt0) REVERT: J 158 ASN cc_start: 0.7736 (p0) cc_final: 0.7398 (p0) REVERT: J 239 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6750 (mm-30) REVERT: K 21 MET cc_start: 0.8258 (mmm) cc_final: 0.7479 (mmm) REVERT: K 41 ASN cc_start: 0.7062 (m-40) cc_final: 0.5921 (p0) REVERT: K 102 PHE cc_start: 0.8506 (t80) cc_final: 0.8049 (t80) REVERT: K 218 CYS cc_start: 0.7645 (m) cc_final: 0.7077 (t) REVERT: L 18 ASP cc_start: 0.6671 (m-30) cc_final: 0.5759 (t0) REVERT: L 20 VAL cc_start: 0.8200 (t) cc_final: 0.7891 (m) REVERT: L 21 MET cc_start: 0.7046 (mmp) cc_final: 0.5407 (mtp) REVERT: L 99 GLU cc_start: 0.8573 (mp0) cc_final: 0.8356 (tm-30) REVERT: L 115 VAL cc_start: -0.4062 (OUTLIER) cc_final: -0.4501 (p) REVERT: P 113 PHE cc_start: 0.3218 (m-10) cc_final: 0.2461 (p90) REVERT: P 185 ILE cc_start: 0.4375 (mm) cc_final: 0.3925 (pt) REVERT: P 238 TYR cc_start: 0.6905 (m-10) cc_final: 0.6553 (m-80) outliers start: 2 outliers final: 1 residues processed: 587 average time/residue: 0.1783 time to fit residues: 175.0142 Evaluate side-chains 456 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 148 optimal weight: 40.0000 chunk 414 optimal weight: 0.4980 chunk 145 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 288 optimal weight: 0.5980 chunk 411 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS G 309 GLN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 ASN ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 HIS ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.116856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096722 restraints weight = 113560.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097269 restraints weight = 94130.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097503 restraints weight = 72345.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098623 restraints weight = 60552.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098594 restraints weight = 52302.992| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33293 Z= 0.180 Angle : 0.777 13.456 45109 Z= 0.401 Chirality : 0.051 0.250 5298 Planarity : 0.005 0.087 5784 Dihedral : 6.901 47.316 4586 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.58 % Favored : 87.37 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.12), residues: 4188 helix: -1.16 (0.13), residues: 1328 sheet: -2.87 (0.20), residues: 523 loop : -3.20 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 225 TYR 0.030 0.002 TYR G 441 PHE 0.029 0.002 PHE J 94 TRP 0.016 0.002 TRP J 111 HIS 0.007 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00404 (33293) covalent geometry : angle 0.77734 (45109) hydrogen bonds : bond 0.04019 ( 957) hydrogen bonds : angle 5.68890 ( 2709) *********************** 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 564 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 1.373 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: A 14 MET cc_start: 0.3369 (ptt) cc_final: 0.2450 (ptm) REVERT: A 104 ILE cc_start: 0.7552 (mm) cc_final: 0.7350 (mm) REVERT: A 187 MET cc_start: 0.7923 (tpt) cc_final: 0.7160 (tpt) REVERT: A 213 ASN cc_start: 0.8530 (p0) cc_final: 0.8264 (p0) REVERT: A 222 GLN cc_start: 0.8211 (mp10) cc_final: 0.7659 (mp10) REVERT: A 274 ASP cc_start: 0.8856 (t0) cc_final: 0.8479 (t0) REVERT: A 298 ASP cc_start: 0.8136 (t70) cc_final: 0.7767 (t0) REVERT: B 20 MET cc_start: 0.3466 (tpp) cc_final: 0.3133 (tpt) REVERT: B 173 VAL cc_start: 0.8528 (t) cc_final: 0.8255 (t) REVERT: B 223 ASN cc_start: 0.7520 (t0) cc_final: 0.7224 (t0) REVERT: B 240 PRO cc_start: 0.8105 (Cg_exo) cc_final: 0.7861 (Cg_endo) REVERT: C 23 LYS cc_start: 0.8346 (pttt) cc_final: 0.7811 (tptm) REVERT: C 34 MET cc_start: 0.7217 (mpp) cc_final: 0.6812 (mpp) REVERT: C 166 MET cc_start: 0.6248 (tpt) cc_final: 0.5681 (tpt) REVERT: C 203 MET cc_start: 0.8312 (ttt) cc_final: 0.7740 (ttp) REVERT: C 238 THR cc_start: 0.8368 (p) cc_final: 0.8143 (p) REVERT: C 302 ILE cc_start: 0.8232 (mt) cc_final: 0.7923 (mt) REVERT: C 325 ILE cc_start: 0.9257 (tp) cc_final: 0.8880 (mp) REVERT: D 139 GLU cc_start: 0.8112 (mp0) cc_final: 0.7887 (mp0) REVERT: D 301 ASP cc_start: 0.7717 (t0) cc_final: 0.7349 (t0) REVERT: D 348 ASP cc_start: 0.7622 (m-30) cc_final: 0.7318 (m-30) REVERT: E 1 MET cc_start: 0.4884 (tpt) cc_final: 0.4489 (tpp) REVERT: E 213 ASP cc_start: 0.7678 (p0) cc_final: 0.7078 (p0) REVERT: E 216 MET cc_start: 0.7546 (mmt) cc_final: 0.7148 (mmt) REVERT: F 91 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7282 (mtt180) REVERT: F 203 HIS cc_start: 0.8003 (m90) cc_final: 0.7687 (m170) REVERT: F 204 LEU cc_start: 0.8993 (tt) cc_final: 0.8733 (tt) REVERT: G 197 SER cc_start: 0.8245 (m) cc_final: 0.7874 (p) REVERT: H 196 MET cc_start: 0.7168 (ppp) cc_final: 0.6495 (ppp) REVERT: H 306 ARG cc_start: 0.7789 (ppt170) cc_final: 0.7236 (ttp80) REVERT: H 310 GLU cc_start: 0.9003 (pp20) cc_final: 0.8629 (pp20) REVERT: H 329 ASN cc_start: 0.8616 (m110) cc_final: 0.7840 (t0) REVERT: I 181 MET cc_start: 0.8835 (mmm) cc_final: 0.8119 (tpp) REVERT: I 260 PHE cc_start: 0.8216 (p90) cc_final: 0.7749 (p90) REVERT: J 48 VAL cc_start: 0.8056 (p) cc_final: 0.7681 (p) REVERT: J 63 GLN cc_start: 0.7190 (tt0) cc_final: 0.6803 (tt0) REVERT: J 239 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7351 (mm-30) REVERT: K 21 MET cc_start: 0.8430 (mmm) cc_final: 0.7601 (mmm) REVERT: K 41 ASN cc_start: 0.7033 (m-40) cc_final: 0.5977 (p0) REVERT: K 102 PHE cc_start: 0.8576 (t80) cc_final: 0.8084 (t80) REVERT: K 218 CYS cc_start: 0.7662 (m) cc_final: 0.7072 (t) REVERT: L 18 ASP cc_start: 0.7092 (m-30) cc_final: 0.6170 (t0) REVERT: L 99 GLU cc_start: 0.8485 (mp0) cc_final: 0.8246 (tm-30) REVERT: P 238 TYR cc_start: 0.7024 (m-10) cc_final: 0.6649 (m-80) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.1827 time to fit residues: 171.6729 Evaluate side-chains 437 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 379 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 181 optimal weight: 50.0000 chunk 401 optimal weight: 50.0000 chunk 233 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN G 182 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.118042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.097780 restraints weight = 112484.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.098454 restraints weight = 92209.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.099069 restraints weight = 69146.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099659 restraints weight = 56938.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099810 restraints weight = 50198.759| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33293 Z= 0.146 Angle : 0.765 14.115 45109 Z= 0.388 Chirality : 0.050 0.275 5298 Planarity : 0.005 0.074 5784 Dihedral : 6.777 48.431 4586 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.37 % Favored : 88.59 % Rotamer: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.12), residues: 4188 helix: -0.99 (0.14), residues: 1319 sheet: -2.83 (0.20), residues: 523 loop : -3.16 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 428 TYR 0.028 0.002 TYR B 304 PHE 0.025 0.002 PHE D 272 TRP 0.015 0.001 TRP J 111 HIS 0.006 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00328 (33293) covalent geometry : angle 0.76478 (45109) hydrogen bonds : bond 0.03752 ( 957) hydrogen bonds : angle 5.56066 ( 2709) *********************** 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 559 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 1.256 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: A 14 MET cc_start: 0.3658 (ptt) cc_final: 0.2948 (ptm) REVERT: A 187 MET cc_start: 0.7879 (tpt) cc_final: 0.7155 (tpt) REVERT: A 222 GLN cc_start: 0.8123 (mp10) cc_final: 0.7644 (mp10) REVERT: A 274 ASP cc_start: 0.8730 (t0) cc_final: 0.8375 (t0) REVERT: A 298 ASP cc_start: 0.8000 (t70) cc_final: 0.7639 (t0) REVERT: B 173 VAL cc_start: 0.8374 (t) cc_final: 0.8115 (t) REVERT: B 222 GLN cc_start: 0.8699 (mm110) cc_final: 0.8364 (mp10) REVERT: B 223 ASN cc_start: 0.7785 (t0) cc_final: 0.7172 (t0) REVERT: B 240 PRO cc_start: 0.7850 (Cg_exo) cc_final: 0.7570 (Cg_endo) REVERT: C 23 LYS cc_start: 0.8330 (pttt) cc_final: 0.7850 (tptm) REVERT: C 34 MET cc_start: 0.7199 (mpp) cc_final: 0.6624 (mpp) REVERT: C 203 MET cc_start: 0.8224 (ttt) cc_final: 0.7699 (ttp) REVERT: C 302 ILE cc_start: 0.8140 (mt) cc_final: 0.7741 (mt) REVERT: C 325 ILE cc_start: 0.9292 (tp) cc_final: 0.8871 (mp) REVERT: D 273 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7502 (mtpt) REVERT: D 301 ASP cc_start: 0.7455 (t0) cc_final: 0.7177 (t0) REVERT: D 348 ASP cc_start: 0.7778 (m-30) cc_final: 0.7480 (m-30) REVERT: E 1 MET cc_start: 0.4618 (tpt) cc_final: 0.4148 (tpp) REVERT: E 69 MET cc_start: 0.3233 (ppp) cc_final: 0.2395 (pmm) REVERT: E 231 TYR cc_start: 0.6224 (p90) cc_final: 0.5998 (p90) REVERT: F 43 LEU cc_start: 0.9196 (tt) cc_final: 0.8994 (tt) REVERT: F 91 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7295 (mtt180) REVERT: F 170 MET cc_start: 0.7605 (tmm) cc_final: 0.7293 (tmm) REVERT: F 204 LEU cc_start: 0.8937 (tt) cc_final: 0.8554 (mp) REVERT: G 400 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7449 (ttmt) REVERT: G 482 LEU cc_start: 0.8542 (tp) cc_final: 0.8195 (tp) REVERT: H 196 MET cc_start: 0.7019 (ppp) cc_final: 0.6398 (ppp) REVERT: H 306 ARG cc_start: 0.7791 (ppt170) cc_final: 0.7256 (ttp80) REVERT: H 310 GLU cc_start: 0.8984 (pp20) cc_final: 0.8721 (pp20) REVERT: H 329 ASN cc_start: 0.8559 (m110) cc_final: 0.7590 (t0) REVERT: H 336 TYR cc_start: 0.8935 (t80) cc_final: 0.8547 (t80) REVERT: H 348 GLU cc_start: 0.7718 (tt0) cc_final: 0.7340 (mt-10) REVERT: H 415 MET cc_start: 0.6536 (mmm) cc_final: 0.5547 (mmm) REVERT: I 181 MET cc_start: 0.8759 (mmm) cc_final: 0.8091 (tpp) REVERT: I 260 PHE cc_start: 0.8239 (p90) cc_final: 0.7789 (p90) REVERT: J 63 GLN cc_start: 0.7160 (tt0) cc_final: 0.6723 (tt0) REVERT: J 239 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7425 (mm-30) REVERT: K 21 MET cc_start: 0.8444 (mmm) cc_final: 0.7725 (mmm) REVERT: K 41 ASN cc_start: 0.7010 (m-40) cc_final: 0.5984 (p0) REVERT: K 102 PHE cc_start: 0.8508 (t80) cc_final: 0.8047 (t80) REVERT: K 218 CYS cc_start: 0.7592 (m) cc_final: 0.7038 (t) REVERT: L 18 ASP cc_start: 0.7043 (m-30) cc_final: 0.6150 (t0) REVERT: L 21 MET cc_start: 0.7435 (mmp) cc_final: 0.5703 (mtp) REVERT: L 99 GLU cc_start: 0.8616 (mp0) cc_final: 0.8411 (tm-30) REVERT: L 131 PHE cc_start: 0.7034 (m-80) cc_final: 0.6686 (m-80) REVERT: P 145 MET cc_start: -0.4621 (ptm) cc_final: -0.4832 (ttp) REVERT: P 185 ILE cc_start: 0.4254 (mm) cc_final: 0.3865 (pt) REVERT: P 238 TYR cc_start: 0.7098 (m-10) cc_final: 0.6684 (m-80) outliers start: 1 outliers final: 0 residues processed: 559 average time/residue: 0.1785 time to fit residues: 167.7766 Evaluate side-chains 442 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 206 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 chunk 26 optimal weight: 0.0270 chunk 114 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 269 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** 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** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.118851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099011 restraints weight = 112188.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.099579 restraints weight = 83216.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.099901 restraints weight = 65912.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100178 restraints weight = 55704.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100494 restraints weight = 52084.888| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3620 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= 0.136 Angle : 0.757 13.692 45109 Z= 0.382 Chirality : 0.050 0.245 5298 Planarity : 0.005 0.068 5784 Dihedral : 6.618 48.248 4586 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.37 % Favored : 88.59 % Rotamer: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.12), residues: 4188 helix: -0.81 (0.14), residues: 1311 sheet: -2.68 (0.21), residues: 518 loop : -3.12 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 155 TYR 0.029 0.002 TYR G 489 PHE 0.032 0.002 PHE J 94 TRP 0.014 0.001 TRP J 111 HIS 0.005 0.001 HIS P 173 Details of bonding type rmsd covalent geometry : bond 0.00308 (33293) covalent geometry : angle 0.75693 (45109) hydrogen bonds : bond 0.03650 ( 957) hydrogen bonds : angle 5.49076 ( 2709) *********************** 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 578 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 577 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.3869 (ptt) cc_final: 0.3494 (ptm) REVERT: A 104 ILE cc_start: 0.7337 (mm) cc_final: 0.7042 (mm) REVERT: A 187 MET cc_start: 0.7828 (tpt) cc_final: 0.7078 (tpt) REVERT: A 222 GLN cc_start: 0.8104 (mp10) cc_final: 0.7519 (mp10) REVERT: A 298 ASP cc_start: 0.8073 (t70) cc_final: 0.7708 (t0) REVERT: B 34 LEU cc_start: 0.8543 (mt) cc_final: 0.8225 (pp) REVERT: B 75 PHE cc_start: 0.7703 (t80) cc_final: 0.7314 (t80) REVERT: B 173 VAL cc_start: 0.8323 (t) cc_final: 0.8097 (t) REVERT: B 222 GLN cc_start: 0.8586 (mm110) cc_final: 0.8367 (mp10) REVERT: B 223 ASN cc_start: 0.7633 (t0) cc_final: 0.7086 (t0) REVERT: B 240 PRO cc_start: 0.7634 (Cg_exo) cc_final: 0.7286 (Cg_endo) REVERT: C 23 LYS cc_start: 0.8213 (pttt) cc_final: 0.7921 (tptm) REVERT: C 34 MET cc_start: 0.7241 (mpp) cc_final: 0.6777 (mpp) REVERT: C 166 MET cc_start: 0.6944 (tpp) cc_final: 0.6368 (tpt) REVERT: C 203 MET cc_start: 0.8096 (ttt) cc_final: 0.7627 (ttp) REVERT: C 302 ILE cc_start: 0.8037 (mt) cc_final: 0.7654 (mt) REVERT: C 325 ILE cc_start: 0.9259 (tp) cc_final: 0.8829 (mp) REVERT: D 139 GLU cc_start: 0.8075 (mp0) cc_final: 0.7830 (mp0) REVERT: D 199 GLN cc_start: 0.8788 (pt0) cc_final: 0.8323 (tt0) REVERT: D 273 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7936 (ttpt) REVERT: D 301 ASP cc_start: 0.7615 (t0) cc_final: 0.7306 (t0) REVERT: D 348 ASP cc_start: 0.7631 (m-30) cc_final: 0.7389 (m-30) REVERT: E 1 MET cc_start: 0.4605 (tpt) cc_final: 0.4194 (tpp) REVERT: E 225 ARG cc_start: 0.8402 (ttt180) cc_final: 0.7020 (mmm-85) REVERT: E 231 TYR cc_start: 0.6695 (p90) cc_final: 0.6439 (p90) REVERT: F 8 MET cc_start: 0.5840 (tpp) cc_final: 0.5534 (tpp) REVERT: F 170 MET cc_start: 0.7606 (tmm) cc_final: 0.7369 (tmm) REVERT: G 482 LEU cc_start: 0.8444 (tp) cc_final: 0.8090 (tp) REVERT: G 484 LEU cc_start: 0.8893 (mp) cc_final: 0.8538 (mt) REVERT: H 196 MET cc_start: 0.6987 (ppp) cc_final: 0.6308 (ppp) REVERT: H 306 ARG cc_start: 0.7874 (ppt170) cc_final: 0.7454 (ttp80) REVERT: H 329 ASN cc_start: 0.8422 (m110) cc_final: 0.7516 (t0) REVERT: H 336 TYR cc_start: 0.8884 (t80) cc_final: 0.8550 (t80) REVERT: I 181 MET cc_start: 0.8734 (mmm) cc_final: 0.8091 (tpp) REVERT: I 260 PHE cc_start: 0.8168 (p90) cc_final: 0.7745 (p90) REVERT: J 63 GLN cc_start: 0.7072 (tt0) cc_final: 0.6636 (tt0) REVERT: J 158 ASN cc_start: 0.7599 (p0) cc_final: 0.7296 (p0) REVERT: J 239 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7252 (mm-30) REVERT: K 21 MET cc_start: 0.8436 (mmm) cc_final: 0.7663 (mmm) REVERT: K 41 ASN cc_start: 0.6991 (m-40) cc_final: 0.5975 (p0) REVERT: K 218 CYS cc_start: 0.7556 (m) cc_final: 0.7022 (t) REVERT: L 18 ASP cc_start: 0.7016 (m-30) cc_final: 0.6109 (t0) REVERT: L 45 MET cc_start: 0.6148 (tmm) cc_final: 0.5574 (tmm) REVERT: L 89 ARG cc_start: 0.6226 (pmt170) cc_final: 0.5889 (pmt170) REVERT: L 99 GLU cc_start: 0.8530 (mp0) cc_final: 0.8244 (tm-30) REVERT: L 131 PHE cc_start: 0.6751 (m-80) cc_final: 0.6450 (m-80) REVERT: P 145 MET cc_start: -0.4537 (ptm) cc_final: -0.4895 (ttp) REVERT: P 185 ILE cc_start: 0.4260 (mm) cc_final: 0.3895 (pt) REVERT: P 238 TYR cc_start: 0.7119 (m-10) cc_final: 0.6682 (m-80) outliers start: 1 outliers final: 0 residues processed: 578 average time/residue: 0.1737 time to fit residues: 167.6495 Evaluate side-chains 455 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 8 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 298 optimal weight: 0.0270 chunk 363 optimal weight: 7.9990 chunk 326 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 182 HIS G 309 GLN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN H 347 GLN H 411 ASN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 HIS J 72 ASN ** J 118 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 = 0.4054 r_free = 0.4054 target = 0.121615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101369 restraints weight = 110041.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102320 restraints weight = 92782.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.103631 restraints weight = 67077.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.103895 restraints weight = 49474.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.104021 restraints weight = 43678.092| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33293 Z= 0.124 Angle : 0.758 13.843 45109 Z= 0.378 Chirality : 0.050 0.222 5298 Planarity : 0.005 0.066 5784 Dihedral : 6.367 47.479 4586 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.41 % Favored : 89.54 % Rotamer: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.12), residues: 4188 helix: -0.73 (0.14), residues: 1317 sheet: -2.63 (0.20), residues: 549 loop : -3.02 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 428 TYR 0.028 0.002 TYR G 214 PHE 0.029 0.002 PHE I 260 TRP 0.020 0.001 TRP H 366 HIS 0.008 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00272 (33293) covalent geometry : angle 0.75811 (45109) hydrogen bonds : bond 0.03516 ( 957) hydrogen bonds : angle 5.35594 ( 2709) *********************** 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 611 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 1.270 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: A 14 MET cc_start: 0.3641 (ptt) cc_final: 0.3426 (ptm) REVERT: A 53 ILE cc_start: 0.8091 (mt) cc_final: 0.7693 (mt) REVERT: A 187 MET cc_start: 0.7716 (tpt) cc_final: 0.6883 (tpt) REVERT: A 222 GLN cc_start: 0.8090 (mp10) cc_final: 0.7611 (mp10) REVERT: A 238 LEU cc_start: 0.8849 (tp) cc_final: 0.8486 (tp) REVERT: A 298 ASP cc_start: 0.8075 (t70) cc_final: 0.7735 (t0) REVERT: B 34 LEU cc_start: 0.8448 (mt) cc_final: 0.8214 (pp) REVERT: B 75 PHE cc_start: 0.7553 (t80) cc_final: 0.7249 (t80) REVERT: B 173 VAL cc_start: 0.8476 (t) cc_final: 0.8140 (t) REVERT: B 223 ASN cc_start: 0.7587 (t0) cc_final: 0.7105 (t0) REVERT: B 240 PRO cc_start: 0.7553 (Cg_exo) cc_final: 0.7342 (Cg_endo) REVERT: C 18 PHE cc_start: 0.8071 (m-10) cc_final: 0.7595 (m-80) REVERT: C 23 LYS cc_start: 0.8438 (pttt) cc_final: 0.8002 (tptt) REVERT: C 34 MET cc_start: 0.7225 (mpp) cc_final: 0.6816 (mpp) REVERT: C 81 MET cc_start: 0.7441 (ppp) cc_final: 0.7163 (ppp) REVERT: C 166 MET cc_start: 0.6873 (tpp) cc_final: 0.6426 (tpt) REVERT: C 302 ILE cc_start: 0.8151 (mt) cc_final: 0.7586 (mt) REVERT: C 325 ILE cc_start: 0.9186 (tp) cc_final: 0.8767 (mp) REVERT: D 135 GLU cc_start: 0.8448 (pm20) cc_final: 0.8212 (pm20) REVERT: D 199 GLN cc_start: 0.8866 (pt0) cc_final: 0.8377 (tt0) REVERT: D 301 ASP cc_start: 0.7585 (t0) cc_final: 0.7269 (t0) REVERT: E 1 MET cc_start: 0.4371 (tpt) cc_final: 0.4108 (tpp) REVERT: E 213 ASP cc_start: 0.7647 (p0) cc_final: 0.7426 (p0) REVERT: E 225 ARG cc_start: 0.8383 (ttt180) cc_final: 0.7083 (mmm-85) REVERT: F 8 MET cc_start: 0.5758 (tpp) cc_final: 0.5506 (tpp) REVERT: F 91 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7264 (mtt180) REVERT: F 170 MET cc_start: 0.7567 (tmm) cc_final: 0.7167 (tmm) REVERT: F 234 ARG cc_start: 0.6749 (tpm170) cc_final: 0.6503 (tpm170) REVERT: G 196 MET cc_start: 0.4864 (tpt) cc_final: 0.4645 (tpt) REVERT: H 196 MET cc_start: 0.6772 (ppp) cc_final: 0.6090 (ppp) REVERT: H 306 ARG cc_start: 0.7850 (ppt170) cc_final: 0.7472 (ttp80) REVERT: H 329 ASN cc_start: 0.8041 (m110) cc_final: 0.7053 (t0) REVERT: H 336 TYR cc_start: 0.8839 (t80) cc_final: 0.8546 (t80) REVERT: H 475 ASN cc_start: 0.8424 (p0) cc_final: 0.7808 (p0) REVERT: H 499 LEU cc_start: 0.8179 (pt) cc_final: 0.7806 (pt) REVERT: I 169 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7622 (ttm110) REVERT: I 181 MET cc_start: 0.8660 (mmm) cc_final: 0.8115 (tpp) REVERT: I 260 PHE cc_start: 0.8017 (p90) cc_final: 0.7724 (p90) REVERT: I 310 CYS cc_start: 0.7210 (p) cc_final: 0.5606 (t) REVERT: J 63 GLN cc_start: 0.6690 (tt0) cc_final: 0.6309 (tt0) REVERT: J 75 LEU cc_start: 0.7595 (pt) cc_final: 0.7370 (pt) REVERT: J 149 LEU cc_start: 0.8334 (tp) cc_final: 0.8126 (tp) REVERT: J 158 ASN cc_start: 0.7548 (p0) cc_final: 0.7212 (p0) REVERT: J 239 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7079 (mm-30) REVERT: K 21 MET cc_start: 0.8292 (mmm) cc_final: 0.7623 (mmm) REVERT: K 41 ASN cc_start: 0.7043 (m-40) cc_final: 0.5814 (p0) REVERT: K 218 CYS cc_start: 0.7543 (m) cc_final: 0.7024 (t) REVERT: L 18 ASP cc_start: 0.6866 (m-30) cc_final: 0.5955 (t0) REVERT: L 21 MET cc_start: 0.6303 (mmp) cc_final: 0.5199 (mtp) REVERT: L 45 MET cc_start: 0.6502 (tmm) cc_final: 0.6269 (tmm) REVERT: L 99 GLU cc_start: 0.8643 (mp0) cc_final: 0.8335 (tm-30) REVERT: L 131 PHE cc_start: 0.6596 (m-80) cc_final: 0.6277 (m-80) REVERT: P 152 MET cc_start: 0.3150 (mmm) cc_final: 0.0496 (ptm) REVERT: P 185 ILE cc_start: 0.4045 (mm) cc_final: 0.3730 (pt) REVERT: P 238 TYR cc_start: 0.6975 (m-10) cc_final: 0.6657 (m-80) REVERT: P 456 TRP cc_start: 0.4935 (m-90) cc_final: 0.4492 (m-90) outliers start: 1 outliers final: 1 residues processed: 611 average time/residue: 0.1786 time to fit residues: 182.5880 Evaluate side-chains 474 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 112 optimal weight: 0.9980 chunk 319 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 373 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN D 132 ASN G 182 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN H 347 GLN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.120524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.100845 restraints weight = 110440.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101589 restraints weight = 95115.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102473 restraints weight = 73161.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102868 restraints weight = 56749.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103038 restraints weight = 51046.501| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33293 Z= 0.133 Angle : 0.760 13.616 45109 Z= 0.381 Chirality : 0.050 0.231 5298 Planarity : 0.005 0.066 5784 Dihedral : 6.292 46.417 4586 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.84 % Favored : 89.11 % Rotamer: Outliers : 0.09 % Allowed : 1.00 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.12), residues: 4188 helix: -0.64 (0.14), residues: 1300 sheet: -2.63 (0.20), residues: 548 loop : -2.92 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 428 TYR 0.031 0.002 TYR C 344 PHE 0.030 0.002 PHE P 113 TRP 0.014 0.001 TRP J 111 HIS 0.007 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00303 (33293) covalent geometry : angle 0.75991 (45109) hydrogen bonds : bond 0.03573 ( 957) hydrogen bonds : angle 5.38005 ( 2709) *********************** 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 578 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 575 time to evaluate : 1.124 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: A 14 MET cc_start: 0.3888 (ptt) cc_final: 0.3584 (ptm) REVERT: A 53 ILE cc_start: 0.7997 (mt) cc_final: 0.7647 (mt) REVERT: A 187 MET cc_start: 0.7645 (tpt) cc_final: 0.7299 (tpt) REVERT: A 222 GLN cc_start: 0.8222 (mp10) cc_final: 0.7958 (mp10) REVERT: A 298 ASP cc_start: 0.8007 (t70) cc_final: 0.7756 (t0) REVERT: B 75 PHE cc_start: 0.7686 (t80) cc_final: 0.7300 (t80) REVERT: B 156 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8466 (tp40) REVERT: B 173 VAL cc_start: 0.8379 (t) cc_final: 0.8065 (t) REVERT: B 222 GLN cc_start: 0.8716 (mm110) cc_final: 0.8010 (mm-40) REVERT: B 223 ASN cc_start: 0.7693 (t0) cc_final: 0.7238 (t0) REVERT: C 18 PHE cc_start: 0.8015 (m-10) cc_final: 0.7745 (m-80) REVERT: C 23 LYS cc_start: 0.8219 (pttt) cc_final: 0.8013 (tptt) REVERT: C 34 MET cc_start: 0.7413 (mpp) cc_final: 0.6936 (mpp) REVERT: C 166 MET cc_start: 0.6938 (tpp) cc_final: 0.6383 (tpt) REVERT: C 302 ILE cc_start: 0.8176 (mt) cc_final: 0.7713 (mt) REVERT: C 325 ILE cc_start: 0.9181 (tp) cc_final: 0.8862 (mp) REVERT: C 347 ASP cc_start: 0.8090 (m-30) cc_final: 0.7232 (t0) REVERT: D 199 GLN cc_start: 0.8907 (pt0) cc_final: 0.8695 (pt0) REVERT: D 288 PHE cc_start: 0.7853 (m-80) cc_final: 0.7167 (m-80) REVERT: D 301 ASP cc_start: 0.7609 (t0) cc_final: 0.7272 (t0) REVERT: E 1 MET cc_start: 0.4985 (tpt) cc_final: 0.4645 (tpp) REVERT: E 213 ASP cc_start: 0.7395 (p0) cc_final: 0.7178 (p0) REVERT: E 225 ARG cc_start: 0.8403 (ttt180) cc_final: 0.7118 (mmm-85) REVERT: F 8 MET cc_start: 0.5799 (tpp) cc_final: 0.5508 (tpp) REVERT: F 91 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7293 (mtt180) REVERT: F 170 MET cc_start: 0.7549 (tmm) cc_final: 0.7161 (tmm) REVERT: G 384 SER cc_start: 0.8202 (m) cc_final: 0.7866 (m) REVERT: G 452 PHE cc_start: 0.6279 (m-80) cc_final: 0.5742 (m-80) REVERT: H 196 MET cc_start: 0.6860 (ppp) cc_final: 0.6056 (ppp) REVERT: H 301 ARG cc_start: 0.7799 (pmt-80) cc_final: 0.7471 (pmt-80) REVERT: H 306 ARG cc_start: 0.7851 (ppt170) cc_final: 0.7489 (ttp80) REVERT: H 329 ASN cc_start: 0.8116 (m110) cc_final: 0.7164 (t0) REVERT: H 336 TYR cc_start: 0.8889 (t80) cc_final: 0.8594 (t80) REVERT: H 415 MET cc_start: 0.6518 (mmm) cc_final: 0.5477 (mmm) REVERT: I 169 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7841 (ttm110) REVERT: I 181 MET cc_start: 0.8691 (mmm) cc_final: 0.8124 (tpp) REVERT: I 260 PHE cc_start: 0.8090 (p90) cc_final: 0.7747 (p90) REVERT: I 347 GLU cc_start: 0.6916 (pm20) cc_final: 0.6684 (pm20) REVERT: J 63 GLN cc_start: 0.6748 (tt0) cc_final: 0.6387 (tt0) REVERT: J 149 LEU cc_start: 0.8354 (tp) cc_final: 0.8129 (tp) REVERT: J 158 ASN cc_start: 0.7654 (p0) cc_final: 0.7371 (p0) REVERT: J 183 MET cc_start: 0.7075 (tmm) cc_final: 0.6463 (tmm) REVERT: J 239 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6787 (mm-30) REVERT: J 329 ASP cc_start: 0.7916 (m-30) cc_final: 0.7370 (p0) REVERT: K 21 MET cc_start: 0.8263 (mmm) cc_final: 0.7659 (mmm) REVERT: K 41 ASN cc_start: 0.6958 (m-40) cc_final: 0.5933 (p0) REVERT: K 218 CYS cc_start: 0.7631 (m) cc_final: 0.7082 (t) REVERT: L 18 ASP cc_start: 0.6902 (m-30) cc_final: 0.6005 (t0) REVERT: L 21 MET cc_start: 0.6464 (mmp) cc_final: 0.5282 (mtp) REVERT: L 99 GLU cc_start: 0.8620 (mp0) cc_final: 0.8415 (tm-30) REVERT: L 131 PHE cc_start: 0.6482 (m-80) cc_final: 0.6122 (m-80) REVERT: P 152 MET cc_start: 0.2765 (mmm) cc_final: -0.0123 (ptt) REVERT: P 185 ILE cc_start: 0.3938 (mm) cc_final: 0.3696 (pt) REVERT: P 238 TYR cc_start: 0.6935 (m-10) cc_final: 0.6650 (m-80) REVERT: P 456 TRP cc_start: 0.4905 (m-90) cc_final: 0.4500 (m-90) outliers start: 3 outliers final: 0 residues processed: 578 average time/residue: 0.1764 time to fit residues: 172.1689 Evaluate side-chains 459 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 268 optimal weight: 0.8980 chunk 273 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 165 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 182 optimal weight: 50.0000 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS J 72 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 ASN P 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.117662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097348 restraints weight = 113212.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.098037 restraints weight = 94316.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098898 restraints weight = 70158.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.099310 restraints weight = 56252.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.099468 restraints weight = 49736.953| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 33293 Z= 0.173 Angle : 0.793 14.138 45109 Z= 0.404 Chirality : 0.051 0.223 5298 Planarity : 0.005 0.085 5784 Dihedral : 6.437 46.502 4586 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.96 % Favored : 87.99 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.12), residues: 4188 helix: -0.74 (0.14), residues: 1305 sheet: -2.75 (0.19), residues: 579 loop : -2.94 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 36 TYR 0.026 0.002 TYR B 304 PHE 0.029 0.002 PHE A 72 TRP 0.017 0.002 TRP J 111 HIS 0.007 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00392 (33293) covalent geometry : angle 0.79325 (45109) hydrogen bonds : bond 0.03829 ( 957) hydrogen bonds : angle 5.52071 ( 2709) ********************** 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 555 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 554 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.4019 (ptt) cc_final: 0.3736 (ptm) REVERT: A 53 ILE cc_start: 0.8163 (mt) cc_final: 0.7777 (mt) REVERT: A 187 MET cc_start: 0.7674 (tpt) cc_final: 0.7087 (tpt) REVERT: A 222 GLN cc_start: 0.8254 (mp10) cc_final: 0.7908 (mp10) REVERT: A 298 ASP cc_start: 0.8116 (t70) cc_final: 0.7700 (t0) REVERT: B 20 MET cc_start: 0.4019 (tpp) cc_final: 0.3757 (tpt) REVERT: B 222 GLN cc_start: 0.8675 (mm110) cc_final: 0.8048 (mm110) REVERT: B 223 ASN cc_start: 0.7651 (t0) cc_final: 0.7255 (t0) REVERT: C 23 LYS cc_start: 0.8319 (pttt) cc_final: 0.7972 (tptt) REVERT: C 166 MET cc_start: 0.7076 (tpp) cc_final: 0.6506 (tpt) REVERT: C 207 LEU cc_start: 0.8986 (pp) cc_final: 0.8703 (pp) REVERT: C 238 THR cc_start: 0.8213 (p) cc_final: 0.7965 (p) REVERT: C 302 ILE cc_start: 0.8113 (mt) cc_final: 0.7753 (mt) REVERT: D 199 GLN cc_start: 0.9010 (pt0) cc_final: 0.8762 (pt0) REVERT: D 301 ASP cc_start: 0.7772 (t0) cc_final: 0.7476 (t0) REVERT: E 1 MET cc_start: 0.5092 (tpt) cc_final: 0.4654 (tpp) REVERT: E 177 ASP cc_start: 0.6932 (t70) cc_final: 0.6716 (t70) REVERT: E 225 ARG cc_start: 0.8483 (ttt180) cc_final: 0.7078 (mmm-85) REVERT: F 8 MET cc_start: 0.5636 (tpp) cc_final: 0.5185 (tpp) REVERT: F 130 MET cc_start: 0.8073 (mmt) cc_final: 0.7683 (tpp) REVERT: F 204 LEU cc_start: 0.9012 (tt) cc_final: 0.8783 (mp) REVERT: G 482 LEU cc_start: 0.8430 (tp) cc_final: 0.8166 (tp) REVERT: H 196 MET cc_start: 0.7007 (ppp) cc_final: 0.6330 (ppp) REVERT: H 306 ARG cc_start: 0.7811 (ppt170) cc_final: 0.7377 (ttp80) REVERT: H 329 ASN cc_start: 0.8479 (m110) cc_final: 0.7725 (t0) REVERT: H 336 TYR cc_start: 0.8902 (t80) cc_final: 0.8617 (t80) REVERT: H 415 MET cc_start: 0.6775 (mmm) cc_final: 0.5754 (mmm) REVERT: I 260 PHE cc_start: 0.8224 (p90) cc_final: 0.7852 (p90) REVERT: I 305 MET cc_start: 0.7556 (ptm) cc_final: 0.7321 (ppp) REVERT: J 48 VAL cc_start: 0.8056 (p) cc_final: 0.7633 (p) REVERT: J 63 GLN cc_start: 0.7113 (tt0) cc_final: 0.6667 (tt0) REVERT: J 149 LEU cc_start: 0.8546 (tp) cc_final: 0.8265 (tp) REVERT: J 158 ASN cc_start: 0.7687 (p0) cc_final: 0.7351 (p0) REVERT: J 181 MET cc_start: 0.8220 (tpp) cc_final: 0.7473 (tpt) REVERT: J 239 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7148 (mm-30) REVERT: J 355 ILE cc_start: 0.8492 (tt) cc_final: 0.7718 (mp) REVERT: K 21 MET cc_start: 0.8551 (mmm) cc_final: 0.7971 (mmm) REVERT: K 41 ASN cc_start: 0.6892 (m-40) cc_final: 0.5657 (p0) REVERT: K 218 CYS cc_start: 0.7604 (m) cc_final: 0.7058 (t) REVERT: L 18 ASP cc_start: 0.7063 (m-30) cc_final: 0.6143 (t0) REVERT: L 21 MET cc_start: 0.7251 (mmp) cc_final: 0.5716 (mtp) REVERT: L 45 MET cc_start: 0.6329 (tmm) cc_final: 0.6078 (tmm) REVERT: L 131 PHE cc_start: 0.6805 (m-80) cc_final: 0.5843 (m-80) REVERT: P 152 MET cc_start: 0.2802 (mmm) cc_final: -0.0156 (ptt) REVERT: P 185 ILE cc_start: 0.4124 (mm) cc_final: 0.3819 (pt) REVERT: P 238 TYR cc_start: 0.6917 (m-10) cc_final: 0.6501 (m-80) REVERT: P 456 TRP cc_start: 0.5108 (m-90) cc_final: 0.4633 (m-90) outliers start: 1 outliers final: 1 residues processed: 555 average time/residue: 0.1757 time to fit residues: 164.7749 Evaluate side-chains 444 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 74 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 384 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 275 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 387 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN G 182 HIS ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN ** H 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.099065 restraints weight = 111891.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100102 restraints weight = 88820.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100683 restraints weight = 65403.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101173 restraints weight = 54447.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101315 restraints weight = 49325.964| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4261 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= 0.135 Angle : 0.775 14.075 45109 Z= 0.387 Chirality : 0.050 0.228 5298 Planarity : 0.005 0.081 5784 Dihedral : 6.300 45.919 4586 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.65 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.12), residues: 4188 helix: -0.61 (0.14), residues: 1293 sheet: -2.56 (0.22), residues: 463 loop : -2.80 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 428 TYR 0.027 0.002 TYR B 304 PHE 0.028 0.002 PHE P 113 TRP 0.016 0.001 TRP D 51 HIS 0.006 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00308 (33293) covalent geometry : angle 0.77472 (45109) hydrogen bonds : bond 0.03652 ( 957) hydrogen bonds : angle 5.39409 ( 2709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.91 seconds wall clock time: 87 minutes 16.18 seconds (5236.18 seconds total)