Starting phenix.real_space_refine on Sun Jun 22 22:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d46_30571/06_2025/7d46_30571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d46_30571/06_2025/7d46_30571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d46_30571/06_2025/7d46_30571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d46_30571/06_2025/7d46_30571.map" model { file = "/net/cci-nas-00/data/ceres_data/7d46_30571/06_2025/7d46_30571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d46_30571/06_2025/7d46_30571.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 142 5.16 5 C 16872 2.51 5 N 4649 2.21 5 O 4973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26636 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2249 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2489 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2515 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2445 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 11, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2445 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 11, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Time building chain proxies: 20.56, per 1000 atoms: 0.77 Number of scatterers: 26636 At special positions: 0 Unit cell: (166.11, 166.11, 160.23, 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 142 16.00 O 4973 8.00 N 4649 7.00 C 16872 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: 9.41 Conformation dependent library (CDL) restraints added in 5.3 seconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6594 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 37 sheets defined 39.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.844A pdb=" N GLU A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.607A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 62 through 75 removed outlier: 4.184A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 4.465A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.079A pdb=" N ALA A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.977A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.595A pdb=" N LYS A 234 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.552A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'B' and resid 2 through 16 removed outlier: 4.468A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.689A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 116 removed outlier: 4.527A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 292 through 305 removed outlier: 3.513A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 removed outlier: 3.670A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 4.372A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 95 Processing helix chain 'C' and resid 129 through 146 removed outlier: 3.750A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.745A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.939A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.972A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.631A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 71 removed outlier: 4.928A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 96 removed outlier: 3.901A pdb=" N ASN D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.068A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.815A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.905A pdb=" N VAL D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.773A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.723A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.869A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 46 removed outlier: 3.930A pdb=" N VAL E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.885A pdb=" N GLU E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.666A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.627A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 removed outlier: 4.071A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 235 Processing helix chain 'E' and resid 277 through 292 removed outlier: 4.291A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.849A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 86 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.215A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.504A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 277 through 292 removed outlier: 4.265A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.960A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.752A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 222 through 239 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.350A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 284 Processing helix chain 'G' and resid 292 through 311 Processing helix chain 'G' and resid 313 through 324 removed outlier: 3.521A pdb=" N GLN G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) 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 339 through 350 Processing helix chain 'G' and resid 369 through 377 Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.500A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 430 removed outlier: 4.576A pdb=" N GLN G 422 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 463 removed outlier: 3.860A pdb=" N LEU G 463 " --> pdb=" O PRO G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 516 removed outlier: 3.741A pdb=" N VAL G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.649A pdb=" N SER H 181 " --> pdb=" O SER H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 239 Processing helix chain 'H' and resid 247 through 267 removed outlier: 5.006A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 284 Processing helix chain 'H' and resid 285 through 287 No H-bonds generated for 'chain 'H' and resid 285 through 287' Processing helix chain 'H' and resid 292 through 311 Processing helix chain 'H' and resid 314 through 324 Processing helix chain 'H' and resid 339 through 351 removed outlier: 4.119A pdb=" N THR H 351 " --> pdb=" O GLN H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 377 Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.847A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 390 through 395' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 removed outlier: 3.800A pdb=" N PHE H 443 " --> pdb=" O THR H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 463 Processing helix chain 'H' and resid 508 through 512 Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.523A pdb=" N ASP I 62 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 98 through 107 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 161 through 175 removed outlier: 3.799A pdb=" N GLU I 175 " --> pdb=" O ARG I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.051A pdb=" N SER I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 262 Processing helix chain 'I' and resid 268 through 279 removed outlier: 3.642A pdb=" N ASN I 279 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 314 Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.608A pdb=" N ASN I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 63 removed outlier: 4.394A pdb=" N ASP J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 63' Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.792A pdb=" N LEU J 68 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.689A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.866A pdb=" N GLU J 175 " --> pdb=" O ARG J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 Processing helix chain 'J' and resid 253 through 262 removed outlier: 3.550A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 322 through 326 Processing helix chain 'J' and resid 338 through 342 removed outlier: 3.528A pdb=" N ASN J 341 " --> pdb=" O SER J 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 6.451A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 286 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.787A pdb=" N ASN A 208 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.656A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.052A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.668A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 314 " --> pdb=" O ALA C 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AA9, first strand: chain 'D' and resid 189 through 193 removed outlier: 5.782A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU D 193 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 217 " --> pdb=" O GLU D 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 236 through 239 Processing sheet with id=AB2, first strand: chain 'D' and resid 324 through 326 removed outlier: 3.850A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 329 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 51 through 52 removed outlier: 7.036A pdb=" N VAL E 51 " --> pdb=" O VAL E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 200 through 207 removed outlier: 3.915A pdb=" N ALA E 202 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU E 128 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE E 266 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET E 130 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS E 268 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET E 132 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 167 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.968A pdb=" N VAL E 408 " --> pdb=" O ILE E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 7 through 8 removed outlier: 4.012A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA F 202 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ARG F 133 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU F 204 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AB9, first strand: chain 'F' and resid 167 through 170 removed outlier: 6.377A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL I 202 " --> pdb=" O PHE I 215 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE I 215 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG I 211 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AC2, first strand: chain 'F' and resid 402 through 405 Processing sheet with id=AC3, first strand: chain 'G' and resid 385 through 387 removed outlier: 3.550A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR G 336 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 499 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 507 " --> pdb=" O VAL G 500 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR G 502 " --> pdb=" O GLY G 505 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 407 through 408 removed outlier: 3.888A pdb=" N VAL G 414 " --> pdb=" O THR G 492 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR G 492 " --> pdb=" O VAL G 414 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 385 through 387 removed outlier: 8.944A pdb=" N LEU H 386 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL H 360 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.735A pdb=" N VAL H 414 " --> pdb=" O THR H 492 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 500 through 502 removed outlier: 3.678A pdb=" N ILE H 507 " --> pdb=" O VAL H 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 120 through 122 removed outlier: 3.637A pdb=" N ALA I 45 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL I 151 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL I 46 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AD1, first strand: chain 'I' and resid 186 through 187 Processing sheet with id=AD2, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.524A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 91 through 94 removed outlier: 7.518A pdb=" N ALA J 45 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE J 94 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU J 47 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL J 46 " --> pdb=" O VAL J 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AD5, first strand: chain 'J' and resid 179 through 182 removed outlier: 4.471A pdb=" N SER J 179 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N HIS J 288 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N MET J 181 " --> pdb=" O HIS J 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 244 through 246 removed outlier: 3.580A pdb=" N LYS J 186 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE J 185 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.434A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 241 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 205 " --> pdb=" O GLU J 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 361 through 362 removed outlier: 6.024A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 373 through 375 removed outlier: 3.540A pdb=" N ASP J 392 " --> pdb=" O ILE J 408 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 395 through 396 removed outlier: 6.707A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 919 hydrogen bonds defined for protein. 2610 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: 13.05 Time building geometry restraints manager: 9.84 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: 8897 1.34 - 1.46: 4331 1.46 - 1.58: 13665 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 27109 Sorted by residual: bond pdb=" CA ASP D 219 " pdb=" C ASP D 219 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.34e-02 5.57e+03 1.51e+01 bond pdb=" CA SER D 334 " pdb=" C SER D 334 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.59e-02 3.96e+03 1.37e+01 bond pdb=" CA ALA H 349 " pdb=" C ALA H 349 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" C VAL B 193 " pdb=" N ILE B 194 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" CA ALA A 219 " pdb=" C ALA A 219 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.40e-02 5.10e+03 7.85e+00 ... (remaining 27104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 35898 2.54 - 5.07: 788 5.07 - 7.61: 79 7.61 - 10.14: 9 10.14 - 12.68: 1 Bond angle restraints: 36775 Sorted by residual: angle pdb=" C SER D 326 " pdb=" N ASN D 327 " pdb=" CA ASN D 327 " ideal model delta sigma weight residual 122.65 113.65 9.00 1.66e+00 3.63e-01 2.94e+01 angle pdb=" N ILE A 42 " pdb=" CA ILE A 42 " pdb=" C ILE A 42 " ideal model delta sigma weight residual 113.71 108.63 5.08 9.50e-01 1.11e+00 2.86e+01 angle pdb=" N ASP I 62 " pdb=" CA ASP I 62 " pdb=" C ASP I 62 " ideal model delta sigma weight residual 113.43 107.83 5.60 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N VAL H 488 " pdb=" CA VAL H 488 " pdb=" C VAL H 488 " ideal model delta sigma weight residual 113.20 109.21 3.99 9.60e-01 1.09e+00 1.73e+01 angle pdb=" N VAL J 66 " pdb=" CA VAL J 66 " pdb=" C VAL J 66 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 ... (remaining 36770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 14333 17.16 - 34.31: 1744 34.31 - 51.47: 348 51.47 - 68.63: 46 68.63 - 85.78: 13 Dihedral angle restraints: 16484 sinusoidal: 6343 harmonic: 10141 Sorted by residual: dihedral pdb=" CA LEU I 431 " pdb=" C LEU I 431 " pdb=" N THR I 432 " pdb=" CA THR I 432 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG H 417 " pdb=" C ARG H 417 " pdb=" N VAL H 418 " pdb=" CA VAL H 418 " ideal model delta harmonic sigma weight residual -180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE C 278 " pdb=" C PHE C 278 " pdb=" N PRO C 279 " pdb=" CA PRO C 279 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 16481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2825 0.046 - 0.092: 1153 0.092 - 0.137: 313 0.137 - 0.183: 33 0.183 - 0.229: 3 Chirality restraints: 4327 Sorted by residual: chirality pdb=" CB ILE I 441 " pdb=" CA ILE I 441 " pdb=" CG1 ILE I 441 " pdb=" CG2 ILE I 441 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE J 355 " pdb=" CA ILE J 355 " pdb=" CG1 ILE J 355 " pdb=" CG2 ILE J 355 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO C 279 " pdb=" N PRO C 279 " pdb=" C PRO C 279 " pdb=" CB PRO C 279 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 4324 not shown) Planarity restraints: 4730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO H 396 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO G 396 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 94 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO F 95 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 95 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 95 " 0.030 5.00e-02 4.00e+02 ... (remaining 4727 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 864 2.67 - 3.23: 27854 3.23 - 3.79: 40213 3.79 - 4.34: 51932 4.34 - 4.90: 86508 Nonbonded interactions: 207371 Sorted by model distance: nonbonded pdb=" NZ LYS F 268 " pdb=" O ASN F 271 " model vdw 2.116 3.120 nonbonded pdb=" NH2 ARG C 228 " pdb=" OD2 ASP G 450 " model vdw 2.138 3.120 nonbonded pdb=" O SER D 74 " pdb=" NH2 ARG D 246 " model vdw 2.142 3.120 nonbonded pdb=" O VAL A 63 " pdb=" OG SER A 67 " model vdw 2.155 3.040 nonbonded pdb=" OG SER E 105 " pdb=" OD1 ASP E 107 " model vdw 2.157 3.040 ... (remaining 207366 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 1 through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or (resid 122 through 127 and (name N or name \ CA or name C or name O or name CB )) or resid 128 through 351)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 41 through 467) } 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: 177.670 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: 0.040 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 73.750 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 27109 Z= 0.347 Angle : 0.930 12.676 36775 Z= 0.539 Chirality : 0.051 0.229 4327 Planarity : 0.005 0.061 4730 Dihedral : 15.192 85.783 9890 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.52 % Favored : 82.43 % Rotamer: Outliers : 0.42 % Allowed : 11.66 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.12), residues: 3437 helix: -2.23 (0.12), residues: 1212 sheet: -4.58 (0.18), residues: 457 loop : -4.00 (0.12), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 51 HIS 0.009 0.002 HIS D 125 PHE 0.033 0.002 PHE A 239 TYR 0.028 0.003 TYR G 441 ARG 0.006 0.001 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.15783 ( 919) hydrogen bonds : angle 6.89255 ( 2610) covalent geometry : bond 0.00776 (27109) covalent geometry : angle 0.92969 (36775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 585 time to evaluate : 3.952 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: A 10 PHE cc_start: 0.7906 (t80) cc_final: 0.7625 (t80) REVERT: A 187 MET cc_start: 0.8834 (tpp) cc_final: 0.8577 (mmm) REVERT: B 1 MET cc_start: 0.2450 (mmm) cc_final: 0.2168 (tpp) REVERT: B 75 PHE cc_start: 0.6977 (t80) cc_final: 0.6693 (t80) REVERT: B 187 MET cc_start: 0.9255 (tpp) cc_final: 0.8600 (tpt) REVERT: B 200 VAL cc_start: 0.8680 (t) cc_final: 0.8337 (t) REVERT: B 304 TYR cc_start: 0.7904 (m-80) cc_final: 0.7426 (m-10) REVERT: C 46 ILE cc_start: 0.8668 (mm) cc_final: 0.8287 (mt) REVERT: C 49 HIS cc_start: 0.7499 (m90) cc_final: 0.7107 (m-70) REVERT: C 51 TRP cc_start: 0.7322 (p90) cc_final: 0.7122 (p-90) REVERT: C 68 MET cc_start: 0.7885 (tpp) cc_final: 0.7371 (mmt) REVERT: C 199 GLN cc_start: 0.8011 (mt0) cc_final: 0.7808 (mt0) REVERT: C 203 MET cc_start: 0.8140 (ttt) cc_final: 0.7854 (ttt) REVERT: C 217 MET cc_start: 0.7943 (ptp) cc_final: 0.7246 (ptp) REVERT: C 226 MET cc_start: 0.8993 (tpt) cc_final: 0.8387 (tpt) REVERT: C 292 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 37 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7210 (mt-10) REVERT: D 166 MET cc_start: 0.8142 (mtp) cc_final: 0.7899 (mtp) REVERT: D 226 MET cc_start: 0.8861 (tpt) cc_final: 0.8200 (tpp) REVERT: D 340 MET cc_start: 0.8806 (mmt) cc_final: 0.8581 (mmm) REVERT: D 342 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7317 (tt0) REVERT: D 347 ASP cc_start: 0.5760 (p0) cc_final: 0.5530 (p0) REVERT: E 41 ASN cc_start: 0.8742 (t0) cc_final: 0.8377 (t0) REVERT: E 44 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6871 (mm-30) REVERT: E 94 TYR cc_start: 0.8773 (t80) cc_final: 0.8531 (t80) REVERT: E 98 LYS cc_start: 0.8046 (tppt) cc_final: 0.7419 (tptt) REVERT: E 120 LEU cc_start: 0.8202 (tp) cc_final: 0.7797 (tp) REVERT: E 132 MET cc_start: 0.9015 (ttm) cc_final: 0.8673 (ttm) REVERT: E 134 LYS cc_start: 0.7283 (ttpt) cc_final: 0.6888 (tttp) REVERT: E 156 ASP cc_start: 0.5791 (p0) cc_final: 0.5459 (p0) REVERT: E 232 LEU cc_start: 0.9119 (tp) cc_final: 0.8723 (tt) REVERT: F 44 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 130 MET cc_start: 0.8428 (ptp) cc_final: 0.8063 (ptm) REVERT: F 132 MET cc_start: 0.8304 (ttm) cc_final: 0.7940 (ttm) REVERT: G 362 ASP cc_start: 0.8997 (t70) cc_final: 0.8664 (t0) REVERT: H 192 LEU cc_start: 0.9386 (mt) cc_final: 0.9022 (tp) REVERT: H 238 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7218 (tp40) REVERT: H 341 LEU cc_start: 0.9269 (tp) cc_final: 0.9067 (tt) REVERT: I 128 TYR cc_start: 0.7496 (p90) cc_final: 0.6894 (p90) REVERT: I 129 ARG cc_start: 0.7385 (mmt-90) cc_final: 0.7068 (mtp85) REVERT: J 80 LEU cc_start: 0.8175 (mt) cc_final: 0.7853 (mp) REVERT: J 81 GLU cc_start: 0.8112 (tp30) cc_final: 0.7891 (tm-30) REVERT: J 128 TYR cc_start: 0.5906 (p90) cc_final: 0.5632 (p90) REVERT: J 266 TYR cc_start: 0.8810 (m-10) cc_final: 0.8308 (m-80) REVERT: J 389 VAL cc_start: 0.8478 (p) cc_final: 0.8248 (p) REVERT: J 412 LEU cc_start: 0.9272 (tt) cc_final: 0.9006 (tt) outliers start: 12 outliers final: 11 residues processed: 596 average time/residue: 0.4071 time to fit residues: 379.7070 Evaluate side-chains 430 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 419 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 312 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 244 GLN A 270 HIS B 170 HIS C 130 GLN C 158 HIS C 188 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 150 ASN D 154 GLN D 160 HIS D 162 ASN D 242 ASN D 261 HIS D 280 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 271 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 ASN G 431 ASN H 254 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN I 376 ASN J 44 GLN J 214 HIS J 352 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116842 restraints weight = 39456.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115914 restraints weight = 47629.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116898 restraints weight = 45199.432| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27109 Z= 0.163 Angle : 0.698 11.600 36775 Z= 0.353 Chirality : 0.047 0.275 4327 Planarity : 0.005 0.071 4730 Dihedral : 5.717 36.346 3755 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.92 % Allowed : 18.51 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.13), residues: 3437 helix: -0.74 (0.14), residues: 1221 sheet: -4.06 (0.20), residues: 457 loop : -3.29 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 51 HIS 0.011 0.001 HIS B 170 PHE 0.022 0.002 PHE D 177 TYR 0.025 0.002 TYR F 38 ARG 0.005 0.000 ARG J 172 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 919) hydrogen bonds : angle 5.04870 ( 2610) covalent geometry : bond 0.00387 (27109) covalent geometry : angle 0.69837 (36775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 519 time to evaluate : 3.336 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: A 113 ASP cc_start: 0.8009 (p0) cc_final: 0.7340 (t0) REVERT: A 187 MET cc_start: 0.8785 (tpp) cc_final: 0.8447 (mmm) REVERT: B 28 ARG cc_start: 0.6506 (ttt180) cc_final: 0.5523 (ptm160) REVERT: B 187 MET cc_start: 0.9196 (tpp) cc_final: 0.8621 (tpt) REVERT: B 200 VAL cc_start: 0.8461 (t) cc_final: 0.8115 (t) REVERT: C 49 HIS cc_start: 0.7138 (m90) cc_final: 0.6757 (m-70) REVERT: C 217 MET cc_start: 0.7619 (ptp) cc_final: 0.6548 (ptp) REVERT: D 223 PHE cc_start: 0.8102 (t80) cc_final: 0.7672 (t80) REVERT: D 280 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.7010 (t0) REVERT: D 340 MET cc_start: 0.8753 (mmt) cc_final: 0.8457 (mmm) REVERT: D 342 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7316 (tt0) REVERT: D 347 ASP cc_start: 0.6178 (p0) cc_final: 0.5892 (p0) REVERT: E 41 ASN cc_start: 0.8645 (t0) cc_final: 0.8315 (t0) REVERT: E 44 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7481 (mm-30) REVERT: E 94 TYR cc_start: 0.8693 (t80) cc_final: 0.8360 (t80) REVERT: E 98 LYS cc_start: 0.7926 (tppt) cc_final: 0.7422 (tptt) REVERT: E 120 LEU cc_start: 0.8040 (tp) cc_final: 0.7748 (tp) REVERT: E 132 MET cc_start: 0.8995 (ttm) cc_final: 0.8584 (ttm) REVERT: E 216 MET cc_start: 0.6908 (tpp) cc_final: 0.6535 (tpp) REVERT: G 362 ASP cc_start: 0.8882 (t70) cc_final: 0.8628 (t0) REVERT: G 386 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7067 (pp) REVERT: H 238 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7266 (tp40) REVERT: H 341 LEU cc_start: 0.9027 (tp) cc_final: 0.8760 (tt) REVERT: H 485 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8995 (pt) REVERT: I 129 ARG cc_start: 0.7324 (mmt-90) cc_final: 0.7075 (mtp85) REVERT: I 289 MET cc_start: 0.8881 (ttm) cc_final: 0.8672 (ttp) REVERT: I 326 ASN cc_start: 0.8698 (t0) cc_final: 0.8441 (t0) REVERT: I 431 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8858 (pp) REVERT: J 80 LEU cc_start: 0.8139 (mt) cc_final: 0.7850 (mp) REVERT: J 128 TYR cc_start: 0.5633 (p90) cc_final: 0.4968 (p90) REVERT: J 266 TYR cc_start: 0.8785 (m-10) cc_final: 0.8252 (m-80) REVERT: J 302 ASN cc_start: 0.8802 (p0) cc_final: 0.8541 (p0) REVERT: J 412 LEU cc_start: 0.8994 (tt) cc_final: 0.8727 (tt) outliers start: 83 outliers final: 46 residues processed: 570 average time/residue: 0.3644 time to fit residues: 336.7940 Evaluate side-chains 481 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 431 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 488 VAL Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 313 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 301 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 300 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS C 158 HIS D 154 GLN D 158 HIS D 280 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 ASN G 478 ASN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 ASN I 248 HIS J 248 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118047 restraints weight = 39019.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117218 restraints weight = 47901.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118584 restraints weight = 45792.086| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27109 Z= 0.147 Angle : 0.655 10.455 36775 Z= 0.328 Chirality : 0.046 0.271 4327 Planarity : 0.005 0.074 4730 Dihedral : 5.366 40.006 3749 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.90 % Allowed : 21.11 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.14), residues: 3437 helix: -0.09 (0.15), residues: 1226 sheet: -3.98 (0.19), residues: 485 loop : -2.90 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 51 HIS 0.012 0.001 HIS B 170 PHE 0.034 0.002 PHE B 285 TYR 0.016 0.002 TYR B 185 ARG 0.007 0.000 ARG J 65 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 919) hydrogen bonds : angle 4.64955 ( 2610) covalent geometry : bond 0.00352 (27109) covalent geometry : angle 0.65506 (36775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 489 time to evaluate : 2.824 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: A 113 ASP cc_start: 0.7811 (p0) cc_final: 0.7450 (t0) REVERT: A 145 LYS cc_start: 0.7359 (mtpt) cc_final: 0.7017 (ptmm) REVERT: B 28 ARG cc_start: 0.6402 (ttt180) cc_final: 0.5382 (ttm110) REVERT: B 187 MET cc_start: 0.9180 (tpp) cc_final: 0.8685 (tpt) REVERT: B 200 VAL cc_start: 0.8363 (t) cc_final: 0.8151 (t) REVERT: C 217 MET cc_start: 0.7540 (ptp) cc_final: 0.6542 (ptp) REVERT: D 143 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: D 245 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8583 (pp) REVERT: D 340 MET cc_start: 0.8740 (mmt) cc_final: 0.8540 (mmm) REVERT: D 342 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7425 (tt0) REVERT: D 347 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6355 (p0) REVERT: E 41 ASN cc_start: 0.8662 (t0) cc_final: 0.8339 (t0) REVERT: E 44 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7434 (mm-30) REVERT: E 94 TYR cc_start: 0.8624 (t80) cc_final: 0.8268 (t80) REVERT: E 98 LYS cc_start: 0.7763 (tppt) cc_final: 0.7493 (tptt) REVERT: E 107 ASP cc_start: 0.6951 (p0) cc_final: 0.6739 (p0) REVERT: E 120 LEU cc_start: 0.8049 (tp) cc_final: 0.7780 (tp) REVERT: E 132 MET cc_start: 0.9043 (ttm) cc_final: 0.8756 (ttm) REVERT: E 216 MET cc_start: 0.6895 (tpp) cc_final: 0.6657 (tpp) REVERT: E 232 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8289 (tt) REVERT: F 272 THR cc_start: 0.7470 (t) cc_final: 0.7210 (t) REVERT: F 286 ARG cc_start: 0.8021 (tmm-80) cc_final: 0.7370 (ttp80) REVERT: G 362 ASP cc_start: 0.8863 (t70) cc_final: 0.8642 (t0) REVERT: G 386 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6951 (pp) REVERT: G 411 ASN cc_start: 0.8321 (p0) cc_final: 0.7816 (p0) REVERT: H 238 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7303 (tp40) REVERT: H 265 GLN cc_start: 0.8533 (tp40) cc_final: 0.7570 (tm-30) REVERT: H 306 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6883 (ttm110) REVERT: H 341 LEU cc_start: 0.8980 (tp) cc_final: 0.8698 (tt) REVERT: I 326 ASN cc_start: 0.8539 (t0) cc_final: 0.8226 (t0) REVERT: I 426 LYS cc_start: 0.8518 (mttt) cc_final: 0.8229 (mttt) REVERT: I 431 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8729 (pp) REVERT: J 128 TYR cc_start: 0.5821 (p90) cc_final: 0.5135 (p90) REVERT: J 266 TYR cc_start: 0.8795 (m-10) cc_final: 0.8281 (m-80) REVERT: J 324 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: J 389 VAL cc_start: 0.8219 (p) cc_final: 0.7919 (p) outliers start: 111 outliers final: 61 residues processed: 561 average time/residue: 0.3424 time to fit residues: 314.9562 Evaluate side-chains 497 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 429 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 274 HIS Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 488 VAL Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 287 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 171 optimal weight: 0.0010 chunk 199 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 333 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS B 170 HIS C 158 HIS D 201 HIS D 280 ASN E 172 ASN E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** 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 = 0.3489 r_free = 0.3489 target = 0.132445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115582 restraints weight = 39653.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114572 restraints weight = 50155.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115372 restraints weight = 47552.127| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 27109 Z= 0.204 Angle : 0.692 10.325 36775 Z= 0.347 Chirality : 0.047 0.253 4327 Planarity : 0.005 0.067 4730 Dihedral : 5.442 43.009 3748 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 5.13 % Allowed : 22.76 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.14), residues: 3437 helix: 0.03 (0.15), residues: 1231 sheet: -3.78 (0.20), residues: 468 loop : -2.79 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 51 HIS 0.013 0.001 HIS B 170 PHE 0.026 0.002 PHE C 177 TYR 0.016 0.002 TYR B 185 ARG 0.005 0.000 ARG E 192 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 919) hydrogen bonds : angle 4.64294 ( 2610) covalent geometry : bond 0.00498 (27109) covalent geometry : angle 0.69220 (36775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 446 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7841 (p0) cc_final: 0.7422 (t0) REVERT: A 145 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7199 (ptmm) REVERT: A 299 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 1 MET cc_start: 0.3586 (tpp) cc_final: 0.3157 (tpp) REVERT: B 28 ARG cc_start: 0.6449 (ttt180) cc_final: 0.5396 (ttm110) REVERT: B 187 MET cc_start: 0.9163 (tpp) cc_final: 0.8617 (tpt) REVERT: B 195 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9198 (p) REVERT: B 200 VAL cc_start: 0.8392 (t) cc_final: 0.8186 (t) REVERT: C 217 MET cc_start: 0.7603 (ptp) cc_final: 0.6751 (ptp) REVERT: D 143 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: D 245 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8602 (pp) REVERT: D 280 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7317 (t0) REVERT: D 342 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7448 (tt0) REVERT: D 347 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6471 (p0) REVERT: E 41 ASN cc_start: 0.8652 (t0) cc_final: 0.8305 (t0) REVERT: E 44 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7520 (mm-30) REVERT: E 94 TYR cc_start: 0.8621 (t80) cc_final: 0.8314 (t80) REVERT: E 98 LYS cc_start: 0.7950 (tppt) cc_final: 0.7417 (tptt) REVERT: E 107 ASP cc_start: 0.7129 (p0) cc_final: 0.6842 (p0) REVERT: E 120 LEU cc_start: 0.8101 (tp) cc_final: 0.7803 (tp) REVERT: E 132 MET cc_start: 0.9037 (ttm) cc_final: 0.8742 (ttm) REVERT: E 216 MET cc_start: 0.6967 (tpp) cc_final: 0.6706 (tpp) REVERT: E 232 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8366 (tt) REVERT: F 55 THR cc_start: 0.5030 (OUTLIER) cc_final: 0.4776 (m) REVERT: F 94 TYR cc_start: 0.8888 (t80) cc_final: 0.8425 (t80) REVERT: F 107 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.6047 (p0) REVERT: F 272 THR cc_start: 0.7347 (t) cc_final: 0.6996 (t) REVERT: F 286 ARG cc_start: 0.8091 (tmm-80) cc_final: 0.7290 (ttp80) REVERT: F 289 ARG cc_start: 0.7172 (ttt-90) cc_final: 0.6208 (tmt170) REVERT: G 256 LEU cc_start: 0.8651 (mt) cc_final: 0.8448 (tt) REVERT: G 362 ASP cc_start: 0.8942 (t70) cc_final: 0.8742 (t0) REVERT: G 386 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7285 (pp) REVERT: H 265 GLN cc_start: 0.8593 (tp40) cc_final: 0.8014 (tm-30) REVERT: H 269 LEU cc_start: 0.8046 (mm) cc_final: 0.7772 (mm) REVERT: H 341 LEU cc_start: 0.9045 (tp) cc_final: 0.8750 (tt) REVERT: I 326 ASN cc_start: 0.8636 (t0) cc_final: 0.8304 (t0) REVERT: I 426 LYS cc_start: 0.8601 (mttt) cc_final: 0.8298 (mttt) REVERT: I 431 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8761 (pp) REVERT: J 88 VAL cc_start: 0.9163 (t) cc_final: 0.8878 (m) REVERT: J 128 TYR cc_start: 0.6022 (p90) cc_final: 0.5168 (p90) REVERT: J 172 ARG cc_start: 0.8167 (tpt-90) cc_final: 0.7945 (tpt-90) REVERT: J 266 TYR cc_start: 0.8836 (m-10) cc_final: 0.8277 (m-80) REVERT: J 324 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: J 389 VAL cc_start: 0.8308 (p) cc_final: 0.8104 (p) outliers start: 146 outliers final: 97 residues processed: 552 average time/residue: 0.3283 time to fit residues: 299.1294 Evaluate side-chains 519 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 411 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 274 HIS Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain H residue 516 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 377 SER Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 242 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS C 158 HIS D 280 ASN E 172 ASN E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN I 452 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115622 restraints weight = 39404.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114892 restraints weight = 54941.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116140 restraints weight = 47853.997| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27109 Z= 0.208 Angle : 0.698 12.026 36775 Z= 0.348 Chirality : 0.047 0.263 4327 Planarity : 0.005 0.076 4730 Dihedral : 5.447 44.136 3748 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 5.90 % Allowed : 23.39 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.14), residues: 3437 helix: 0.11 (0.15), residues: 1230 sheet: -3.78 (0.19), residues: 485 loop : -2.67 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 51 HIS 0.010 0.001 HIS E 190 PHE 0.028 0.002 PHE D 177 TYR 0.016 0.002 TYR B 185 ARG 0.005 0.000 ARG H 306 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 919) hydrogen bonds : angle 4.62800 ( 2610) covalent geometry : bond 0.00504 (27109) covalent geometry : angle 0.69779 (36775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 446 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7939 (p0) cc_final: 0.7619 (t0) REVERT: A 145 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7586 (ptmm) REVERT: B 1 MET cc_start: 0.3624 (tpp) cc_final: 0.3213 (tpp) REVERT: B 28 ARG cc_start: 0.6512 (ttt180) cc_final: 0.5418 (ttm110) REVERT: B 76 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5430 (tp) REVERT: B 187 MET cc_start: 0.9261 (tpp) cc_final: 0.8698 (tpt) REVERT: B 195 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9214 (p) REVERT: B 304 TYR cc_start: 0.7667 (m-80) cc_final: 0.7252 (m-10) REVERT: C 128 GLN cc_start: 0.5788 (tm-30) cc_final: 0.5352 (tm-30) REVERT: C 217 MET cc_start: 0.7651 (ptp) cc_final: 0.6808 (ptp) REVERT: C 246 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8034 (mtp180) REVERT: D 144 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8446 (tp) REVERT: D 175 GLU cc_start: 0.8025 (tp30) cc_final: 0.7683 (tm-30) REVERT: D 245 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8631 (pp) REVERT: D 342 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7426 (tt0) REVERT: D 347 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6438 (p0) REVERT: E 41 ASN cc_start: 0.8626 (t0) cc_final: 0.8316 (t0) REVERT: E 44 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7592 (mm-30) REVERT: E 94 TYR cc_start: 0.8635 (t80) cc_final: 0.8385 (t80) REVERT: E 98 LYS cc_start: 0.7879 (tppt) cc_final: 0.7394 (tptt) REVERT: E 107 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6586 (p0) REVERT: E 120 LEU cc_start: 0.8103 (tp) cc_final: 0.7829 (tp) REVERT: E 132 MET cc_start: 0.9037 (ttm) cc_final: 0.8711 (ttm) REVERT: E 216 MET cc_start: 0.6938 (tpp) cc_final: 0.6722 (tpp) REVERT: E 232 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8494 (tt) REVERT: F 94 TYR cc_start: 0.8935 (t80) cc_final: 0.8556 (t80) REVERT: F 107 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.6028 (p0) REVERT: F 272 THR cc_start: 0.7338 (t) cc_final: 0.6981 (t) REVERT: F 286 ARG cc_start: 0.8000 (tmm-80) cc_final: 0.7388 (ttp80) REVERT: G 256 LEU cc_start: 0.8682 (mt) cc_final: 0.8469 (tt) REVERT: G 386 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7311 (pp) REVERT: G 504 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7592 (pp) REVERT: H 265 GLN cc_start: 0.8577 (tp40) cc_final: 0.7971 (tm-30) REVERT: H 269 LEU cc_start: 0.8014 (mm) cc_final: 0.7516 (mt) REVERT: H 341 LEU cc_start: 0.9035 (tp) cc_final: 0.8749 (tt) REVERT: I 47 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8006 (tp) REVERT: I 168 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.6771 (t70) REVERT: I 326 ASN cc_start: 0.8743 (t0) cc_final: 0.8464 (t0) REVERT: I 426 LYS cc_start: 0.8637 (mttt) cc_final: 0.8319 (mttt) REVERT: I 431 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8783 (pp) REVERT: J 88 VAL cc_start: 0.9144 (t) cc_final: 0.8876 (m) REVERT: J 128 TYR cc_start: 0.6129 (p90) cc_final: 0.5199 (p90) REVERT: J 266 TYR cc_start: 0.8825 (m-10) cc_final: 0.8274 (m-80) REVERT: J 324 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: J 389 VAL cc_start: 0.8340 (p) cc_final: 0.8124 (p) outliers start: 168 outliers final: 115 residues processed: 568 average time/residue: 0.3419 time to fit residues: 321.7057 Evaluate side-chains 542 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 412 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 274 HIS Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain H residue 516 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 168 HIS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 289 MET Chi-restraints excluded: chain J residue 305 MET Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 377 SER Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 256 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 chunk 165 optimal weight: 0.0270 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 243 optimal weight: 0.0970 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS B 170 HIS C 158 HIS D 242 ASN D 280 ASN E 172 ASN E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN G 274 HIS H 265 GLN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119738 restraints weight = 38532.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119022 restraints weight = 51869.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120138 restraints weight = 44553.010| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27109 Z= 0.127 Angle : 0.640 13.753 36775 Z= 0.316 Chirality : 0.045 0.257 4327 Planarity : 0.004 0.066 4730 Dihedral : 5.093 45.947 3748 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.71 % Allowed : 25.29 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3437 helix: 0.39 (0.15), residues: 1234 sheet: -3.39 (0.20), residues: 483 loop : -2.43 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 51 HIS 0.015 0.001 HIS B 170 PHE 0.020 0.001 PHE D 177 TYR 0.015 0.001 TYR D 337 ARG 0.005 0.000 ARG H 306 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 919) hydrogen bonds : angle 4.34282 ( 2610) covalent geometry : bond 0.00302 (27109) covalent geometry : angle 0.63953 (36775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 455 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7388 (ptmm) REVERT: B 1 MET cc_start: 0.3534 (tpp) cc_final: 0.3129 (tpp) REVERT: B 28 ARG cc_start: 0.6379 (ttt180) cc_final: 0.5442 (ttm110) REVERT: B 187 MET cc_start: 0.9131 (tpp) cc_final: 0.8398 (tpt) REVERT: B 195 VAL cc_start: 0.9392 (OUTLIER) cc_final: 0.9166 (p) REVERT: B 304 TYR cc_start: 0.7635 (m-80) cc_final: 0.7177 (m-10) REVERT: C 17 SER cc_start: 0.8800 (p) cc_final: 0.8348 (t) REVERT: C 97 HIS cc_start: 0.6809 (t70) cc_final: 0.6396 (t-170) REVERT: C 128 GLN cc_start: 0.5849 (tm-30) cc_final: 0.5567 (tm-30) REVERT: C 217 MET cc_start: 0.7345 (ptp) cc_final: 0.6727 (ptp) REVERT: D 144 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8355 (tp) REVERT: D 245 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8579 (pp) REVERT: D 342 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7427 (tt0) REVERT: D 347 ASP cc_start: 0.6375 (OUTLIER) cc_final: 0.6155 (p0) REVERT: E 44 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 94 TYR cc_start: 0.8671 (t80) cc_final: 0.8398 (t80) REVERT: E 107 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6401 (p0) REVERT: E 120 LEU cc_start: 0.8003 (tp) cc_final: 0.7754 (tp) REVERT: E 132 MET cc_start: 0.9105 (ttm) cc_final: 0.8817 (ttm) REVERT: E 209 LYS cc_start: 0.7979 (tppt) cc_final: 0.7451 (tppt) REVERT: E 216 MET cc_start: 0.6819 (tpp) cc_final: 0.6594 (tpp) REVERT: E 232 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8403 (tt) REVERT: F 43 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7860 (mp) REVERT: F 94 TYR cc_start: 0.8681 (t80) cc_final: 0.8335 (t80) REVERT: G 247 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7044 (tm-30) REVERT: G 386 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7033 (pp) REVERT: G 504 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7322 (pp) REVERT: H 265 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8007 (tm-30) REVERT: I 168 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6565 (t70) REVERT: I 326 ASN cc_start: 0.8605 (t0) cc_final: 0.8319 (t0) REVERT: I 426 LYS cc_start: 0.8566 (mttt) cc_final: 0.8233 (mttt) REVERT: I 431 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8717 (pp) REVERT: J 88 VAL cc_start: 0.9140 (t) cc_final: 0.8843 (m) REVERT: J 128 TYR cc_start: 0.6018 (p90) cc_final: 0.5068 (p90) REVERT: J 266 TYR cc_start: 0.8818 (m-10) cc_final: 0.8263 (m-80) REVERT: J 291 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.9002 (m) REVERT: J 389 VAL cc_start: 0.8271 (p) cc_final: 0.7987 (p) REVERT: J 412 LEU cc_start: 0.8932 (tt) cc_final: 0.8707 (tt) outliers start: 134 outliers final: 83 residues processed: 549 average time/residue: 0.3304 time to fit residues: 300.1921 Evaluate side-chains 499 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 404 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 274 HIS Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 168 HIS Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 289 MET Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 264 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 0.0570 chunk 169 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 116 HIS C 44 GLN C 158 HIS ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN G 478 ASN H 274 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 464 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121226 restraints weight = 38741.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121051 restraints weight = 44898.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121692 restraints weight = 37779.676| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27109 Z= 0.140 Angle : 0.648 12.085 36775 Z= 0.320 Chirality : 0.045 0.280 4327 Planarity : 0.004 0.070 4730 Dihedral : 4.997 47.422 3747 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.57 % Allowed : 25.85 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 3437 helix: 0.49 (0.15), residues: 1249 sheet: -3.24 (0.21), residues: 477 loop : -2.37 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 51 HIS 0.014 0.001 HIS B 116 PHE 0.028 0.002 PHE F 266 TYR 0.027 0.001 TYR D 337 ARG 0.009 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 919) hydrogen bonds : angle 4.29088 ( 2610) covalent geometry : bond 0.00339 (27109) covalent geometry : angle 0.64840 (36775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 432 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7098 (tt) REVERT: A 145 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7428 (ptmm) REVERT: A 180 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7098 (t0) REVERT: A 187 MET cc_start: 0.8870 (tpt) cc_final: 0.8610 (tpt) REVERT: B 1 MET cc_start: 0.3595 (tpp) cc_final: 0.3179 (tpp) REVERT: B 28 ARG cc_start: 0.6369 (ttt180) cc_final: 0.5453 (ttm110) REVERT: B 195 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9164 (p) REVERT: B 304 TYR cc_start: 0.7549 (m-80) cc_final: 0.7204 (m-10) REVERT: C 17 SER cc_start: 0.8790 (p) cc_final: 0.8340 (t) REVERT: C 217 MET cc_start: 0.7420 (ptp) cc_final: 0.6821 (ptp) REVERT: D 245 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8624 (pp) REVERT: D 262 SER cc_start: 0.9068 (t) cc_final: 0.8743 (p) REVERT: D 342 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7448 (tt0) REVERT: D 347 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.6089 (p0) REVERT: E 44 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7709 (mm-30) REVERT: E 94 TYR cc_start: 0.8719 (t80) cc_final: 0.8455 (t80) REVERT: E 107 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.6366 (p0) REVERT: E 120 LEU cc_start: 0.8019 (tp) cc_final: 0.7766 (tp) REVERT: E 132 MET cc_start: 0.9121 (ttm) cc_final: 0.8809 (ttm) REVERT: E 172 ASN cc_start: 0.7490 (t0) cc_final: 0.6944 (t0) REVERT: E 178 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: E 232 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8296 (tt) REVERT: F 43 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7823 (mp) REVERT: F 94 TYR cc_start: 0.8731 (t80) cc_final: 0.8395 (t80) REVERT: G 247 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7040 (tm-30) REVERT: G 386 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7309 (pp) REVERT: G 504 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7320 (pp) REVERT: H 265 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7712 (tm-30) REVERT: I 168 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6557 (t70) REVERT: I 326 ASN cc_start: 0.8657 (t0) cc_final: 0.8360 (t0) REVERT: I 426 LYS cc_start: 0.8455 (mttt) cc_final: 0.8176 (mttt) REVERT: I 431 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8737 (pp) REVERT: J 80 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7737 (mp) REVERT: J 88 VAL cc_start: 0.9134 (t) cc_final: 0.8798 (m) REVERT: J 128 TYR cc_start: 0.6146 (p90) cc_final: 0.5029 (p90) REVERT: J 266 TYR cc_start: 0.8785 (m-10) cc_final: 0.8235 (m-80) REVERT: J 291 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9046 (m) REVERT: J 389 VAL cc_start: 0.8119 (p) cc_final: 0.7824 (p) outliers start: 130 outliers final: 96 residues processed: 523 average time/residue: 0.3314 time to fit residues: 285.1947 Evaluate side-chains 511 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 400 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 168 HIS Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 289 MET Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 302 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 283 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 225 optimal weight: 0.0170 chunk 315 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS C 158 HIS ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN H 274 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120462 restraints weight = 38861.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119919 restraints weight = 48903.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121218 restraints weight = 43118.917| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27109 Z= 0.142 Angle : 0.655 11.534 36775 Z= 0.322 Chirality : 0.045 0.325 4327 Planarity : 0.004 0.065 4730 Dihedral : 4.972 53.185 3747 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.95 % Allowed : 25.78 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.15), residues: 3437 helix: 0.56 (0.15), residues: 1247 sheet: -3.11 (0.20), residues: 531 loop : -2.35 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 51 HIS 0.013 0.001 HIS B 116 PHE 0.022 0.002 PHE C 177 TYR 0.025 0.001 TYR D 337 ARG 0.008 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 919) hydrogen bonds : angle 4.25424 ( 2610) covalent geometry : bond 0.00346 (27109) covalent geometry : angle 0.65540 (36775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 421 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7125 (tt) REVERT: A 145 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7416 (ptmm) REVERT: A 180 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7150 (t0) REVERT: A 187 MET cc_start: 0.8867 (tpt) cc_final: 0.8610 (tpt) REVERT: B 1 MET cc_start: 0.3590 (tpp) cc_final: 0.3207 (tpp) REVERT: B 28 ARG cc_start: 0.6391 (ttt180) cc_final: 0.5567 (ttm110) REVERT: B 195 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9180 (p) REVERT: B 304 TYR cc_start: 0.7436 (m-80) cc_final: 0.7205 (m-10) REVERT: C 14 ARG cc_start: 0.7439 (ttt180) cc_final: 0.7158 (ttp-170) REVERT: C 17 SER cc_start: 0.8805 (p) cc_final: 0.8366 (t) REVERT: C 97 HIS cc_start: 0.6778 (t70) cc_final: 0.6396 (t-170) REVERT: C 184 LYS cc_start: 0.7556 (mppt) cc_final: 0.7159 (mttm) REVERT: C 217 MET cc_start: 0.7418 (ptp) cc_final: 0.6670 (ptp) REVERT: D 144 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8326 (tp) REVERT: D 245 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8661 (pp) REVERT: D 262 SER cc_start: 0.9034 (t) cc_final: 0.8591 (p) REVERT: D 340 MET cc_start: 0.8860 (mmm) cc_final: 0.8400 (mmm) REVERT: D 342 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7377 (tt0) REVERT: D 347 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.6039 (p0) REVERT: E 43 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8000 (mp) REVERT: E 44 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 107 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6245 (p0) REVERT: E 120 LEU cc_start: 0.8048 (tp) cc_final: 0.7769 (tp) REVERT: E 132 MET cc_start: 0.9126 (ttm) cc_final: 0.8755 (mtp) REVERT: E 157 PHE cc_start: 0.7337 (m-80) cc_final: 0.6945 (m-10) REVERT: E 172 ASN cc_start: 0.7310 (t0) cc_final: 0.6890 (t0) REVERT: E 178 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: E 209 LYS cc_start: 0.8001 (tppt) cc_final: 0.7528 (tppt) REVERT: E 232 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8304 (tt) REVERT: F 27 LEU cc_start: 0.8100 (pp) cc_final: 0.7857 (pt) REVERT: F 43 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7909 (mp) REVERT: F 69 MET cc_start: 0.4332 (tmm) cc_final: 0.4077 (tmm) REVERT: F 94 TYR cc_start: 0.8776 (t80) cc_final: 0.8483 (t80) REVERT: G 247 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7047 (tm-30) REVERT: G 386 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7314 (pp) REVERT: G 504 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7266 (pp) REVERT: H 265 GLN cc_start: 0.8563 (tp-100) cc_final: 0.7797 (tm-30) REVERT: H 269 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7391 (mt) REVERT: I 168 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.6538 (t70) REVERT: I 326 ASN cc_start: 0.8680 (t0) cc_final: 0.8388 (t0) REVERT: I 426 LYS cc_start: 0.8405 (mttt) cc_final: 0.7973 (mtpt) REVERT: I 431 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8775 (pp) REVERT: J 80 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7762 (mp) REVERT: J 88 VAL cc_start: 0.9048 (t) cc_final: 0.8720 (m) REVERT: J 128 TYR cc_start: 0.6181 (p90) cc_final: 0.4969 (p90) REVERT: J 266 TYR cc_start: 0.8808 (m-10) cc_final: 0.8244 (m-80) REVERT: J 291 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9005 (m) REVERT: J 389 VAL cc_start: 0.8143 (p) cc_final: 0.7832 (p) outliers start: 141 outliers final: 101 residues processed: 521 average time/residue: 0.3205 time to fit residues: 277.2908 Evaluate side-chains 523 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 404 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 393 TYR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 168 HIS Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 289 MET Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 302 optimal weight: 2.9990 chunk 243 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 86 optimal weight: 0.0370 chunk 215 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS C 158 HIS C 261 HIS ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 ASN H 274 HIS ** H 448 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 = 0.3550 r_free = 0.3550 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121330 restraints weight = 38560.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120380 restraints weight = 48560.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121393 restraints weight = 44236.042| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27109 Z= 0.130 Angle : 0.655 13.621 36775 Z= 0.321 Chirality : 0.045 0.367 4327 Planarity : 0.004 0.064 4730 Dihedral : 4.904 55.450 3747 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.81 % Allowed : 26.41 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 3437 helix: 0.64 (0.15), residues: 1244 sheet: -2.99 (0.21), residues: 527 loop : -2.26 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 51 HIS 0.012 0.001 HIS B 116 PHE 0.030 0.001 PHE B 239 TYR 0.024 0.001 TYR D 337 ARG 0.010 0.000 ARG I 121 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 919) hydrogen bonds : angle 4.19358 ( 2610) covalent geometry : bond 0.00312 (27109) covalent geometry : angle 0.65491 (36775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 421 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.5956 (pm20) cc_final: 0.5533 (pm20) REVERT: A 60 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6835 (t70) REVERT: A 101 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7114 (tt) REVERT: A 137 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8240 (p) REVERT: A 180 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7108 (t0) REVERT: B 1 MET cc_start: 0.3579 (tpp) cc_final: 0.3161 (tpp) REVERT: B 28 ARG cc_start: 0.6432 (ttt180) cc_final: 0.5423 (ttm110) REVERT: B 118 PHE cc_start: 0.7753 (m-10) cc_final: 0.7512 (m-80) REVERT: B 195 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9167 (p) REVERT: B 304 TYR cc_start: 0.7345 (m-80) cc_final: 0.7135 (m-10) REVERT: C 14 ARG cc_start: 0.7423 (ttt180) cc_final: 0.7131 (ttp-170) REVERT: C 17 SER cc_start: 0.8880 (p) cc_final: 0.8495 (t) REVERT: C 97 HIS cc_start: 0.6777 (t70) cc_final: 0.6412 (t-170) REVERT: C 184 LYS cc_start: 0.7609 (mppt) cc_final: 0.7314 (mttm) REVERT: C 217 MET cc_start: 0.7283 (ptp) cc_final: 0.6512 (ptp) REVERT: C 277 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7812 (mm-40) REVERT: D 144 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8299 (tp) REVERT: D 148 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (mmp) REVERT: D 230 ASN cc_start: 0.8158 (m110) cc_final: 0.7847 (m-40) REVERT: D 245 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8626 (pp) REVERT: D 262 SER cc_start: 0.8991 (t) cc_final: 0.8572 (p) REVERT: D 342 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7350 (tt0) REVERT: D 347 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6068 (p0) REVERT: E 44 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7718 (mm-30) REVERT: E 75 ILE cc_start: 0.7893 (pt) cc_final: 0.7638 (pt) REVERT: E 107 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6109 (p0) REVERT: E 157 PHE cc_start: 0.7171 (m-80) cc_final: 0.6751 (m-80) REVERT: E 172 ASN cc_start: 0.7287 (t0) cc_final: 0.6877 (t0) REVERT: E 178 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: E 194 ARG cc_start: 0.8571 (tpt-90) cc_final: 0.8319 (ttt90) REVERT: E 216 MET cc_start: 0.7120 (tpp) cc_final: 0.6360 (tpp) REVERT: E 232 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8248 (tt) REVERT: F 1 MET cc_start: 0.7732 (tpp) cc_final: 0.7443 (mmm) REVERT: F 27 LEU cc_start: 0.7776 (pp) cc_final: 0.7494 (pt) REVERT: F 43 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7882 (mp) REVERT: F 94 TYR cc_start: 0.8721 (t80) cc_final: 0.8423 (t80) REVERT: G 247 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7010 (tm-30) REVERT: G 386 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7281 (pp) REVERT: G 504 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7161 (pp) REVERT: H 265 GLN cc_start: 0.8528 (tp-100) cc_final: 0.7794 (tm-30) REVERT: H 269 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7224 (mt) REVERT: H 499 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7850 (mm) REVERT: I 133 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7441 (t70) REVERT: I 168 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.6545 (t70) REVERT: I 326 ASN cc_start: 0.8639 (t0) cc_final: 0.8345 (t0) REVERT: I 426 LYS cc_start: 0.8382 (mttt) cc_final: 0.7948 (mtpt) REVERT: J 80 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7744 (mp) REVERT: J 88 VAL cc_start: 0.9013 (t) cc_final: 0.8674 (m) REVERT: J 128 TYR cc_start: 0.6110 (p90) cc_final: 0.4890 (p90) REVERT: J 239 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8346 (mt-10) REVERT: J 266 TYR cc_start: 0.8809 (m-10) cc_final: 0.8251 (m-80) REVERT: J 291 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.8996 (m) REVERT: J 389 VAL cc_start: 0.8142 (p) cc_final: 0.7820 (p) outliers start: 137 outliers final: 94 residues processed: 516 average time/residue: 0.3389 time to fit residues: 290.1687 Evaluate side-chains 513 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 398 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 393 TYR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 168 HIS Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 289 MET Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 59 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 335 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 116 HIS C 158 HIS ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120890 restraints weight = 38589.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119845 restraints weight = 49396.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120976 restraints weight = 45321.467| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27109 Z= 0.142 Angle : 0.664 13.478 36775 Z= 0.325 Chirality : 0.045 0.316 4327 Planarity : 0.004 0.064 4730 Dihedral : 4.898 55.871 3747 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.53 % Allowed : 27.01 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 3437 helix: 0.69 (0.15), residues: 1237 sheet: -2.90 (0.21), residues: 527 loop : -2.21 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 51 HIS 0.010 0.001 HIS B 116 PHE 0.027 0.002 PHE B 239 TYR 0.024 0.002 TYR D 337 ARG 0.009 0.000 ARG I 121 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 919) hydrogen bonds : angle 4.19445 ( 2610) covalent geometry : bond 0.00347 (27109) covalent geometry : angle 0.66401 (36775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 411 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.5977 (pm20) cc_final: 0.5605 (pm20) REVERT: A 60 ASP cc_start: 0.7389 (p0) cc_final: 0.6861 (t70) REVERT: A 101 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 137 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 180 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7021 (t0) REVERT: B 1 MET cc_start: 0.3147 (tpp) cc_final: 0.2694 (tpp) REVERT: B 28 ARG cc_start: 0.6433 (ttt180) cc_final: 0.5424 (ttm110) REVERT: B 118 PHE cc_start: 0.7822 (m-10) cc_final: 0.7615 (m-80) REVERT: B 195 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9178 (p) REVERT: C 17 SER cc_start: 0.8883 (p) cc_final: 0.8496 (t) REVERT: C 97 HIS cc_start: 0.6785 (t70) cc_final: 0.6421 (t-170) REVERT: C 184 LYS cc_start: 0.7547 (mppt) cc_final: 0.7154 (mttm) REVERT: C 217 MET cc_start: 0.7397 (ptp) cc_final: 0.6667 (ptp) REVERT: C 277 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7765 (mm-40) REVERT: D 144 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 148 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7874 (mmp) REVERT: D 230 ASN cc_start: 0.8193 (m110) cc_final: 0.7898 (m-40) REVERT: D 245 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8631 (pp) REVERT: D 262 SER cc_start: 0.8974 (t) cc_final: 0.8558 (p) REVERT: D 340 MET cc_start: 0.8835 (mmm) cc_final: 0.8442 (mmm) REVERT: D 342 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7349 (tt0) REVERT: D 347 ASP cc_start: 0.6345 (OUTLIER) cc_final: 0.6078 (p0) REVERT: E 44 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7719 (mm-30) REVERT: E 75 ILE cc_start: 0.7884 (pt) cc_final: 0.7643 (pt) REVERT: E 98 LYS cc_start: 0.7555 (tptt) cc_final: 0.7313 (tttt) REVERT: E 107 ASP cc_start: 0.6500 (OUTLIER) cc_final: 0.6144 (p0) REVERT: E 132 MET cc_start: 0.9083 (mtt) cc_final: 0.8741 (mtp) REVERT: E 157 PHE cc_start: 0.7192 (m-80) cc_final: 0.6776 (m-10) REVERT: E 167 LEU cc_start: 0.8612 (pt) cc_final: 0.8410 (pt) REVERT: E 172 ASN cc_start: 0.7188 (t0) cc_final: 0.6810 (t0) REVERT: E 178 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: E 194 ARG cc_start: 0.8560 (tpt-90) cc_final: 0.8327 (ttt90) REVERT: E 216 MET cc_start: 0.7122 (tpp) cc_final: 0.6330 (tpp) REVERT: E 232 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8255 (tt) REVERT: F 27 LEU cc_start: 0.7847 (pp) cc_final: 0.7556 (pt) REVERT: F 43 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7878 (mp) REVERT: F 94 TYR cc_start: 0.8697 (t80) cc_final: 0.8443 (t80) REVERT: G 247 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6955 (tm-30) REVERT: G 386 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7291 (pp) REVERT: G 397 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7831 (mt-10) REVERT: G 504 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7224 (pp) REVERT: H 265 GLN cc_start: 0.8567 (tp-100) cc_final: 0.7839 (tm-30) REVERT: H 269 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7217 (mt) REVERT: H 499 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7902 (mm) REVERT: I 133 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7460 (t70) REVERT: I 166 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7427 (tm-30) REVERT: I 168 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.6422 (t70) REVERT: I 326 ASN cc_start: 0.8656 (t0) cc_final: 0.8367 (t0) REVERT: I 426 LYS cc_start: 0.8395 (mttt) cc_final: 0.7854 (mtpt) REVERT: I 431 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8796 (pp) REVERT: J 80 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7761 (mp) REVERT: J 88 VAL cc_start: 0.9057 (t) cc_final: 0.8741 (m) REVERT: J 128 TYR cc_start: 0.6176 (p90) cc_final: 0.4922 (p90) REVERT: J 266 TYR cc_start: 0.8806 (m-10) cc_final: 0.8238 (m-80) REVERT: J 291 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.8976 (m) REVERT: J 389 VAL cc_start: 0.8140 (p) cc_final: 0.7766 (p) outliers start: 129 outliers final: 99 residues processed: 506 average time/residue: 0.3362 time to fit residues: 284.4795 Evaluate side-chains 515 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 395 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 456 GLU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 504 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 393 TYR Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 420 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 168 HIS Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 340 HIS Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 377 SER Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 448 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 164 optimal weight: 0.0570 chunk 143 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 339 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 316 optimal weight: 0.4980 chunk 317 optimal weight: 0.6980 chunk 41 optimal weight: 0.0060 chunk 284 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 HIS ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS F 60 GLN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123524 restraints weight = 38372.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122853 restraints weight = 46706.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124232 restraints weight = 41113.909| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27109 Z= 0.127 Angle : 0.654 13.231 36775 Z= 0.320 Chirality : 0.045 0.307 4327 Planarity : 0.004 0.064 4730 Dihedral : 4.795 57.548 3747 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.32 % Allowed : 27.43 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 3437 helix: 0.79 (0.15), residues: 1238 sheet: -2.77 (0.22), residues: 518 loop : -2.11 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 51 HIS 0.009 0.001 HIS E 115 PHE 0.026 0.001 PHE B 239 TYR 0.022 0.001 TYR D 337 ARG 0.009 0.000 ARG I 121 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 919) hydrogen bonds : angle 4.13681 ( 2610) covalent geometry : bond 0.00304 (27109) covalent geometry : angle 0.65353 (36775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8858.19 seconds wall clock time: 156 minutes 17.60 seconds (9377.60 seconds total)