Starting phenix.real_space_refine on Sun Aug 24 16:58:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqs_34953/08_2025/8hqs_34953_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqs_34953/08_2025/8hqs_34953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hqs_34953/08_2025/8hqs_34953_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqs_34953/08_2025/8hqs_34953_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hqs_34953/08_2025/8hqs_34953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqs_34953/08_2025/8hqs_34953.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2622 atoms to isotropic. 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 89 5.16 5 C 12240 2.51 5 N 3259 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19224 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3136 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain breaks: 1 Chain: "B" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3231 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 8, 'TRANS': 399} Chain breaks: 2 Chain: "D" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2576 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 1 Chain: "E" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4271 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Chain: "F" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2575 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2264 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Chain: "H" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1171 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain breaks: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.21 Number of scatterers: 19224 At special positions: 0 Unit cell: (170.24, 163.856, 124.488, 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 89 16.00 O 3636 8.00 N 3259 7.00 C 12240 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: 1.55 Conformation dependent library (CDL) restraints added in 827.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 14 sheets defined 53.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.694A pdb=" N LEU A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.601A pdb=" N ILE A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 removed outlier: 4.168A pdb=" N PHE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 103' Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.622A pdb=" N ARG A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.520A pdb=" N ILE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 230 Processing helix chain 'A' and resid 912 through 945 Proline residue: A 927 - end of helix Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 987 through 1002 Processing helix chain 'A' and resid 1023 through 1038 removed outlier: 3.697A pdb=" N ALA A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 36 removed outlier: 3.507A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.515A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 143' Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 249 through 280 Processing helix chain 'B' and resid 940 through 984 removed outlier: 3.596A pdb=" N LYS B 984 " --> pdb=" O ARG B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 987 No H-bonds generated for 'chain 'B' and resid 985 through 987' Processing helix chain 'B' and resid 1020 through 1037 Processing helix chain 'B' and resid 1049 through 1054 removed outlier: 3.783A pdb=" N MET B1053 " --> pdb=" O ASP B1050 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP B1054 " --> pdb=" O VAL B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1071 removed outlier: 4.257A pdb=" N ASP B1071 " --> pdb=" O LYS B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.602A pdb=" N ALA D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.549A pdb=" N LEU D 185 " --> pdb=" O PRO D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.593A pdb=" N ALA D 221 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 243 removed outlier: 3.828A pdb=" N VAL D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 254 Processing helix chain 'D' and resid 256 through 262 Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 300 through 316 removed outlier: 3.722A pdb=" N ARG D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 328 through 338 removed outlier: 3.636A pdb=" N PHE D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 387 through 403 Processing helix chain 'D' and resid 404 through 410 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 427 through 441 removed outlier: 3.673A pdb=" N GLU D 431 " --> pdb=" O CYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 463 removed outlier: 4.023A pdb=" N SER D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 43 through 54 removed outlier: 4.194A pdb=" N GLN E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 79 through 91 Proline residue: E 85 - end of helix Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.761A pdb=" N GLU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 142 Processing helix chain 'E' and resid 190 through 195 removed outlier: 3.677A pdb=" N GLU E 193 " --> pdb=" O SER E 190 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN E 194 " --> pdb=" O CYS E 191 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 190 through 195' Processing helix chain 'E' and resid 203 through 209 Processing helix chain 'E' and resid 213 through 225 Processing helix chain 'E' and resid 229 through 239 Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 278 removed outlier: 3.556A pdb=" N GLN E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 287 removed outlier: 3.680A pdb=" N SER E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 302 Processing helix chain 'E' and resid 309 through 313 removed outlier: 4.417A pdb=" N ASP E 312 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 313 " --> pdb=" O PRO E 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 309 through 313' Processing helix chain 'E' and resid 339 through 364 removed outlier: 4.156A pdb=" N ARG E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 Processing helix chain 'E' and resid 394 through 403 removed outlier: 3.704A pdb=" N PHE E 398 " --> pdb=" O ASP E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 430 Processing helix chain 'E' and resid 437 through 442 Processing helix chain 'E' and resid 444 through 458 Processing helix chain 'E' and resid 471 through 498 Processing helix chain 'E' and resid 505 through 529 removed outlier: 3.558A pdb=" N LEU E 509 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 546 Processing helix chain 'F' and resid 13 through 28 Processing helix chain 'F' and resid 33 through 46 Processing helix chain 'F' and resid 56 through 79 removed outlier: 4.098A pdb=" N ASP F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 97 removed outlier: 3.714A pdb=" N VAL F 94 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR F 95 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 168 Processing helix chain 'F' and resid 182 through 195 removed outlier: 3.566A pdb=" N GLU F 186 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 219 removed outlier: 3.782A pdb=" N PHE F 219 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 237 Processing helix chain 'F' and resid 251 through 258 removed outlier: 3.698A pdb=" N ILE F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.675A pdb=" N MET F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 25 through 42 removed outlier: 3.783A pdb=" N ARG G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN G 42 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 63 removed outlier: 3.614A pdb=" N GLN G 52 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 83 Processing helix chain 'G' and resid 93 through 99 removed outlier: 4.368A pdb=" N MET G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN G 98 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 151 removed outlier: 4.137A pdb=" N GLU G 149 " --> pdb=" O HIS G 145 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE G 151 " --> pdb=" O TYR G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 195 Processing helix chain 'G' and resid 201 through 212 removed outlier: 3.652A pdb=" N THR G 210 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE G 211 " --> pdb=" O PHE G 207 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 237 Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 267 through 277 removed outlier: 4.021A pdb=" N GLU G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 286 Processing helix chain 'G' and resid 289 through 298 Processing helix chain 'H' and resid 221 through 227 Processing helix chain 'H' and resid 241 through 245 Processing helix chain 'H' and resid 308 through 313 removed outlier: 4.240A pdb=" N ILE H 313 " --> pdb=" O PHE H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.632A pdb=" N THR H 328 " --> pdb=" O ASN H 324 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU H 331 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS H 333 " --> pdb=" O SER H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 373 removed outlier: 3.601A pdb=" N LYS H 363 " --> pdb=" O ASP H 359 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU H 364 " --> pdb=" O SER H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 395 removed outlier: 4.074A pdb=" N TRP H 387 " --> pdb=" O ASP H 383 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 388 " --> pdb=" O MET H 384 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H 393 " --> pdb=" O LYS H 389 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 59 removed outlier: 6.352A pdb=" N THR A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE A 42 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS A 117 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS A 44 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR A 115 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 50 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 109 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A 140 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP A 149 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1045 through 1046 removed outlier: 8.024A pdb=" N ASN A 65 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA4, first strand: chain 'A' and resid 953 through 956 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.955A pdb=" N HIS B 155 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 85 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 153 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 87 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS B 151 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.176A pdb=" N ASN B 105 " --> pdb=" O ILE B1079 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 989 through 995 Processing sheet with id=AA8, first strand: chain 'D' and resid 198 through 199 Processing sheet with id=AA9, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AB1, first strand: chain 'F' and resid 206 through 208 removed outlier: 5.825A pdb=" N SER F 207 " --> pdb=" O ILE F 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 240 through 242 Processing sheet with id=AB3, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.773A pdb=" N ILE G 124 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN G 89 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 199 through 200 removed outlier: 3.999A pdb=" N ILE G 199 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 305 through 306 removed outlier: 3.644A pdb=" N GLU H 340 " --> pdb=" O THR H 348 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2658 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: 2.97 Time building geometry restraints manager: 2.04 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: 6272 1.34 - 1.46: 3299 1.46 - 1.58: 9856 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 19562 Sorted by residual: bond pdb=" N GLY F 297 " pdb=" CA GLY F 297 " ideal model delta sigma weight residual 1.451 1.476 -0.025 8.60e-03 1.35e+04 8.76e+00 bond pdb=" N ILE G 254 " pdb=" CA ILE G 254 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N ASN F 293 " pdb=" CA ASN F 293 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.97e+00 bond pdb=" N THR F 296 " pdb=" CA THR F 296 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.88e+00 bond pdb=" N GLU G 252 " pdb=" CA GLU G 252 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.76e+00 ... (remaining 19557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 25805 1.71 - 3.41: 492 3.41 - 5.12: 56 5.12 - 6.82: 20 6.82 - 8.53: 5 Bond angle restraints: 26378 Sorted by residual: angle pdb=" N ILE B1091 " pdb=" CA ILE B1091 " pdb=" C ILE B1091 " ideal model delta sigma weight residual 113.71 108.86 4.85 9.50e-01 1.11e+00 2.61e+01 angle pdb=" C THR G 168 " pdb=" CA THR G 168 " pdb=" CB THR G 168 " ideal model delta sigma weight residual 115.79 109.99 5.80 1.19e+00 7.06e-01 2.37e+01 angle pdb=" CA GLY F 297 " pdb=" C GLY F 297 " pdb=" O GLY F 297 " ideal model delta sigma weight residual 121.78 117.74 4.04 9.10e-01 1.21e+00 1.97e+01 angle pdb=" N GLU F 292 " pdb=" CA GLU F 292 " pdb=" C GLU F 292 " ideal model delta sigma weight residual 114.56 109.27 5.29 1.27e+00 6.20e-01 1.73e+01 angle pdb=" N ILE F 279 " pdb=" CA ILE F 279 " pdb=" C ILE F 279 " ideal model delta sigma weight residual 113.53 109.60 3.93 9.80e-01 1.04e+00 1.61e+01 ... (remaining 26373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11179 17.73 - 35.46: 649 35.46 - 53.19: 103 53.19 - 70.92: 17 70.92 - 88.65: 12 Dihedral angle restraints: 11960 sinusoidal: 4939 harmonic: 7021 Sorted by residual: dihedral pdb=" CA PHE B 187 " pdb=" C PHE B 187 " pdb=" N SER B 188 " pdb=" CA SER B 188 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE E 239 " pdb=" C ILE E 239 " pdb=" N TRP E 240 " pdb=" CA TRP E 240 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PRO H 302 " pdb=" C PRO H 302 " pdb=" N GLU H 303 " pdb=" CA GLU H 303 " ideal model delta harmonic sigma weight residual 180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 11957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2474 0.052 - 0.105: 430 0.105 - 0.157: 87 0.157 - 0.209: 4 0.209 - 0.262: 1 Chirality restraints: 2996 Sorted by residual: chirality pdb=" CB ILE H 396 " pdb=" CA ILE H 396 " pdb=" CG1 ILE H 396 " pdb=" CG2 ILE H 396 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE G 254 " pdb=" N ILE G 254 " pdb=" C ILE G 254 " pdb=" CB ILE G 254 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA VAL B 175 " pdb=" N VAL B 175 " pdb=" C VAL B 175 " pdb=" CB VAL B 175 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.23e-01 ... (remaining 2993 not shown) Planarity restraints: 3371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 187 " -0.024 2.00e-02 2.50e+03 1.94e-02 6.61e+00 pdb=" CG PHE B 187 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 187 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 187 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 187 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 187 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 187 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 346 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO H 347 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 347 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 347 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 242 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO H 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 243 " -0.021 5.00e-02 4.00e+02 ... (remaining 3368 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1694 2.74 - 3.28: 20566 3.28 - 3.82: 32057 3.82 - 4.36: 38182 4.36 - 4.90: 64189 Nonbonded interactions: 156688 Sorted by model distance: nonbonded pdb=" OH TYR E 20 " pdb=" OD2 ASP E 140 " model vdw 2.203 3.040 nonbonded pdb=" O GLU E 23 " pdb=" OH TYR E 126 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU E 516 " pdb=" OH TYR E 539 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR F 20 " pdb=" O PRO G 130 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 35 " pdb=" OE1 GLU A 133 " model vdw 2.241 3.040 ... (remaining 156683 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 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 : 0.003 0.036 19562 Z= 0.164 Angle : 0.569 8.527 26378 Z= 0.325 Chirality : 0.041 0.262 2996 Planarity : 0.003 0.051 3371 Dihedral : 11.427 88.648 7390 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 0.60 % Allowed : 1.48 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2357 helix: 1.84 (0.15), residues: 1146 sheet: 0.72 (0.46), residues: 163 loop : -1.14 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 491 TYR 0.015 0.001 TYR B 161 PHE 0.044 0.002 PHE B 187 TRP 0.012 0.001 TRP E 220 HIS 0.003 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00284 (19562) covalent geometry : angle 0.56858 (26378) hydrogen bonds : bond 0.13259 ( 909) hydrogen bonds : angle 5.28974 ( 2658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5373 (mtt180) cc_final: 0.4840 (ptm160) REVERT: A 1032 MET cc_start: 0.4348 (tmm) cc_final: 0.4086 (ptm) REVERT: A 1067 MET cc_start: 0.1696 (ptm) cc_final: 0.1168 (mmm) REVERT: A 1092 PHE cc_start: 0.5176 (m-80) cc_final: 0.4848 (m-80) REVERT: E 409 GLN cc_start: 0.8035 (tp40) cc_final: 0.7591 (tp-100) REVERT: E 472 TYR cc_start: 0.7664 (t80) cc_final: 0.7446 (t80) REVERT: E 510 GLU cc_start: 0.7341 (tp30) cc_final: 0.7097 (mt-10) REVERT: F 158 MET cc_start: 0.0877 (tpp) cc_final: 0.0112 (tpp) REVERT: F 166 MET cc_start: 0.0072 (mmm) cc_final: -0.0130 (mmm) REVERT: G 97 MET cc_start: 0.4724 (tpp) cc_final: 0.3917 (tpp) REVERT: G 248 ASP cc_start: -0.1388 (OUTLIER) cc_final: -0.3727 (t0) outliers start: 13 outliers final: 3 residues processed: 207 average time/residue: 0.1447 time to fit residues: 45.6471 Evaluate side-chains 114 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 287 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 200 optimal weight: 30.0000 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 199 ASN B 940 GLN D 171 GLN D 285 ASN F 101 ASN F 115 ASN F 164 GLN F 215 ASN F 244 GLN F 293 ASN F 303 GLN G 52 GLN G 142 GLN G 224 ASN G 290 HIS ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 377 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.242849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163872 restraints weight = 34224.423| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.38 r_work: 0.3387 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19562 Z= 0.146 Angle : 0.517 7.632 26378 Z= 0.271 Chirality : 0.041 0.164 2996 Planarity : 0.004 0.049 3371 Dihedral : 4.548 54.374 2578 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.06 % Allowed : 6.37 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2357 helix: 1.77 (0.15), residues: 1164 sheet: 0.59 (0.45), residues: 163 loop : -1.01 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 491 TYR 0.016 0.001 TYR D 222 PHE 0.035 0.001 PHE B 187 TRP 0.012 0.001 TRP D 200 HIS 0.011 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00332 (19562) covalent geometry : angle 0.51734 (26378) hydrogen bonds : bond 0.04236 ( 909) hydrogen bonds : angle 4.32213 ( 2658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5638 (mtt180) cc_final: 0.4926 (ptm160) REVERT: A 1032 MET cc_start: 0.4778 (tmm) cc_final: 0.4490 (ptm) REVERT: A 1067 MET cc_start: 0.1664 (ptm) cc_final: 0.1320 (mmm) REVERT: A 1092 PHE cc_start: 0.5290 (m-80) cc_final: 0.4735 (m-80) REVERT: B 1055 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7179 (tp-100) REVERT: E 249 ASP cc_start: 0.8578 (m-30) cc_final: 0.8318 (m-30) REVERT: E 409 GLN cc_start: 0.8188 (tp40) cc_final: 0.7656 (tp-100) REVERT: E 510 GLU cc_start: 0.7524 (tp30) cc_final: 0.7122 (mt-10) REVERT: G 97 MET cc_start: 0.3841 (tpp) cc_final: 0.3416 (tpp) REVERT: G 248 ASP cc_start: -0.2525 (OUTLIER) cc_final: -0.3645 (t0) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.1472 time to fit residues: 31.6170 Evaluate side-chains 110 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 172 optimal weight: 8.9990 chunk 125 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN D 171 GLN D 397 ASN D 442 ASN E 430 GLN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 377 HIS ** H 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.240512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156805 restraints weight = 34331.668| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.12 r_work: 0.3398 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 19562 Z= 0.197 Angle : 0.537 9.145 26378 Z= 0.280 Chirality : 0.043 0.164 2996 Planarity : 0.004 0.057 3371 Dihedral : 4.288 42.844 2571 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.34 % Allowed : 7.94 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2357 helix: 1.63 (0.15), residues: 1161 sheet: 0.29 (0.44), residues: 163 loop : -1.03 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 291 TYR 0.021 0.002 TYR D 222 PHE 0.026 0.002 PHE B 187 TRP 0.012 0.001 TRP D 200 HIS 0.011 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00463 (19562) covalent geometry : angle 0.53656 (26378) hydrogen bonds : bond 0.04329 ( 909) hydrogen bonds : angle 4.26510 ( 2658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5545 (mtt180) cc_final: 0.4839 (ptm160) REVERT: A 1032 MET cc_start: 0.5117 (tmm) cc_final: 0.4861 (ptm) REVERT: A 1067 MET cc_start: 0.1705 (ptm) cc_final: 0.1371 (mmt) REVERT: A 1092 PHE cc_start: 0.5308 (m-80) cc_final: 0.4746 (m-80) REVERT: B 200 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: E 409 GLN cc_start: 0.8151 (tp40) cc_final: 0.7509 (tp-100) REVERT: E 510 GLU cc_start: 0.7495 (tp30) cc_final: 0.7259 (mt-10) REVERT: G 97 MET cc_start: 0.3916 (tpp) cc_final: 0.3490 (tpp) REVERT: G 248 ASP cc_start: -0.2265 (OUTLIER) cc_final: -0.3551 (t0) outliers start: 29 outliers final: 12 residues processed: 127 average time/residue: 0.1345 time to fit residues: 27.1648 Evaluate side-chains 107 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain G residue 248 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 31 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 224 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 229 optimal weight: 0.0040 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 955 ASN D 171 GLN G 25 ASN ** H 324 ASN ** 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 = 0.4818 r_free = 0.4818 target = 0.239580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159852 restraints weight = 33983.713| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 4.55 r_work: 0.3352 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 19562 Z= 0.178 Angle : 0.506 7.576 26378 Z= 0.266 Chirality : 0.042 0.192 2996 Planarity : 0.003 0.051 3371 Dihedral : 4.146 40.351 2570 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 1.80 % Allowed : 8.64 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2357 helix: 1.70 (0.15), residues: 1161 sheet: 0.24 (0.44), residues: 163 loop : -1.05 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 388 TYR 0.018 0.001 TYR D 222 PHE 0.031 0.001 PHE E 546 TRP 0.012 0.001 TRP D 200 HIS 0.008 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00419 (19562) covalent geometry : angle 0.50559 (26378) hydrogen bonds : bond 0.04048 ( 909) hydrogen bonds : angle 4.13896 ( 2658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5631 (mtt180) cc_final: 0.4936 (ptm160) REVERT: A 1067 MET cc_start: 0.1706 (ptm) cc_final: 0.1281 (mmt) REVERT: A 1092 PHE cc_start: 0.5334 (m-80) cc_final: 0.4758 (m-80) REVERT: B 944 MET cc_start: 0.7733 (mmt) cc_final: 0.7444 (mmt) REVERT: E 409 GLN cc_start: 0.8254 (tp40) cc_final: 0.7661 (tp-100) REVERT: G 248 ASP cc_start: -0.2495 (OUTLIER) cc_final: -0.3500 (t0) outliers start: 39 outliers final: 18 residues processed: 131 average time/residue: 0.1384 time to fit residues: 29.1159 Evaluate side-chains 112 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 80 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN D 171 GLN D 285 ASN E 292 ASN F 303 GLN F 306 HIS G 25 ASN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 381 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 = 0.4790 r_free = 0.4790 target = 0.237152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.159967 restraints weight = 33622.285| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 4.20 r_work: 0.3313 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 19562 Z= 0.284 Angle : 0.608 8.536 26378 Z= 0.316 Chirality : 0.045 0.174 2996 Planarity : 0.004 0.047 3371 Dihedral : 4.490 40.426 2570 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 1.94 % Allowed : 10.35 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2357 helix: 1.38 (0.15), residues: 1158 sheet: 0.04 (0.45), residues: 163 loop : -1.19 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 388 TYR 0.022 0.002 TYR E 492 PHE 0.033 0.002 PHE E 463 TRP 0.012 0.002 TRP D 200 HIS 0.008 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00677 (19562) covalent geometry : angle 0.60838 (26378) hydrogen bonds : bond 0.04811 ( 909) hydrogen bonds : angle 4.35783 ( 2658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5819 (mtt180) cc_final: 0.5079 (ptm160) REVERT: A 1067 MET cc_start: 0.1381 (ptm) cc_final: 0.1042 (mmt) REVERT: A 1092 PHE cc_start: 0.5125 (m-80) cc_final: 0.4554 (m-80) REVERT: E 291 ARG cc_start: 0.7217 (tpp-160) cc_final: 0.6995 (mpp-170) REVERT: E 409 GLN cc_start: 0.8245 (tp40) cc_final: 0.7640 (tp-100) REVERT: E 512 LEU cc_start: 0.8656 (mt) cc_final: 0.8426 (tp) REVERT: G 248 ASP cc_start: -0.2525 (OUTLIER) cc_final: -0.3624 (t0) outliers start: 42 outliers final: 23 residues processed: 135 average time/residue: 0.1235 time to fit residues: 26.4693 Evaluate side-chains 118 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 39 CYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 121 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 88 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 0.0370 chunk 117 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 34 optimal weight: 30.0000 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN D 211 GLN E 319 HIS ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.240466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163080 restraints weight = 33923.452| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 4.68 r_work: 0.3376 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19562 Z= 0.113 Angle : 0.471 6.917 26378 Z= 0.248 Chirality : 0.040 0.172 2996 Planarity : 0.003 0.047 3371 Dihedral : 4.061 37.777 2570 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 1.34 % Allowed : 11.45 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2357 helix: 1.80 (0.15), residues: 1155 sheet: 0.24 (0.45), residues: 163 loop : -1.07 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 291 TYR 0.016 0.001 TYR A 998 PHE 0.026 0.001 PHE E 463 TRP 0.014 0.001 TRP E 220 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00250 (19562) covalent geometry : angle 0.47103 (26378) hydrogen bonds : bond 0.03746 ( 909) hydrogen bonds : angle 4.02711 ( 2658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5873 (mtt180) cc_final: 0.5118 (ptm160) REVERT: A 1067 MET cc_start: 0.1371 (ptm) cc_final: 0.0927 (mmm) REVERT: A 1092 PHE cc_start: 0.5039 (m-80) cc_final: 0.4563 (m-80) REVERT: E 512 LEU cc_start: 0.8699 (mt) cc_final: 0.8479 (tp) REVERT: G 248 ASP cc_start: -0.2597 (OUTLIER) cc_final: -0.3610 (t0) outliers start: 29 outliers final: 21 residues processed: 124 average time/residue: 0.1397 time to fit residues: 26.9731 Evaluate side-chains 117 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 546 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain H residue 351 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 109 optimal weight: 0.0060 chunk 164 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 130 optimal weight: 0.2980 chunk 133 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN D 382 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.238601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157594 restraints weight = 33832.047| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.21 r_work: 0.3394 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19562 Z= 0.175 Angle : 0.516 12.412 26378 Z= 0.267 Chirality : 0.041 0.152 2996 Planarity : 0.003 0.048 3371 Dihedral : 4.098 36.333 2570 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 1.52 % Allowed : 11.73 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2357 helix: 1.71 (0.15), residues: 1164 sheet: 0.34 (0.45), residues: 160 loop : -1.09 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.015 0.001 TYR E 492 PHE 0.020 0.001 PHE E 546 TRP 0.011 0.001 TRP D 200 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00412 (19562) covalent geometry : angle 0.51560 (26378) hydrogen bonds : bond 0.04019 ( 909) hydrogen bonds : angle 4.07256 ( 2658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5870 (mtt180) cc_final: 0.5112 (ptm160) REVERT: A 969 MET cc_start: 0.4344 (mmp) cc_final: 0.3916 (mmp) REVERT: A 1067 MET cc_start: 0.1331 (ptm) cc_final: 0.0865 (mmm) REVERT: A 1092 PHE cc_start: 0.5027 (m-80) cc_final: 0.4522 (m-80) REVERT: D 445 THR cc_start: 0.8434 (p) cc_final: 0.8154 (p) REVERT: E 512 LEU cc_start: 0.8674 (mt) cc_final: 0.8445 (tp) REVERT: G 248 ASP cc_start: -0.2628 (OUTLIER) cc_final: -0.3680 (t0) outliers start: 33 outliers final: 25 residues processed: 124 average time/residue: 0.1258 time to fit residues: 24.9307 Evaluate side-chains 120 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 1055 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain E residue 546 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain H residue 351 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 123 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 187 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN E 406 ASN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.239896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.162126 restraints weight = 33891.548| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.38 r_work: 0.3359 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19562 Z= 0.120 Angle : 0.483 12.659 26378 Z= 0.249 Chirality : 0.040 0.147 2996 Planarity : 0.003 0.067 3371 Dihedral : 3.942 36.052 2570 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 1.48 % Allowed : 12.01 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2357 helix: 1.86 (0.15), residues: 1163 sheet: 0.44 (0.45), residues: 160 loop : -1.08 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 291 TYR 0.013 0.001 TYR E 82 PHE 0.019 0.001 PHE E 546 TRP 0.012 0.001 TRP E 220 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00271 (19562) covalent geometry : angle 0.48313 (26378) hydrogen bonds : bond 0.03629 ( 909) hydrogen bonds : angle 3.93118 ( 2658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.2819 (OUTLIER) cc_final: 0.2188 (t0) REVERT: A 147 ARG cc_start: 0.5802 (mtt180) cc_final: 0.5053 (ptm160) REVERT: A 1067 MET cc_start: 0.1310 (ptm) cc_final: 0.0832 (mmm) REVERT: A 1092 PHE cc_start: 0.5076 (m-80) cc_final: 0.4558 (m-80) REVERT: D 445 THR cc_start: 0.8376 (p) cc_final: 0.8118 (p) REVERT: G 248 ASP cc_start: -0.3122 (OUTLIER) cc_final: -0.3825 (t0) REVERT: H 370 ARG cc_start: -0.0787 (OUTLIER) cc_final: -0.1038 (mtp85) outliers start: 32 outliers final: 23 residues processed: 124 average time/residue: 0.1243 time to fit residues: 24.4975 Evaluate side-chains 118 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain E residue 546 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 370 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 146 optimal weight: 0.2980 chunk 208 optimal weight: 40.0000 chunk 184 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.240242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163216 restraints weight = 33711.653| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 4.70 r_work: 0.3384 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19562 Z= 0.110 Angle : 0.481 12.508 26378 Z= 0.247 Chirality : 0.039 0.145 2996 Planarity : 0.003 0.050 3371 Dihedral : 3.836 35.701 2570 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 1.43 % Allowed : 12.33 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 2357 helix: 1.96 (0.15), residues: 1166 sheet: 0.56 (0.45), residues: 158 loop : -1.01 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 291 TYR 0.013 0.001 TYR E 82 PHE 0.031 0.001 PHE E 463 TRP 0.013 0.001 TRP E 220 HIS 0.003 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00245 (19562) covalent geometry : angle 0.48113 (26378) hydrogen bonds : bond 0.03482 ( 909) hydrogen bonds : angle 3.84509 ( 2658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.2483 (OUTLIER) cc_final: 0.1994 (t0) REVERT: A 147 ARG cc_start: 0.5775 (mtt180) cc_final: 0.5010 (ptm160) REVERT: A 969 MET cc_start: 0.4578 (mmp) cc_final: 0.4079 (mmp) REVERT: A 1067 MET cc_start: 0.1404 (ptm) cc_final: 0.0817 (mmm) REVERT: A 1092 PHE cc_start: 0.4961 (m-80) cc_final: 0.4456 (m-80) REVERT: D 445 THR cc_start: 0.8318 (p) cc_final: 0.8070 (p) REVERT: G 248 ASP cc_start: -0.2938 (OUTLIER) cc_final: -0.3602 (t0) REVERT: H 370 ARG cc_start: -0.0842 (OUTLIER) cc_final: -0.1110 (mtp85) outliers start: 31 outliers final: 24 residues processed: 117 average time/residue: 0.1100 time to fit residues: 20.8510 Evaluate side-chains 119 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain E residue 546 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 370 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 17 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 177 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 61 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1056 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN F 59 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.239097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163606 restraints weight = 34024.589| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 4.75 r_work: 0.3384 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19562 Z= 0.150 Angle : 0.506 11.331 26378 Z= 0.260 Chirality : 0.040 0.152 2996 Planarity : 0.003 0.049 3371 Dihedral : 3.917 35.635 2570 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 1.29 % Allowed : 12.66 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.18), residues: 2357 helix: 1.90 (0.15), residues: 1160 sheet: 0.53 (0.45), residues: 158 loop : -1.01 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.013 0.001 TYR D 222 PHE 0.034 0.001 PHE E 463 TRP 0.011 0.001 TRP E 525 HIS 0.005 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00350 (19562) covalent geometry : angle 0.50585 (26378) hydrogen bonds : bond 0.03772 ( 909) hydrogen bonds : angle 3.92606 ( 2658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.2538 (OUTLIER) cc_final: 0.2260 (t0) REVERT: A 147 ARG cc_start: 0.5764 (mtt180) cc_final: 0.4976 (ptm160) REVERT: A 969 MET cc_start: 0.4883 (mmp) cc_final: 0.4409 (mmp) REVERT: A 1067 MET cc_start: 0.1529 (ptm) cc_final: 0.0873 (mmm) REVERT: A 1092 PHE cc_start: 0.5061 (m-80) cc_final: 0.4573 (m-80) REVERT: D 445 THR cc_start: 0.8326 (p) cc_final: 0.8066 (p) REVERT: E 291 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6786 (mmt90) REVERT: E 512 LEU cc_start: 0.8704 (mt) cc_final: 0.8465 (tp) REVERT: G 248 ASP cc_start: -0.3318 (OUTLIER) cc_final: -0.3932 (t0) REVERT: H 370 ARG cc_start: -0.0779 (OUTLIER) cc_final: -0.1005 (mtp85) outliers start: 28 outliers final: 25 residues processed: 117 average time/residue: 0.1377 time to fit residues: 25.4309 Evaluate side-chains 123 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain E residue 546 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain H residue 351 ILE Chi-restraints excluded: chain H residue 370 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 113 optimal weight: 0.1980 chunk 186 optimal weight: 7.9990 chunk 123 optimal weight: 0.0030 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 0.0270 chunk 144 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN H 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.240322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162962 restraints weight = 33939.776| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.80 r_work: 0.3405 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19562 Z= 0.106 Angle : 0.483 11.908 26378 Z= 0.248 Chirality : 0.039 0.141 2996 Planarity : 0.003 0.048 3371 Dihedral : 3.814 35.467 2570 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 1.29 % Allowed : 12.70 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.18), residues: 2357 helix: 2.06 (0.15), residues: 1157 sheet: 0.48 (0.45), residues: 160 loop : -0.94 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1062 TYR 0.013 0.001 TYR E 82 PHE 0.033 0.001 PHE E 463 TRP 0.013 0.001 TRP E 525 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00235 (19562) covalent geometry : angle 0.48283 (26378) hydrogen bonds : bond 0.03458 ( 909) hydrogen bonds : angle 3.82109 ( 2658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6975.88 seconds wall clock time: 119 minutes 43.42 seconds (7183.42 seconds total)