Starting phenix.real_space_refine on Wed Jun 18 17:17:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqs_34953/06_2025/8hqs_34953_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqs_34953/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqs_34953/06_2025/8hqs_34953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqs_34953/06_2025/8hqs_34953.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqs_34953/06_2025/8hqs_34953_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqs_34953/06_2025/8hqs_34953_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.53, per 1000 atoms: 0.81 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: 5.41 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.07 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: 5.77 Time building geometry restraints manager: 6.33 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: 21.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 48.250 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.300 ------------------------------------------------------------------------------- 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 : 11.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP E 220 HIS 0.003 0.001 HIS D 359 PHE 0.044 0.002 PHE B 187 TYR 0.015 0.001 TYR B 161 ARG 0.003 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.13259 ( 909) hydrogen bonds : angle 5.28974 ( 2658) covalent geometry : bond 0.00284 (19562) covalent geometry : angle 0.56858 (26378) *********************** 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 : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5373 (mtt180) cc_final: 0.4878 (ptm160) REVERT: A 1032 MET cc_start: 0.4348 (tmm) cc_final: 0.4093 (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: 0.7012 (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: 0.3918 (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: 0.3286 time to fit residues: 103.4488 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 : 2.108 ------------------------------------------------------------------------------- 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 198 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 0.0770 chunk 60 optimal weight: 0.2980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 184 optimal weight: 20.0000 chunk 71 optimal weight: 0.3980 chunk 112 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.243655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.170280 restraints weight = 34601.793| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 4.88 r_work: 0.3556 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19562 Z= 0.117 Angle : 0.504 11.157 26378 Z= 0.263 Chirality : 0.041 0.167 2996 Planarity : 0.003 0.050 3371 Dihedral : 4.490 54.071 2578 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.02 % Allowed : 6.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2357 helix: 1.87 (0.15), residues: 1163 sheet: 0.67 (0.45), residues: 163 loop : -0.99 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 200 HIS 0.011 0.001 HIS A1058 PHE 0.034 0.001 PHE B 187 TYR 0.014 0.001 TYR H 327 ARG 0.006 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 909) hydrogen bonds : angle 4.25788 ( 2658) covalent geometry : bond 0.00254 (19562) covalent geometry : angle 0.50442 (26378) *********************** 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 148 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5619 (mtt180) cc_final: 0.4919 (ptm160) REVERT: A 1032 MET cc_start: 0.4762 (tmm) cc_final: 0.4467 (ptm) REVERT: A 1067 MET cc_start: 0.1679 (ptm) cc_final: 0.1336 (mmm) REVERT: A 1092 PHE cc_start: 0.5280 (m-80) cc_final: 0.4652 (m-80) REVERT: B 1055 GLN cc_start: 0.7552 (tp-100) cc_final: 0.7146 (tp-100) REVERT: D 213 MET cc_start: 0.7571 (mtp) cc_final: 0.7321 (mtp) REVERT: E 394 ASP cc_start: 0.7990 (t70) cc_final: 0.7597 (p0) REVERT: E 409 GLN cc_start: 0.8070 (tp40) cc_final: 0.7552 (tp-100) REVERT: E 510 GLU cc_start: 0.7486 (tp30) cc_final: 0.7020 (mt-10) REVERT: G 97 MET cc_start: 0.4003 (tpp) cc_final: 0.3615 (tpp) REVERT: G 248 ASP cc_start: -0.2644 (OUTLIER) cc_final: -0.3773 (t0) outliers start: 22 outliers final: 11 residues processed: 143 average time/residue: 0.3260 time to fit residues: 70.8690 Evaluate side-chains 113 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU 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 168 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 292 MET 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 92 optimal weight: 0.0980 chunk 155 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 199 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 227 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN B 95 HIS B 199 ASN D 171 GLN ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 442 ASN F 293 ASN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 377 HIS H 395 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.241012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162312 restraints weight = 33972.001| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 4.69 r_work: 0.3340 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19562 Z= 0.177 Angle : 0.526 11.087 26378 Z= 0.274 Chirality : 0.042 0.164 2996 Planarity : 0.004 0.049 3371 Dihedral : 4.220 41.615 2571 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.06 % Allowed : 8.04 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2357 helix: 1.70 (0.15), residues: 1170 sheet: 0.36 (0.44), residues: 165 loop : -0.99 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 200 HIS 0.010 0.001 HIS D 359 PHE 0.033 0.002 PHE E 546 TYR 0.020 0.001 TYR D 222 ARG 0.005 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 909) hydrogen bonds : angle 4.21376 ( 2658) covalent geometry : bond 0.00415 (19562) covalent geometry : angle 0.52646 (26378) *********************** 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 119 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5532 (mtt180) cc_final: 0.4824 (ptm160) REVERT: A 1032 MET cc_start: 0.5150 (tmm) cc_final: 0.4742 (ptm) REVERT: A 1067 MET cc_start: 0.1670 (ptm) cc_final: 0.1348 (mmt) REVERT: A 1092 PHE cc_start: 0.5347 (m-80) cc_final: 0.4781 (m-80) REVERT: B 944 MET cc_start: 0.7789 (mmt) cc_final: 0.7492 (mmt) REVERT: E 409 GLN cc_start: 0.8261 (tp40) cc_final: 0.7618 (tp-100) REVERT: E 510 GLU cc_start: 0.7698 (tp30) cc_final: 0.7294 (mt-10) REVERT: G 97 MET cc_start: 0.3774 (tpp) cc_final: 0.3400 (tpp) REVERT: G 248 ASP cc_start: -0.2214 (OUTLIER) cc_final: -0.3429 (t0) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.3035 time to fit residues: 54.8285 Evaluate side-chains 102 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 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 267 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 460 CYS 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 119 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN D 171 GLN D 285 ASN E 430 GLN G 25 ASN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.240079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163544 restraints weight = 34063.091| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.92 r_work: 0.3338 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 19562 Z= 0.195 Angle : 0.527 11.633 26378 Z= 0.274 Chirality : 0.042 0.154 2996 Planarity : 0.003 0.047 3371 Dihedral : 4.190 39.724 2570 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 1.76 % Allowed : 8.82 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2357 helix: 1.70 (0.15), residues: 1160 sheet: 0.34 (0.44), residues: 165 loop : -1.02 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 200 HIS 0.016 0.001 HIS B 95 PHE 0.023 0.001 PHE B 187 TYR 0.019 0.001 TYR E 492 ARG 0.005 0.000 ARG E 351 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 909) hydrogen bonds : angle 4.16732 ( 2658) covalent geometry : bond 0.00460 (19562) covalent geometry : angle 0.52669 (26378) *********************** 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 135 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5647 (mtt180) cc_final: 0.4923 (ptm160) REVERT: A 1067 MET cc_start: 0.1759 (ptm) cc_final: 0.1359 (mmt) REVERT: A 1092 PHE cc_start: 0.5251 (m-80) cc_final: 0.4677 (m-80) REVERT: B 200 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: E 409 GLN cc_start: 0.8244 (tp40) cc_final: 0.7656 (tp-100) REVERT: E 460 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6821 (p) REVERT: G 97 MET cc_start: 0.3849 (tpp) cc_final: 0.3426 (tpp) REVERT: G 248 ASP cc_start: -0.2544 (OUTLIER) cc_final: -0.3530 (t0) outliers start: 38 outliers final: 18 residues processed: 128 average time/residue: 0.3015 time to fit residues: 62.4553 Evaluate side-chains 109 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 VAL 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 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 460 CYS 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 214 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 201 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.238814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159314 restraints weight = 34001.188| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.63 r_work: 0.3385 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 19562 Z= 0.202 Angle : 0.538 11.257 26378 Z= 0.279 Chirality : 0.042 0.146 2996 Planarity : 0.003 0.047 3371 Dihedral : 4.200 37.674 2570 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 1.85 % Allowed : 9.88 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2357 helix: 1.66 (0.15), residues: 1159 sheet: 0.31 (0.45), residues: 163 loop : -1.06 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 200 HIS 0.009 0.001 HIS D 359 PHE 0.032 0.002 PHE E 463 TYR 0.018 0.001 TYR D 222 ARG 0.005 0.000 ARG H 388 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 909) hydrogen bonds : angle 4.13370 ( 2658) covalent geometry : bond 0.00477 (19562) covalent geometry : angle 0.53808 (26378) *********************** 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 140 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5562 (mtt180) cc_final: 0.4914 (ptm160) REVERT: A 1067 MET cc_start: 0.1546 (ptm) cc_final: 0.1141 (mmt) REVERT: A 1092 PHE cc_start: 0.5134 (m-80) cc_final: 0.4570 (m-80) REVERT: E 409 GLN cc_start: 0.8232 (tp40) cc_final: 0.7634 (tp-100) REVERT: E 460 CYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6920 (p) REVERT: F 128 GLU cc_start: -0.3397 (OUTLIER) cc_final: -0.3852 (pm20) REVERT: G 248 ASP cc_start: -0.2423 (OUTLIER) cc_final: -0.3665 (t0) outliers start: 40 outliers final: 23 residues processed: 135 average time/residue: 0.3106 time to fit residues: 66.9131 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 : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR 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 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 215 LEU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 324 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 267 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 460 CYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 128 GLU 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 46 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 117 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 0.2980 chunk 220 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 203 optimal weight: 20.0000 chunk 101 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- 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 E 319 HIS F 303 GLN F 306 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.240303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164376 restraints weight = 33998.078| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.87 r_work: 0.3344 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19562 Z= 0.125 Angle : 0.478 11.126 26378 Z= 0.249 Chirality : 0.040 0.186 2996 Planarity : 0.003 0.047 3371 Dihedral : 3.971 36.086 2570 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.43 % Allowed : 11.09 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2357 helix: 1.88 (0.15), residues: 1159 sheet: 0.45 (0.45), residues: 163 loop : -1.06 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 220 HIS 0.005 0.001 HIS D 359 PHE 0.027 0.001 PHE E 546 TYR 0.012 0.001 TYR D 222 ARG 0.004 0.000 ARG E 351 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 909) hydrogen bonds : angle 3.96940 ( 2658) covalent geometry : bond 0.00283 (19562) covalent geometry : angle 0.47818 (26378) *********************** 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 128 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5775 (mtt180) cc_final: 0.5067 (ptm160) REVERT: A 1067 MET cc_start: 0.1187 (ptm) cc_final: 0.0766 (mmm) REVERT: A 1092 PHE cc_start: 0.5028 (m-80) cc_final: 0.4538 (m-80) REVERT: E 460 CYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6830 (p) REVERT: G 248 ASP cc_start: -0.2579 (OUTLIER) cc_final: -0.3516 (t0) outliers start: 31 outliers final: 16 residues processed: 122 average time/residue: 0.3079 time to fit residues: 60.1298 Evaluate side-chains 111 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR 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 139 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 460 CYS 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 323 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 25 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 67 optimal weight: 0.0970 chunk 94 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ** 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 = 0.4816 r_free = 0.4816 target = 0.239406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160836 restraints weight = 33664.566| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 4.56 r_work: 0.3336 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19562 Z= 0.159 Angle : 0.510 11.775 26378 Z= 0.263 Chirality : 0.041 0.137 2996 Planarity : 0.003 0.069 3371 Dihedral : 4.026 36.039 2570 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 1.57 % Allowed : 11.45 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2357 helix: 1.83 (0.15), residues: 1160 sheet: 0.58 (0.45), residues: 161 loop : -1.06 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 200 HIS 0.007 0.001 HIS D 359 PHE 0.023 0.001 PHE E 546 TYR 0.015 0.001 TYR E 492 ARG 0.004 0.000 ARG E 351 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 909) hydrogen bonds : angle 3.97498 ( 2658) covalent geometry : bond 0.00371 (19562) covalent geometry : angle 0.51037 (26378) *********************** 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 134 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5845 (mtt180) cc_final: 0.5107 (ptm160) REVERT: A 969 MET cc_start: 0.4379 (mmp) cc_final: 0.4000 (mmp) REVERT: A 1067 MET cc_start: 0.1269 (ptm) cc_final: 0.0845 (mmm) REVERT: A 1092 PHE cc_start: 0.5072 (m-80) cc_final: 0.4583 (m-80) REVERT: E 460 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6968 (p) REVERT: E 461 PHE cc_start: 0.7537 (t80) cc_final: 0.7256 (t80) REVERT: G 248 ASP cc_start: -0.2742 (OUTLIER) cc_final: -0.3595 (t0) outliers start: 34 outliers final: 22 residues processed: 127 average time/residue: 0.4011 time to fit residues: 82.0320 Evaluate side-chains 119 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 1029 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 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 96 SER 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 306 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 460 CYS 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 236 ILE Chi-restraints excluded: chain H residue 323 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 149 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 0.0170 chunk 190 optimal weight: 20.0000 chunk 135 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2422 ------------------------------------------------------------------------------- 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** A1058 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN D 171 GLN D 382 GLN E 406 ASN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 381 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.237632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160654 restraints weight = 33907.693| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 4.59 r_work: 0.3315 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 19562 Z= 0.260 Angle : 0.606 11.591 26378 Z= 0.310 Chirality : 0.044 0.147 2996 Planarity : 0.004 0.044 3371 Dihedral : 4.347 36.252 2570 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 1.71 % Allowed : 12.01 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2357 helix: 1.50 (0.15), residues: 1166 sheet: 0.18 (0.45), residues: 160 loop : -1.10 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 200 HIS 0.012 0.001 HIS A1058 PHE 0.025 0.002 PHE E 546 TYR 0.020 0.002 TYR E 492 ARG 0.005 0.000 ARG E 351 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 909) hydrogen bonds : angle 4.23552 ( 2658) covalent geometry : bond 0.00617 (19562) covalent geometry : angle 0.60595 (26378) *********************** 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 133 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5750 (mtt180) cc_final: 0.4999 (ptm160) REVERT: A 1067 MET cc_start: 0.1515 (ptm) cc_final: 0.0809 (mmm) REVERT: A 1092 PHE cc_start: 0.5030 (m-80) cc_final: 0.4546 (m-80) REVERT: E 291 ARG cc_start: 0.7178 (tpp-160) cc_final: 0.6831 (mmt90) REVERT: E 460 CYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6981 (p) REVERT: E 461 PHE cc_start: 0.7504 (t80) cc_final: 0.7272 (t80) REVERT: E 512 LEU cc_start: 0.8709 (mt) cc_final: 0.8464 (tp) REVERT: G 248 ASP cc_start: -0.3262 (OUTLIER) cc_final: -0.3730 (t0) REVERT: H 370 ARG cc_start: -0.0806 (OUTLIER) cc_final: -0.1026 (mtp85) outliers start: 37 outliers final: 24 residues processed: 127 average time/residue: 0.3221 time to fit residues: 65.6727 Evaluate side-chains 117 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 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 96 SER Chi-restraints excluded: chain E residue 139 ILE 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 E residue 406 ASN Chi-restraints excluded: chain E residue 460 CYS 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 236 ILE Chi-restraints excluded: chain H residue 312 ILE 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 221 optimal weight: 20.0000 chunk 129 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 159 optimal weight: 0.0010 chunk 3 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN F 59 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.239863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.159112 restraints weight = 34102.709| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 4.71 r_work: 0.3358 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19562 Z= 0.137 Angle : 0.509 11.931 26378 Z= 0.262 Chirality : 0.040 0.138 2996 Planarity : 0.003 0.044 3371 Dihedral : 4.068 36.058 2570 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 1.02 % Allowed : 12.89 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2357 helix: 1.76 (0.15), residues: 1163 sheet: 0.20 (0.43), residues: 176 loop : -1.06 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 220 HIS 0.006 0.001 HIS A1058 PHE 0.023 0.001 PHE E 546 TYR 0.013 0.001 TYR E 82 ARG 0.004 0.000 ARG D 384 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 909) hydrogen bonds : angle 3.99170 ( 2658) covalent geometry : bond 0.00314 (19562) covalent geometry : angle 0.50857 (26378) *********************** 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 116 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5799 (mtt180) cc_final: 0.5028 (ptm160) REVERT: A 969 MET cc_start: 0.4811 (mmp) cc_final: 0.4342 (mmp) REVERT: A 1067 MET cc_start: 0.1414 (ptm) cc_final: 0.0608 (mmm) REVERT: A 1092 PHE cc_start: 0.5037 (m-80) cc_final: 0.4550 (m-80) REVERT: E 341 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7930 (tt) REVERT: E 460 CYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6918 (p) REVERT: E 461 PHE cc_start: 0.7577 (t80) cc_final: 0.7366 (t80) REVERT: E 512 LEU cc_start: 0.8747 (mt) cc_final: 0.8497 (tp) REVERT: G 248 ASP cc_start: -0.3669 (OUTLIER) cc_final: -0.4061 (t0) outliers start: 22 outliers final: 14 residues processed: 111 average time/residue: 0.3236 time to fit residues: 57.3645 Evaluate side-chains 112 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR 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 255 VAL Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 460 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 218 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 280 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.238521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155180 restraints weight = 34011.458| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.80 r_work: 0.3390 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19562 Z= 0.194 Angle : 0.551 11.917 26378 Z= 0.282 Chirality : 0.042 0.138 2996 Planarity : 0.003 0.044 3371 Dihedral : 4.146 36.136 2570 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 1.15 % Allowed : 12.66 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2357 helix: 1.67 (0.15), residues: 1166 sheet: 0.21 (0.45), residues: 160 loop : -1.04 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 200 HIS 0.008 0.001 HIS D 359 PHE 0.028 0.002 PHE E 463 TYR 0.035 0.001 TYR A 127 ARG 0.004 0.000 ARG A1062 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 909) hydrogen bonds : angle 4.07566 ( 2658) covalent geometry : bond 0.00456 (19562) covalent geometry : angle 0.55070 (26378) ********************** 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 122 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.5702 (mtt180) cc_final: 0.4964 (ptm160) REVERT: A 1067 MET cc_start: 0.1263 (ptm) cc_final: 0.0472 (mmm) REVERT: A 1092 PHE cc_start: 0.4958 (m-80) cc_final: 0.4456 (m-80) REVERT: E 291 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6757 (mmt90) REVERT: E 460 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6931 (p) REVERT: E 512 LEU cc_start: 0.8804 (mt) cc_final: 0.8497 (tp) REVERT: G 248 ASP cc_start: -0.3745 (OUTLIER) cc_final: -0.4116 (t0) outliers start: 25 outliers final: 20 residues processed: 117 average time/residue: 0.3217 time to fit residues: 60.8588 Evaluate side-chains 118 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 1029 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 172 LYS 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 96 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 460 CYS 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 236 ILE Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 351 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 120 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 172 optimal weight: 0.0010 chunk 209 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.238305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162670 restraints weight = 33839.795| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 4.98 r_work: 0.3336 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3806 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= 0.180 Angle : 0.532 12.070 26378 Z= 0.273 Chirality : 0.041 0.138 2996 Planarity : 0.003 0.044 3371 Dihedral : 4.110 36.143 2570 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 1.20 % Allowed : 12.70 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2357 helix: 1.71 (0.15), residues: 1165 sheet: 0.21 (0.45), residues: 160 loop : -1.10 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 200 HIS 0.006 0.001 HIS D 359 PHE 0.022 0.001 PHE E 546 TYR 0.015 0.001 TYR E 492 ARG 0.005 0.000 ARG D 384 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 909) hydrogen bonds : angle 4.02804 ( 2658) covalent geometry : bond 0.00423 (19562) covalent geometry : angle 0.53199 (26378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15996.92 seconds wall clock time: 278 minutes 26.42 seconds (16706.42 seconds total)