Starting phenix.real_space_refine on Thu Feb 5 05:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0j_64665/02_2026/9v0j_64665.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0j_64665/02_2026/9v0j_64665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v0j_64665/02_2026/9v0j_64665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0j_64665/02_2026/9v0j_64665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v0j_64665/02_2026/9v0j_64665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0j_64665/02_2026/9v0j_64665.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9594 2.51 5 N 2518 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14747 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2716 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 18, 'ASN:plan1': 3, 'ASP:plan': 13, 'GLN:plan1': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3045 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 385} Chain breaks: 6 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 7, 'GLN:plan1': 6, 'GLU:plan': 9, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 150 Chain: "C" Number of atoms: 6981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 6981 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 920} Chain breaks: 15 Unresolved non-hydrogen bonds: 934 Unresolved non-hydrogen angles: 1169 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'ARG:plan': 14, 'HIS:plan': 6, 'ASP:plan': 38, 'GLU:plan': 43, 'ASN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 7, 'GLN:plan1': 15, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 570 Chain: "D" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2005 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 18, 'TRANS': 273} Chain breaks: 6 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 6, 'TYR:plan': 5, 'ARG:plan': 7, 'GLU:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 173 Time building chain proxies: 3.54, per 1000 atoms: 0.24 Number of scatterers: 14747 At special positions: 0 Unit cell: (110.5, 112.2, 199.75, 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 70 16.00 O 2565 8.00 N 2518 7.00 C 9594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 682.0 milliseconds 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 23 sheets defined 37.2% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.589A pdb=" N THR A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 94 through 97 removed outlier: 4.516A pdb=" N ALA A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.594A pdb=" N VAL A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.597A pdb=" N LYS A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 127 through 141 removed outlier: 3.658A pdb=" N ILE A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.830A pdb=" N LEU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.535A pdb=" N ALA B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 135 through 161 removed outlier: 3.523A pdb=" N VAL B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.688A pdb=" N ASP B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.830A pdb=" N CYS B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.607A pdb=" N ILE B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 279 through 288 removed outlier: 3.718A pdb=" N VAL B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.597A pdb=" N GLN B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 319 removed outlier: 3.657A pdb=" N TRP B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 removed outlier: 3.628A pdb=" N SER B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 366 through 369 removed outlier: 3.575A pdb=" N SER B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 506 through 516 Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 536 through 547 removed outlier: 3.698A pdb=" N PHE B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.570A pdb=" N VAL C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 238 through 242 removed outlier: 3.739A pdb=" N ILE C 242 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.580A pdb=" N LEU C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 305 through 318 removed outlier: 3.612A pdb=" N ALA C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 360 removed outlier: 3.581A pdb=" N MET C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 removed outlier: 3.930A pdb=" N ASP C 463 " --> pdb=" O TYR C 459 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 749 Processing helix chain 'C' and resid 796 through 809 removed outlier: 3.577A pdb=" N GLU C 800 " --> pdb=" O GLN C 796 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 806 " --> pdb=" O PHE C 802 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 807 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN C 809 " --> pdb=" O GLN C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 917 through 927 removed outlier: 3.709A pdb=" N LEU C 921 " --> pdb=" O LYS C 917 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 922 " --> pdb=" O TRP C 918 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 962 removed outlier: 3.656A pdb=" N THR C 956 " --> pdb=" O CYS C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 994 Processing helix chain 'C' and resid 1178 through 1186 Processing helix chain 'C' and resid 1208 through 1218 removed outlier: 4.095A pdb=" N ASN C1216 " --> pdb=" O HIS C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1223 through 1237 Processing helix chain 'C' and resid 1286 through 1291 Processing helix chain 'C' and resid 1394 through 1412 Processing helix chain 'C' and resid 1468 through 1479 removed outlier: 3.798A pdb=" N ARG C1479 " --> pdb=" O ALA C1475 " (cutoff:3.500A) Processing helix chain 'C' and resid 1567 through 1581 removed outlier: 3.872A pdb=" N ARG C1571 " --> pdb=" O LYS C1567 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C1575 " --> pdb=" O ARG C1571 " (cutoff:3.500A) Processing helix chain 'C' and resid 1582 through 1584 No H-bonds generated for 'chain 'C' and resid 1582 through 1584' Processing helix chain 'C' and resid 1585 through 1599 removed outlier: 3.541A pdb=" N SER C1593 " --> pdb=" O THR C1589 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C1596 " --> pdb=" O THR C1592 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS C1597 " --> pdb=" O SER C1593 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET C1598 " --> pdb=" O CYS C1594 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS C1599 " --> pdb=" O LEU C1595 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 removed outlier: 4.199A pdb=" N ARG D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.937A pdb=" N GLY D 107 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 178 through 203 removed outlier: 3.736A pdb=" N GLU D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP D 195 " --> pdb=" O CYS D 191 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 247 removed outlier: 3.881A pdb=" N ARG D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 247 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 285 removed outlier: 3.508A pdb=" N CYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY D 285 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 319 removed outlier: 3.535A pdb=" N ALA D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 339 through 345 removed outlier: 4.048A pdb=" N PHE D 345 " --> pdb=" O TYR D 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 27 removed outlier: 6.263A pdb=" N HIS A 16 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 23 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 14 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A 9 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU A 82 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 27 removed outlier: 6.263A pdb=" N HIS A 16 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 23 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 14 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A 9 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU A 82 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 58 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU B 85 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 123 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 9 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER B 14 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU B 22 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 148 Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 177 Processing sheet with id=AA5, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AA6, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 373 removed outlier: 3.628A pdb=" N VAL B 372 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 333 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR B 408 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N HIS B 524 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL B 410 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 372 through 373 removed outlier: 3.628A pdb=" N VAL B 372 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 333 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.286A pdb=" N VAL C 10 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 134 removed outlier: 4.627A pdb=" N LEU C 144 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 131 through 134 removed outlier: 6.089A pdb=" N ALA C 141 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR C 103 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 143 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 124 through 127 Processing sheet with id=AB4, first strand: chain 'C' and resid 243 through 244 removed outlier: 4.410A pdb=" N PHE C 250 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 218 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN C 260 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 216 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N MET C 170 " --> pdb=" O MET C 332 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL C 334 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR C 172 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE C 336 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE C 174 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP C 365 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER C 333 " --> pdb=" O ASP C 365 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL C 367 " --> pdb=" O SER C 333 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 335 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.713A pdb=" N VAL C 216 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN C 260 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 218 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE C 250 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N TYR C 251 " --> pdb=" O THR C 889 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N SER C 891 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP C 253 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS C 893 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR C 255 " --> pdb=" O CYS C 893 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 343 removed outlier: 6.690A pdb=" N PHE C 343 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 756 through 757 removed outlier: 3.729A pdb=" N ILE C 814 " --> pdb=" O TRP C 853 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TRP C 853 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1351 through 1357 removed outlier: 6.389A pdb=" N GLU C1385 " --> pdb=" O HIS C1375 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1205 through 1206 Processing sheet with id=AC1, first strand: chain 'C' and resid 1254 through 1255 removed outlier: 6.563A pdb=" N ALA C1297 " --> pdb=" O PHE C1378 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1439 through 1442 removed outlier: 3.846A pdb=" N ALA C1549 " --> pdb=" O PHE C1510 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL C1509 " --> pdb=" O HIS C1504 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 59 through 64 removed outlier: 6.932A pdb=" N PHE D 17 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL D 63 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN D 15 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 16 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'D' and resid 166 through 167 removed outlier: 6.725A pdb=" N TYR D 94 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR D 152 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 96 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLN D 154 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE D 98 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR D 156 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU D 100 " --> pdb=" O TYR D 156 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP D 101 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N LEU D 325 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE D 291 " --> pdb=" O LEU D 325 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2319 1.31 - 1.44: 4138 1.44 - 1.56: 8537 1.56 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 15094 Sorted by residual: bond pdb=" CA ASP D 301 " pdb=" C ASP D 301 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.34e-02 5.57e+03 2.64e+01 bond pdb=" CA CYS D 302 " pdb=" C CYS D 302 " ideal model delta sigma weight residual 1.527 1.457 0.070 1.41e-02 5.03e+03 2.47e+01 bond pdb=" C GLU D 72 " pdb=" O GLU D 72 " ideal model delta sigma weight residual 1.238 1.189 0.050 1.21e-02 6.83e+03 1.70e+01 bond pdb=" N ASP D 71 " pdb=" CA ASP D 71 " ideal model delta sigma weight residual 1.463 1.408 0.055 1.36e-02 5.41e+03 1.65e+01 bond pdb=" C CYS D 302 " pdb=" O CYS D 302 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.32e-02 5.74e+03 1.47e+01 ... (remaining 15089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 20523 3.40 - 6.79: 101 6.79 - 10.19: 14 10.19 - 13.58: 1 13.58 - 16.98: 2 Bond angle restraints: 20641 Sorted by residual: angle pdb=" N ASP D 71 " pdb=" CA ASP D 71 " pdb=" C ASP D 71 " ideal model delta sigma weight residual 107.71 90.73 16.98 1.90e+00 2.77e-01 7.98e+01 angle pdb=" C GLU D 72 " pdb=" N PRO D 73 " pdb=" CA PRO D 73 " ideal model delta sigma weight residual 119.84 128.77 -8.93 1.25e+00 6.40e-01 5.10e+01 angle pdb=" N ILE B 276 " pdb=" CA ILE B 276 " pdb=" C ILE B 276 " ideal model delta sigma weight residual 112.83 107.88 4.95 9.90e-01 1.02e+00 2.50e+01 angle pdb=" C TRP B 396 " pdb=" N MET B 397 " pdb=" CA MET B 397 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" CA TRP D 92 " pdb=" CB TRP D 92 " pdb=" CG TRP D 92 " ideal model delta sigma weight residual 113.60 121.22 -7.62 1.90e+00 2.77e-01 1.61e+01 ... (remaining 20636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7812 17.94 - 35.89: 790 35.89 - 53.83: 199 53.83 - 71.78: 34 71.78 - 89.72: 9 Dihedral angle restraints: 8844 sinusoidal: 2898 harmonic: 5946 Sorted by residual: dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N ARG B 165 " pdb=" CA ARG B 165 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA SER D 253 " pdb=" C SER D 253 " pdb=" N ASN D 254 " pdb=" CA ASN D 254 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLN B 399 " pdb=" C GLN B 399 " pdb=" N ARG B 400 " pdb=" CA ARG B 400 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 8841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2283 0.087 - 0.174: 177 0.174 - 0.260: 1 0.260 - 0.347: 0 0.347 - 0.434: 2 Chirality restraints: 2463 Sorted by residual: chirality pdb=" CA CYS D 302 " pdb=" N CYS D 302 " pdb=" C CYS D 302 " pdb=" CB CYS D 302 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA ASP D 301 " pdb=" N ASP D 301 " pdb=" C ASP D 301 " pdb=" CB ASP D 301 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ASP D 71 " pdb=" N ASP D 71 " pdb=" C ASP D 71 " pdb=" CB ASP D 71 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2460 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 274 " 0.065 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO B 275 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 275 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 275 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 75 " 0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO D 76 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 76 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 76 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 34 " -0.020 2.00e-02 2.50e+03 1.60e-02 6.37e+00 pdb=" CG TRP D 34 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 34 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP D 34 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 34 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 34 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 34 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 34 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 34 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 34 " -0.002 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 184 2.63 - 3.20: 13106 3.20 - 3.77: 22069 3.77 - 4.33: 28868 4.33 - 4.90: 48025 Nonbonded interactions: 112252 Sorted by model distance: nonbonded pdb=" O VAL B 285 " pdb=" OG1 THR B 289 " model vdw 2.067 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OE2 GLU C 193 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLN B 296 " pdb=" OH TYR B 531 " model vdw 2.158 3.040 nonbonded pdb=" O GLU A 138 " pdb=" OG SER A 142 " model vdw 2.170 3.040 nonbonded pdb=" OG SER A 13 " pdb=" O LYS A 22 " model vdw 2.183 3.040 ... (remaining 112247 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.004 0.070 15094 Z= 0.213 Angle : 0.693 16.978 20641 Z= 0.371 Chirality : 0.045 0.434 2463 Planarity : 0.005 0.099 2610 Dihedral : 15.996 89.720 4962 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.84 % Favored : 92.65 % Rotamer: Outliers : 4.95 % Allowed : 23.78 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1959 helix: 0.12 (0.21), residues: 667 sheet: -0.05 (0.27), residues: 383 loop : -1.19 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 242 TYR 0.013 0.001 TYR C 775 PHE 0.012 0.001 PHE B 124 TRP 0.044 0.001 TRP D 34 HIS 0.007 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00424 (15094) covalent geometry : angle 0.69349 (20641) hydrogen bonds : bond 0.16889 ( 604) hydrogen bonds : angle 6.80360 ( 1722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 90 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8954 (pmm) cc_final: 0.8603 (pmm) REVERT: A 327 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: A 351 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: A 362 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6220 (t80) REVERT: B 85 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8636 (tm-30) REVERT: B 282 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8303 (mp) REVERT: B 359 HIS cc_start: 0.5352 (OUTLIER) cc_final: 0.4427 (m90) REVERT: B 530 MET cc_start: 0.7475 (mmm) cc_final: 0.7203 (tpt) REVERT: C 226 TYR cc_start: 0.7945 (m-80) cc_final: 0.7688 (m-80) REVERT: C 308 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 965 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6200 (m170) REVERT: C 1234 MET cc_start: 0.9548 (tpp) cc_final: 0.9297 (tmm) REVERT: C 1515 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.7131 (p90) REVERT: C 1573 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9090 (tt) REVERT: D 50 MET cc_start: 0.6553 (ppp) cc_final: 0.6222 (ppp) REVERT: D 59 GLU cc_start: 0.2368 (tp30) cc_final: 0.1816 (tm-30) REVERT: D 313 MET cc_start: 0.9275 (mtm) cc_final: 0.8938 (mtm) outliers start: 67 outliers final: 38 residues processed: 152 average time/residue: 0.3885 time to fit residues: 67.9512 Evaluate side-chains 128 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 864 THR Chi-restraints excluded: chain C residue 895 SER Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain C residue 1563 THR Chi-restraints excluded: chain C residue 1573 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS A 371 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 296 GLN C 797 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.077147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057277 restraints weight = 66886.354| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.92 r_work: 0.3142 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15094 Z= 0.146 Angle : 0.627 15.245 20641 Z= 0.313 Chirality : 0.043 0.177 2463 Planarity : 0.004 0.079 2610 Dihedral : 6.968 59.567 2203 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.97 % Favored : 93.67 % Rotamer: Outliers : 4.73 % Allowed : 23.71 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1959 helix: 0.26 (0.21), residues: 691 sheet: 0.10 (0.27), residues: 385 loop : -1.22 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 95 TYR 0.013 0.001 TYR C1429 PHE 0.013 0.001 PHE B 124 TRP 0.030 0.001 TRP D 34 HIS 0.006 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00334 (15094) covalent geometry : angle 0.62710 (20641) hydrogen bonds : bond 0.03812 ( 604) hydrogen bonds : angle 5.30081 ( 1722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 90 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9058 (pmm) cc_final: 0.8832 (pmm) REVERT: A 327 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: A 351 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: A 362 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6226 (t80) REVERT: A 369 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6267 (mp) REVERT: B 85 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8811 (tm-30) REVERT: B 135 ASP cc_start: 0.8389 (t0) cc_final: 0.8128 (t0) REVERT: B 163 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8751 (tm) REVERT: B 359 HIS cc_start: 0.5335 (OUTLIER) cc_final: 0.4462 (m90) REVERT: C 101 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8554 (mm-30) REVERT: C 226 TYR cc_start: 0.7902 (m-80) cc_final: 0.7423 (m-80) REVERT: C 308 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 965 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6398 (m170) REVERT: C 1234 MET cc_start: 0.9554 (tpp) cc_final: 0.9284 (tmm) REVERT: C 1515 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.7116 (p90) REVERT: D 50 MET cc_start: 0.6816 (ppp) cc_final: 0.6549 (ppp) REVERT: D 59 GLU cc_start: 0.2075 (tp30) cc_final: 0.1832 (tm-30) REVERT: D 148 GLU cc_start: 0.7332 (mp0) cc_final: 0.7091 (mp0) outliers start: 64 outliers final: 23 residues processed: 149 average time/residue: 0.3928 time to fit residues: 66.8023 Evaluate side-chains 116 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 864 THR Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.0170 chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.076253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.056296 restraints weight = 68095.692| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.96 r_work: 0.3114 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15094 Z= 0.198 Angle : 0.641 16.024 20641 Z= 0.317 Chirality : 0.044 0.199 2463 Planarity : 0.004 0.058 2610 Dihedral : 6.548 56.723 2174 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.58 % Favored : 93.11 % Rotamer: Outliers : 5.02 % Allowed : 24.30 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1959 helix: 0.35 (0.21), residues: 691 sheet: 0.14 (0.27), residues: 385 loop : -1.28 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 295 TYR 0.012 0.001 TYR C 775 PHE 0.013 0.001 PHE C 254 TRP 0.026 0.001 TRP D 34 HIS 0.007 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00457 (15094) covalent geometry : angle 0.64068 (20641) hydrogen bonds : bond 0.03755 ( 604) hydrogen bonds : angle 5.12608 ( 1722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 83 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9095 (pmm) cc_final: 0.8860 (pmm) REVERT: A 204 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7497 (mtm-85) REVERT: A 327 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: A 351 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: A 362 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6192 (t80) REVERT: A 369 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6238 (mp) REVERT: B 85 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8703 (tm-30) REVERT: B 135 ASP cc_start: 0.8451 (t0) cc_final: 0.8087 (t0) REVERT: B 163 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8855 (tm) REVERT: B 282 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 359 HIS cc_start: 0.5361 (OUTLIER) cc_final: 0.4490 (m90) REVERT: C 101 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: C 226 TYR cc_start: 0.7953 (m-80) cc_final: 0.7495 (m-80) REVERT: C 308 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: C 965 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6493 (m170) REVERT: C 1515 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7174 (p90) REVERT: D 50 MET cc_start: 0.6914 (ppp) cc_final: 0.6617 (ppp) REVERT: D 59 GLU cc_start: 0.1973 (tp30) cc_final: 0.1659 (tm-30) REVERT: D 148 GLU cc_start: 0.7540 (mp0) cc_final: 0.7238 (mp0) REVERT: D 240 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7254 (mmt) REVERT: D 301 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8078 (p0) outliers start: 68 outliers final: 33 residues processed: 143 average time/residue: 0.4409 time to fit residues: 71.6914 Evaluate side-chains 130 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 864 THR Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 48 optimal weight: 0.4980 chunk 147 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 176 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 161 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.0060 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 20 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.078078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.058299 restraints weight = 67209.314| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.97 r_work: 0.3166 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15094 Z= 0.098 Angle : 0.589 14.140 20641 Z= 0.287 Chirality : 0.042 0.163 2463 Planarity : 0.004 0.050 2610 Dihedral : 6.239 55.184 2174 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.41 % Favored : 94.33 % Rotamer: Outliers : 4.43 % Allowed : 25.18 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1959 helix: 0.53 (0.21), residues: 689 sheet: 0.58 (0.28), residues: 366 loop : -1.13 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.008 0.001 TYR C 775 PHE 0.011 0.001 PHE B 124 TRP 0.019 0.001 TRP D 34 HIS 0.005 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00226 (15094) covalent geometry : angle 0.58890 (20641) hydrogen bonds : bond 0.02891 ( 604) hydrogen bonds : angle 4.74774 ( 1722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 98 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9202 (pmm) cc_final: 0.8819 (pmm) REVERT: A 204 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8579 (ttm110) REVERT: A 327 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: A 351 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: A 362 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6185 (t80) REVERT: B 85 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8714 (tm-30) REVERT: B 135 ASP cc_start: 0.8322 (t0) cc_final: 0.7897 (t0) REVERT: B 163 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8871 (tm) REVERT: B 282 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8545 (mt) REVERT: B 359 HIS cc_start: 0.5273 (OUTLIER) cc_final: 0.4470 (m90) REVERT: C 105 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8700 (tptt) REVERT: C 226 TYR cc_start: 0.7872 (m-80) cc_final: 0.7446 (m-80) REVERT: C 308 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: C 965 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6487 (m170) REVERT: C 1515 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6972 (p90) REVERT: C 1574 LYS cc_start: 0.9463 (tppt) cc_final: 0.9080 (tppp) REVERT: C 1578 ASP cc_start: 0.9192 (m-30) cc_final: 0.8911 (m-30) REVERT: D 50 MET cc_start: 0.6900 (ppp) cc_final: 0.6586 (ppp) REVERT: D 59 GLU cc_start: 0.2017 (tp30) cc_final: 0.1652 (tm-30) REVERT: D 132 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9130 (mm) REVERT: D 148 GLU cc_start: 0.7540 (mp0) cc_final: 0.7243 (mp0) REVERT: D 267 THR cc_start: 0.8190 (p) cc_final: 0.7633 (t) REVERT: D 301 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8022 (p0) outliers start: 60 outliers final: 21 residues processed: 152 average time/residue: 0.4214 time to fit residues: 73.0672 Evaluate side-chains 122 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 150 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.077554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.057748 restraints weight = 67571.780| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.98 r_work: 0.3151 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15094 Z= 0.124 Angle : 0.591 14.889 20641 Z= 0.289 Chirality : 0.042 0.226 2463 Planarity : 0.004 0.054 2610 Dihedral : 6.073 53.608 2169 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.98 % Rotamer: Outliers : 4.43 % Allowed : 25.48 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1959 helix: 0.62 (0.21), residues: 688 sheet: 0.46 (0.27), residues: 387 loop : -1.02 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 283 TYR 0.010 0.001 TYR C 775 PHE 0.019 0.001 PHE C1311 TRP 0.017 0.001 TRP D 34 HIS 0.006 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00292 (15094) covalent geometry : angle 0.59129 (20641) hydrogen bonds : bond 0.02952 ( 604) hydrogen bonds : angle 4.69580 ( 1722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 86 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9213 (pmm) cc_final: 0.8805 (pmm) REVERT: A 204 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8543 (ttm110) REVERT: A 327 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: A 351 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: A 362 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6189 (t80) REVERT: B 85 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8726 (tm-30) REVERT: B 135 ASP cc_start: 0.8361 (t0) cc_final: 0.7913 (t0) REVERT: B 163 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (tm) REVERT: B 282 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 359 HIS cc_start: 0.5319 (OUTLIER) cc_final: 0.4525 (m90) REVERT: C 105 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8672 (tptt) REVERT: C 226 TYR cc_start: 0.7832 (m-80) cc_final: 0.7425 (m-80) REVERT: C 308 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: C 965 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.6500 (m170) REVERT: C 1515 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6978 (p90) REVERT: C 1574 LYS cc_start: 0.9483 (tppt) cc_final: 0.9105 (tppp) REVERT: C 1578 ASP cc_start: 0.9195 (m-30) cc_final: 0.8924 (m-30) REVERT: D 95 ARG cc_start: 0.7780 (mpt180) cc_final: 0.7071 (mpp80) REVERT: D 132 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9145 (mm) REVERT: D 148 GLU cc_start: 0.7632 (mp0) cc_final: 0.7398 (mp0) REVERT: D 240 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7069 (mmt) REVERT: D 267 THR cc_start: 0.8189 (p) cc_final: 0.7628 (t) REVERT: D 301 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8000 (p0) outliers start: 60 outliers final: 30 residues processed: 140 average time/residue: 0.4044 time to fit residues: 64.4217 Evaluate side-chains 130 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1372 CYS Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1476 ILE Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 186 optimal weight: 0.0470 chunk 191 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 182 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.078302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.058546 restraints weight = 67428.244| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.97 r_work: 0.3174 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15094 Z= 0.101 Angle : 0.586 13.934 20641 Z= 0.283 Chirality : 0.042 0.194 2463 Planarity : 0.004 0.044 2610 Dihedral : 5.964 55.387 2169 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.31 % Favored : 94.44 % Rotamer: Outliers : 4.14 % Allowed : 25.85 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1959 helix: 0.71 (0.21), residues: 690 sheet: 0.61 (0.27), residues: 381 loop : -0.96 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 283 TYR 0.008 0.001 TYR C 775 PHE 0.016 0.001 PHE C1311 TRP 0.017 0.001 TRP D 34 HIS 0.005 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00238 (15094) covalent geometry : angle 0.58637 (20641) hydrogen bonds : bond 0.02704 ( 604) hydrogen bonds : angle 4.55974 ( 1722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 89 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9221 (pmm) cc_final: 0.8893 (pmm) REVERT: A 204 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8518 (ttm110) REVERT: A 327 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: A 362 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6079 (t80) REVERT: B 85 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8765 (tm-30) REVERT: B 135 ASP cc_start: 0.8327 (t0) cc_final: 0.7888 (t0) REVERT: B 282 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 359 HIS cc_start: 0.5347 (OUTLIER) cc_final: 0.4575 (m90) REVERT: C 105 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8683 (tptt) REVERT: C 226 TYR cc_start: 0.7799 (m-80) cc_final: 0.7437 (m-80) REVERT: C 308 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8197 (mm-30) REVERT: C 965 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6527 (m170) REVERT: C 1515 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6937 (p90) REVERT: C 1574 LYS cc_start: 0.9476 (tppt) cc_final: 0.9093 (tppp) REVERT: C 1578 ASP cc_start: 0.9127 (m-30) cc_final: 0.8852 (m-30) REVERT: D 50 MET cc_start: 0.6997 (ppp) cc_final: 0.6760 (ppp) REVERT: D 95 ARG cc_start: 0.7757 (mpt180) cc_final: 0.7084 (mpp80) REVERT: D 132 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9192 (mm) REVERT: D 148 GLU cc_start: 0.7674 (mp0) cc_final: 0.7473 (mp0) REVERT: D 267 THR cc_start: 0.8184 (p) cc_final: 0.7627 (t) REVERT: D 301 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7943 (p0) outliers start: 56 outliers final: 27 residues processed: 140 average time/residue: 0.4054 time to fit residues: 64.5053 Evaluate side-chains 124 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 0.0570 chunk 101 optimal weight: 0.0570 chunk 168 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 565 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.078617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058832 restraints weight = 66414.736| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 4.01 r_work: 0.3190 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15094 Z= 0.094 Angle : 0.576 13.399 20641 Z= 0.279 Chirality : 0.042 0.171 2463 Planarity : 0.004 0.044 2610 Dihedral : 5.688 58.426 2167 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.21 % Favored : 94.54 % Rotamer: Outliers : 3.40 % Allowed : 26.81 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1959 helix: 0.82 (0.21), residues: 690 sheet: 0.72 (0.27), residues: 375 loop : -0.93 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 127 TYR 0.011 0.001 TYR D 187 PHE 0.013 0.001 PHE C1311 TRP 0.019 0.001 TRP D 34 HIS 0.004 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00221 (15094) covalent geometry : angle 0.57618 (20641) hydrogen bonds : bond 0.02571 ( 604) hydrogen bonds : angle 4.44376 ( 1722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9218 (pmm) cc_final: 0.8902 (pmm) REVERT: A 204 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8520 (ttm110) REVERT: A 327 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: A 362 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6065 (t80) REVERT: B 85 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: B 135 ASP cc_start: 0.8348 (t0) cc_final: 0.7879 (t0) REVERT: B 282 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 359 HIS cc_start: 0.5394 (OUTLIER) cc_final: 0.4567 (m90) REVERT: B 530 MET cc_start: 0.7574 (tpp) cc_final: 0.7302 (tpt) REVERT: C 308 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8210 (mm-30) REVERT: C 965 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.6808 (m170) REVERT: C 1578 ASP cc_start: 0.9108 (m-30) cc_final: 0.8681 (p0) REVERT: D 95 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7120 (mpp80) REVERT: D 267 THR cc_start: 0.8209 (p) cc_final: 0.7650 (t) REVERT: D 301 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7800 (p0) outliers start: 46 outliers final: 31 residues processed: 131 average time/residue: 0.4470 time to fit residues: 66.3833 Evaluate side-chains 128 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1470 HIS Chi-restraints excluded: chain C residue 1476 ILE Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 32 optimal weight: 3.9990 chunk 181 optimal weight: 0.0370 chunk 24 optimal weight: 0.0870 chunk 145 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 172 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.078165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.058327 restraints weight = 66691.572| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.00 r_work: 0.3173 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15094 Z= 0.113 Angle : 0.589 13.414 20641 Z= 0.285 Chirality : 0.042 0.164 2463 Planarity : 0.004 0.065 2610 Dihedral : 5.530 57.578 2163 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 3.91 % Allowed : 26.22 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1959 helix: 0.81 (0.21), residues: 696 sheet: 0.82 (0.27), residues: 376 loop : -0.97 (0.22), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 283 TYR 0.009 0.001 TYR C 775 PHE 0.013 0.001 PHE C1311 TRP 0.021 0.001 TRP D 34 HIS 0.005 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00270 (15094) covalent geometry : angle 0.58874 (20641) hydrogen bonds : bond 0.02675 ( 604) hydrogen bonds : angle 4.47730 ( 1722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9222 (pmm) cc_final: 0.8878 (pmm) REVERT: A 204 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8523 (ttm110) REVERT: A 327 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 362 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6066 (t80) REVERT: B 85 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: B 135 ASP cc_start: 0.8378 (t0) cc_final: 0.7933 (t0) REVERT: B 282 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8596 (mt) REVERT: B 359 HIS cc_start: 0.5369 (OUTLIER) cc_final: 0.4550 (m90) REVERT: B 530 MET cc_start: 0.7625 (tpp) cc_final: 0.7406 (tpt) REVERT: C 105 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8626 (tptt) REVERT: C 308 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: C 965 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6568 (m170) REVERT: C 1578 ASP cc_start: 0.9145 (m-30) cc_final: 0.8905 (m-30) REVERT: D 95 ARG cc_start: 0.7707 (mpt180) cc_final: 0.7056 (mpp80) REVERT: D 178 GLN cc_start: 0.8752 (tp40) cc_final: 0.8073 (mp10) REVERT: D 267 THR cc_start: 0.8203 (p) cc_final: 0.7639 (t) REVERT: D 301 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.7837 (p0) REVERT: D 313 MET cc_start: 0.9236 (mtm) cc_final: 0.8810 (mtm) outliers start: 53 outliers final: 30 residues processed: 137 average time/residue: 0.4114 time to fit residues: 64.7083 Evaluate side-chains 125 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1476 ILE Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 184 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 GLN C1478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.075199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055260 restraints weight = 69322.225| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.95 r_work: 0.3082 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 15094 Z= 0.362 Angle : 0.729 16.024 20641 Z= 0.366 Chirality : 0.047 0.229 2463 Planarity : 0.005 0.056 2610 Dihedral : 6.201 54.226 2160 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.15 % Favored : 92.60 % Rotamer: Outliers : 4.14 % Allowed : 25.92 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1959 helix: 0.44 (0.20), residues: 696 sheet: 0.21 (0.26), residues: 398 loop : -1.09 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 283 TYR 0.021 0.002 TYR C 775 PHE 0.017 0.002 PHE C1480 TRP 0.028 0.002 TRP D 34 HIS 0.009 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00827 (15094) covalent geometry : angle 0.72912 (20641) hydrogen bonds : bond 0.04090 ( 604) hydrogen bonds : angle 5.14532 ( 1722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 79 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9173 (pmm) cc_final: 0.8758 (pmm) REVERT: A 204 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (ttm110) REVERT: A 327 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: A 362 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 85 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8764 (tm-30) REVERT: B 135 ASP cc_start: 0.8583 (t0) cc_final: 0.8123 (t0) REVERT: B 282 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 359 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4696 (m90) REVERT: C 105 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8521 (tptt) REVERT: C 226 TYR cc_start: 0.7956 (m-80) cc_final: 0.7588 (m-80) REVERT: C 308 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8484 (mm-30) REVERT: C 965 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6347 (m170) REVERT: C 1515 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7392 (p90) REVERT: D 21 LYS cc_start: 0.8374 (tppt) cc_final: 0.8095 (tppt) REVERT: D 95 ARG cc_start: 0.7705 (mpt180) cc_final: 0.7053 (mpp80) REVERT: D 178 GLN cc_start: 0.8864 (tp40) cc_final: 0.8173 (mp10) REVERT: D 240 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7024 (mmt) REVERT: D 267 THR cc_start: 0.8306 (p) cc_final: 0.7724 (t) REVERT: D 301 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8042 (p0) REVERT: D 313 MET cc_start: 0.9300 (mtm) cc_final: 0.8852 (mtm) outliers start: 56 outliers final: 35 residues processed: 131 average time/residue: 0.4150 time to fit residues: 62.6376 Evaluate side-chains 123 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 76 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 864 THR Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1476 ILE Chi-restraints excluded: chain C residue 1515 TYR Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 122 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 199 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.077073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057300 restraints weight = 66884.806| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.94 r_work: 0.3142 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15094 Z= 0.127 Angle : 0.630 13.820 20641 Z= 0.305 Chirality : 0.043 0.230 2463 Planarity : 0.004 0.052 2610 Dihedral : 5.841 52.365 2160 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.10 % Favored : 94.64 % Rotamer: Outliers : 3.10 % Allowed : 26.88 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1959 helix: 0.68 (0.21), residues: 695 sheet: 0.48 (0.27), residues: 378 loop : -0.94 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 283 TYR 0.012 0.001 TYR D 187 PHE 0.011 0.001 PHE C1311 TRP 0.028 0.001 TRP D 34 HIS 0.004 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00301 (15094) covalent geometry : angle 0.62955 (20641) hydrogen bonds : bond 0.02982 ( 604) hydrogen bonds : angle 4.75181 ( 1722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9162 (pmm) cc_final: 0.8778 (pmm) REVERT: A 204 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8615 (ttm110) REVERT: A 327 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: A 362 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6044 (t80) REVERT: B 85 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8733 (tm-30) REVERT: B 121 MET cc_start: 0.8727 (ttm) cc_final: 0.8372 (ttm) REVERT: B 135 ASP cc_start: 0.8428 (t0) cc_final: 0.7972 (t0) REVERT: B 282 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 359 HIS cc_start: 0.5401 (OUTLIER) cc_final: 0.4665 (m90) REVERT: B 530 MET cc_start: 0.7496 (tpp) cc_final: 0.7121 (tpt) REVERT: C 226 TYR cc_start: 0.7857 (m-80) cc_final: 0.7442 (m-80) REVERT: C 280 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: C 965 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6383 (m170) REVERT: C 1578 ASP cc_start: 0.9208 (m-30) cc_final: 0.8976 (m-30) REVERT: D 95 ARG cc_start: 0.7688 (mpt180) cc_final: 0.7113 (mpp80) REVERT: D 178 GLN cc_start: 0.8820 (tp40) cc_final: 0.8131 (mp10) REVERT: D 267 THR cc_start: 0.8213 (p) cc_final: 0.7648 (t) REVERT: D 301 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.7983 (p0) REVERT: D 313 MET cc_start: 0.9284 (mtm) cc_final: 0.8778 (mtm) outliers start: 42 outliers final: 29 residues processed: 124 average time/residue: 0.4656 time to fit residues: 65.1903 Evaluate side-chains 121 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 965 HIS Chi-restraints excluded: chain C residue 1353 THR Chi-restraints excluded: chain C residue 1358 VAL Chi-restraints excluded: chain C residue 1419 VAL Chi-restraints excluded: chain C residue 1476 ILE Chi-restraints excluded: chain C residue 1557 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 75 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.077314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057400 restraints weight = 66756.319| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.00 r_work: 0.3144 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15094 Z= 0.128 Angle : 0.618 14.003 20641 Z= 0.299 Chirality : 0.043 0.223 2463 Planarity : 0.004 0.056 2610 Dihedral : 5.594 52.403 2157 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 3.25 % Allowed : 26.74 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1959 helix: 0.74 (0.21), residues: 702 sheet: 0.49 (0.27), residues: 394 loop : -0.94 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 283 TYR 0.010 0.001 TYR C1429 PHE 0.011 0.001 PHE C1311 TRP 0.037 0.001 TRP D 34 HIS 0.005 0.001 HIS B 525 Details of bonding type rmsd covalent geometry : bond 0.00304 (15094) covalent geometry : angle 0.61787 (20641) hydrogen bonds : bond 0.02863 ( 604) hydrogen bonds : angle 4.65138 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5233.88 seconds wall clock time: 90 minutes 4.28 seconds (5404.28 seconds total)