Starting phenix.real_space_refine on Tue Aug 26 01:09:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sor_40669/08_2025/8sor_40669_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sor_40669/08_2025/8sor_40669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sor_40669/08_2025/8sor_40669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sor_40669/08_2025/8sor_40669.map" model { file = "/net/cci-nas-00/data/ceres_data/8sor_40669/08_2025/8sor_40669_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sor_40669/08_2025/8sor_40669_trim.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 10196 2.51 5 N 2776 2.21 5 O 2988 1.98 5 H 16046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32094 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4237 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 13, 'TRANS': 248} Chain breaks: 2 Chain: "C" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4385 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Chain: "D" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4943 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 5, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 18502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 18502 Classifications: {'peptide': 1156} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1102} Chain breaks: 6 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.18 Number of scatterers: 32094 At special positions: 0 Unit cell: (91.43, 157.215, 218.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 2 15.00 O 2988 8.00 N 2776 7.00 C 10196 6.00 H 16046 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 335 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 925.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 19 sheets defined 53.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 12 through 16 removed outlier: 4.437A pdb=" N ASP B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 16' Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.697A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 190 through 212 removed outlier: 3.543A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.618A pdb=" N ALA C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 205 removed outlier: 3.710A pdb=" N ASP C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.539A pdb=" N TYR C 280 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 322 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 340 through 362 removed outlier: 3.726A pdb=" N THR C 345 " --> pdb=" O LYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'D' and resid 138 through 266 removed outlier: 3.699A pdb=" N GLN D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 299 through 322 Processing helix chain 'D' and resid 364 through 385 Processing helix chain 'D' and resid 421 through 449 removed outlier: 3.662A pdb=" N ASN D 449 " --> pdb=" O SER D 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 24 through 27 removed outlier: 3.700A pdb=" N GLU A 27 " --> pdb=" O HIS A 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.666A pdb=" N SER A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 142 Processing helix chain 'A' and resid 180 through 187 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 236 through 254 removed outlier: 4.205A pdb=" N ASP A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.009A pdb=" N TYR A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.995A pdb=" N GLY A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 removed outlier: 4.103A pdb=" N LEU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 417 Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.641A pdb=" N ASN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.797A pdb=" N ILE A 456 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.556A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 504 removed outlier: 4.778A pdb=" N ALA A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 545 Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.611A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 569 through 582 removed outlier: 4.410A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 590 through 609 removed outlier: 3.744A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 630 through 646 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.625A pdb=" N TYR A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 668 through 685 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.645A pdb=" N LEU A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 737 through 754 removed outlier: 3.550A pdb=" N LEU A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 790 through 807 Processing helix chain 'A' and resid 821 through 825 Processing helix chain 'A' and resid 939 through 966 Processing helix chain 'A' and resid 1022 through 1026 Processing helix chain 'A' and resid 1072 through 1076 removed outlier: 4.417A pdb=" N LYS A1075 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1142 removed outlier: 3.539A pdb=" N SER A1141 " --> pdb=" O ASP A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1276 Processing sheet with id=AA1, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 96 removed outlier: 7.236A pdb=" N TRP B 87 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER B 25 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 19 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N MET B 218 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU B 26 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR B 216 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 139 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.591A pdb=" N GLY B 123 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 112 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.796A pdb=" N SER C 260 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 276 through 277 removed outlier: 4.370A pdb=" N THR D 284 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 283 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 331 Processing sheet with id=AA9, first strand: chain 'D' and resid 394 through 396 Processing sheet with id=AB1, first strand: chain 'A' and resid 30 through 34 removed outlier: 3.851A pdb=" N LYS A 30 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 89 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB3, first strand: chain 'A' and resid 175 through 176 removed outlier: 6.657A pdb=" N LEU A 175 " --> pdb=" O VAL A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 985 through 988 removed outlier: 6.379A pdb=" N VAL A1356 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A 988 " --> pdb=" O VAL A1354 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A1354 " --> pdb=" O HIS A 988 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A1344 " --> pdb=" O THR A1337 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A1337 " --> pdb=" O PHE A1344 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A1346 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A1335 " --> pdb=" O VAL A1346 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A1348 " --> pdb=" O THR A1333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 996 through 1001 removed outlier: 3.816A pdb=" N ARG A 998 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A1011 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A1019 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1045 through 1050 removed outlier: 3.687A pdb=" N THR A1047 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A1086 " --> pdb=" O LEU A1068 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1098 through 1105 removed outlier: 6.741A pdb=" N ALA A1115 " --> pdb=" O VAL A1099 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N MET A1101 " --> pdb=" O ALA A1113 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A1113 " --> pdb=" O MET A1101 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N HIS A1103 " --> pdb=" O VAL A1111 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A1111 " --> pdb=" O HIS A1103 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A1124 " --> pdb=" O LEU A1112 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A1121 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A1134 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A1123 " --> pdb=" O ALA A1132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1144 through 1149 removed outlier: 3.529A pdb=" N TRP A1168 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS A1167 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A1176 " --> pdb=" O CYS A1167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1191 through 1192 removed outlier: 3.541A pdb=" N SER A1211 " --> pdb=" O ALA A1202 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A1210 " --> pdb=" O THR A1223 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A1223 " --> pdb=" O VAL A1210 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET A1212 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A1221 " --> pdb=" O GLU A1299 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL A1301 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A1223 " --> pdb=" O VAL A1301 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU A1303 " --> pdb=" O THR A1223 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP A1225 " --> pdb=" O GLU A1303 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1242 through 1248 removed outlier: 7.037A pdb=" N ALA A1259 " --> pdb=" O HIS A1243 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A1245 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A1257 " --> pdb=" O ILE A1245 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS A1247 " --> pdb=" O ILE A1255 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A1255 " --> pdb=" O CYS A1247 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.29 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16008 1.03 - 1.23: 62 1.23 - 1.42: 6780 1.42 - 1.62: 9444 1.62 - 1.81: 132 Bond restraints: 32426 Sorted by residual: bond pdb=" N CYS D 137 " pdb=" CA CYS D 137 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C4 ADP A1401 " pdb=" C5 ADP A1401 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N CYS D 137 " pdb=" H CYS D 137 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C5 ADP A1401 " pdb=" C6 ADP A1401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CA TYR D 333 " pdb=" C TYR D 333 " ideal model delta sigma weight residual 1.524 1.501 0.023 2.25e-02 1.98e+03 1.03e+00 ... (remaining 32421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 58642 7.08 - 14.16: 1 14.16 - 21.24: 0 21.24 - 28.32: 0 28.32 - 35.40: 6 Bond angle restraints: 58649 Sorted by residual: angle pdb=" C PHE D 390 " pdb=" CA PHE D 390 " pdb=" HA PHE D 390 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C SER B 212 " pdb=" CA SER B 212 " pdb=" HA SER B 212 " ideal model delta sigma weight residual 109.00 74.16 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CB PHE D 390 " pdb=" CA PHE D 390 " pdb=" HA PHE D 390 " ideal model delta sigma weight residual 109.00 74.33 34.67 3.00e+00 1.11e-01 1.34e+02 angle pdb=" CB SER B 212 " pdb=" CA SER B 212 " pdb=" HA SER B 212 " ideal model delta sigma weight residual 109.00 74.94 34.06 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N SER B 212 " pdb=" CA SER B 212 " pdb=" HA SER B 212 " ideal model delta sigma weight residual 110.00 76.05 33.95 3.00e+00 1.11e-01 1.28e+02 ... (remaining 58644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13674 17.56 - 35.13: 1118 35.13 - 52.69: 300 52.69 - 70.26: 79 70.26 - 87.82: 14 Dihedral angle restraints: 15185 sinusoidal: 8322 harmonic: 6863 Sorted by residual: dihedral pdb=" CB CYS C 308 " pdb=" SG CYS C 308 " pdb=" SG CYS C 335 " pdb=" CB CYS C 335 " ideal model delta sinusoidal sigma weight residual 93.00 159.05 -66.05 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA HIS A 988 " pdb=" C HIS A 988 " pdb=" N LEU A 989 " pdb=" CA LEU A 989 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 15182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2278 0.075 - 0.150: 175 0.150 - 0.226: 0 0.226 - 0.301: 0 0.301 - 0.376: 2 Chirality restraints: 2455 Sorted by residual: chirality pdb=" CA SER B 212 " pdb=" N SER B 212 " pdb=" C SER B 212 " pdb=" CB SER B 212 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA PHE D 390 " pdb=" N PHE D 390 " pdb=" C PHE D 390 " pdb=" CB PHE D 390 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ILE D 276 " pdb=" N ILE D 276 " pdb=" C ILE D 276 " pdb=" CB ILE D 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 2452 not shown) Planarity restraints: 4718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1083 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A1084 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1084 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1084 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 661 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 662 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 62 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 63 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.020 5.00e-02 4.00e+02 ... (remaining 4715 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 530 2.07 - 2.70: 53276 2.70 - 3.34: 96831 3.34 - 3.97: 119027 3.97 - 4.60: 191880 Nonbonded interactions: 461544 Sorted by model distance: nonbonded pdb=" OE1 GLN A1305 " pdb=" H GLN A1305 " model vdw 1.438 2.450 nonbonded pdb=" OE1 GLN D 281 " pdb=" H GLN D 281 " model vdw 1.502 2.450 nonbonded pdb=" O ALA A 238 " pdb="HH11 ARG A 301 " model vdw 1.532 2.450 nonbonded pdb=" HE1 TRP B 146 " pdb=" O PRO B 160 " model vdw 1.539 2.450 nonbonded pdb="HD22 ASN A 997 " pdb=" OD1 ASN A1013 " model vdw 1.541 2.450 ... (remaining 461539 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 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: 0.190 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 30.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 0.036 16381 Z= 0.181 Angle : 0.616 7.097 22138 Z= 0.344 Chirality : 0.040 0.376 2455 Planarity : 0.003 0.039 2826 Dihedral : 14.389 87.823 6168 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 7.72 % Favored : 92.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.19), residues: 1956 helix: 1.15 (0.17), residues: 951 sheet: -1.44 (0.32), residues: 243 loop : -0.99 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1292 TYR 0.015 0.002 TYR A 702 PHE 0.014 0.001 PHE A 38 TRP 0.013 0.001 TRP C 111 HIS 0.008 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00387 (16380) covalent geometry : angle 0.61498 (22136) SS BOND : bond 0.01420 ( 1) SS BOND : angle 4.05669 ( 2) hydrogen bonds : bond 0.14319 ( 881) hydrogen bonds : angle 6.48300 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 964 MET cc_start: 0.4690 (mmt) cc_final: 0.4488 (mmt) outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.2810 time to fit residues: 64.5233 Evaluate side-chains 148 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain A residue 355 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 252 ASN D 271 ASN A 777 GLN A1131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.112976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097584 restraints weight = 89013.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097243 restraints weight = 103958.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098474 restraints weight = 88403.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098517 restraints weight = 61937.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098669 restraints weight = 62275.042| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.0521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16381 Z= 0.210 Angle : 0.595 6.991 22138 Z= 0.319 Chirality : 0.042 0.377 2455 Planarity : 0.004 0.044 2826 Dihedral : 5.697 63.270 2160 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 0.62 % Allowed : 8.40 % Favored : 90.98 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1956 helix: 1.41 (0.16), residues: 945 sheet: -1.61 (0.32), residues: 242 loop : -1.10 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.018 0.002 TYR A 702 PHE 0.014 0.002 PHE A1008 TRP 0.012 0.001 TRP C 111 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00468 (16380) covalent geometry : angle 0.59539 (22136) SS BOND : bond 0.00810 ( 1) SS BOND : angle 0.36143 ( 2) hydrogen bonds : bond 0.05031 ( 881) hydrogen bonds : angle 5.18360 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5594 (mm-30) REVERT: A 108 ASP cc_start: 0.8248 (m-30) cc_final: 0.7996 (m-30) outliers start: 11 outliers final: 9 residues processed: 170 average time/residue: 0.3285 time to fit residues: 80.8341 Evaluate side-chains 167 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain D residue 394 TYR Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 185 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 446 GLN A 777 GLN A1005 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098213 restraints weight = 88700.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098147 restraints weight = 103772.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098745 restraints weight = 89407.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098954 restraints weight = 72530.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099022 restraints weight = 65570.336| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16381 Z= 0.168 Angle : 0.556 7.023 22138 Z= 0.294 Chirality : 0.041 0.380 2455 Planarity : 0.004 0.044 2826 Dihedral : 5.527 58.047 2157 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 0.85 % Allowed : 8.46 % Favored : 90.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 1956 helix: 1.59 (0.16), residues: 946 sheet: -1.62 (0.32), residues: 246 loop : -1.11 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.015 0.001 TYR A 702 PHE 0.016 0.001 PHE A1008 TRP 0.013 0.001 TRP C 111 HIS 0.008 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00375 (16380) covalent geometry : angle 0.55600 (22136) SS BOND : bond 0.01968 ( 1) SS BOND : angle 2.00383 ( 2) hydrogen bonds : bond 0.04541 ( 881) hydrogen bonds : angle 4.91940 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 ASN cc_start: 0.7785 (t0) cc_final: 0.7515 (t0) REVERT: A 108 ASP cc_start: 0.8129 (m-30) cc_final: 0.7848 (m-30) REVERT: A 1025 MET cc_start: 0.7559 (mmt) cc_final: 0.7211 (mmt) outliers start: 15 outliers final: 11 residues processed: 171 average time/residue: 0.2903 time to fit residues: 73.9359 Evaluate side-chains 167 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 394 TYR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098188 restraints weight = 88677.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098295 restraints weight = 103113.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098686 restraints weight = 89193.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098913 restraints weight = 76399.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099045 restraints weight = 66818.822| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16381 Z= 0.170 Angle : 0.546 7.128 22138 Z= 0.288 Chirality : 0.041 0.377 2455 Planarity : 0.004 0.043 2826 Dihedral : 5.401 54.165 2157 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.13 % Allowed : 8.68 % Favored : 90.19 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.19), residues: 1956 helix: 1.73 (0.17), residues: 945 sheet: -1.66 (0.32), residues: 246 loop : -1.12 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.015 0.001 TYR A 702 PHE 0.015 0.001 PHE A1008 TRP 0.012 0.001 TRP C 111 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00380 (16380) covalent geometry : angle 0.54620 (22136) SS BOND : bond 0.00080 ( 1) SS BOND : angle 1.28836 ( 2) hydrogen bonds : bond 0.04303 ( 881) hydrogen bonds : angle 4.78007 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5717 (mm-30) REVERT: D 317 LEU cc_start: 0.8440 (mt) cc_final: 0.8159 (mt) REVERT: A 108 ASP cc_start: 0.8114 (m-30) cc_final: 0.7821 (m-30) REVERT: A 1025 MET cc_start: 0.7556 (mmt) cc_final: 0.7193 (mmt) outliers start: 20 outliers final: 16 residues processed: 175 average time/residue: 0.3155 time to fit residues: 80.1121 Evaluate side-chains 170 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 394 TYR Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098035 restraints weight = 88954.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098024 restraints weight = 105294.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098555 restraints weight = 93237.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098890 restraints weight = 73738.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099029 restraints weight = 64331.942| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16381 Z= 0.164 Angle : 0.540 7.614 22138 Z= 0.284 Chirality : 0.041 0.377 2455 Planarity : 0.004 0.042 2826 Dihedral : 5.319 51.204 2157 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.01 % Allowed : 9.70 % Favored : 89.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 1956 helix: 1.81 (0.17), residues: 946 sheet: -1.66 (0.32), residues: 245 loop : -1.12 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.014 0.001 TYR A 702 PHE 0.015 0.001 PHE A1008 TRP 0.011 0.001 TRP C 111 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00369 (16380) covalent geometry : angle 0.53978 (22136) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.50592 ( 2) hydrogen bonds : bond 0.04165 ( 881) hydrogen bonds : angle 4.70335 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 317 LEU cc_start: 0.8427 (mt) cc_final: 0.8147 (mt) REVERT: A 108 ASP cc_start: 0.8066 (m-30) cc_final: 0.7818 (m-30) REVERT: A 1025 MET cc_start: 0.7523 (mmt) cc_final: 0.7141 (mmt) outliers start: 18 outliers final: 17 residues processed: 171 average time/residue: 0.2977 time to fit residues: 75.9679 Evaluate side-chains 171 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097651 restraints weight = 88715.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.097394 restraints weight = 102235.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097635 restraints weight = 97137.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097959 restraints weight = 83068.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098124 restraints weight = 71831.978| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16381 Z= 0.182 Angle : 0.545 7.499 22138 Z= 0.286 Chirality : 0.041 0.375 2455 Planarity : 0.004 0.044 2826 Dihedral : 5.266 50.026 2157 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 1.30 % Allowed : 9.58 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 1956 helix: 1.85 (0.17), residues: 940 sheet: -1.83 (0.32), residues: 250 loop : -1.12 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 980 TYR 0.015 0.001 TYR A 702 PHE 0.016 0.001 PHE A1008 TRP 0.011 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00409 (16380) covalent geometry : angle 0.54506 (22136) SS BOND : bond 0.00221 ( 1) SS BOND : angle 2.26549 ( 2) hydrogen bonds : bond 0.04146 ( 881) hydrogen bonds : angle 4.66191 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5637 (mm-30) REVERT: D 317 LEU cc_start: 0.8442 (mt) cc_final: 0.8158 (mt) REVERT: A 108 ASP cc_start: 0.8085 (m-30) cc_final: 0.7833 (m-30) REVERT: A 1025 MET cc_start: 0.7521 (mmt) cc_final: 0.7163 (mmt) outliers start: 23 outliers final: 18 residues processed: 183 average time/residue: 0.2956 time to fit residues: 79.9465 Evaluate side-chains 179 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097645 restraints weight = 88876.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097571 restraints weight = 103779.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098001 restraints weight = 93245.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098346 restraints weight = 74142.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098354 restraints weight = 68389.456| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16381 Z= 0.160 Angle : 0.536 7.661 22138 Z= 0.280 Chirality : 0.040 0.374 2455 Planarity : 0.004 0.042 2826 Dihedral : 5.208 49.199 2157 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 1.30 % Allowed : 9.92 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.19), residues: 1956 helix: 1.88 (0.17), residues: 947 sheet: -1.83 (0.32), residues: 251 loop : -1.09 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 980 TYR 0.014 0.001 TYR A 702 PHE 0.028 0.001 PHE A 272 TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00361 (16380) covalent geometry : angle 0.53616 (22136) SS BOND : bond 0.00255 ( 1) SS BOND : angle 1.92406 ( 2) hydrogen bonds : bond 0.04034 ( 881) hydrogen bonds : angle 4.58412 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 317 LEU cc_start: 0.8415 (mt) cc_final: 0.8125 (mt) REVERT: A 108 ASP cc_start: 0.8064 (m-30) cc_final: 0.7823 (m-30) REVERT: A 1025 MET cc_start: 0.7503 (mmt) cc_final: 0.7048 (mmt) outliers start: 23 outliers final: 22 residues processed: 182 average time/residue: 0.3369 time to fit residues: 89.6417 Evaluate side-chains 184 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 164 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097353 restraints weight = 88825.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097410 restraints weight = 104298.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097883 restraints weight = 90424.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098170 restraints weight = 77593.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098343 restraints weight = 68212.125| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16381 Z= 0.174 Angle : 0.542 7.612 22138 Z= 0.284 Chirality : 0.041 0.373 2455 Planarity : 0.004 0.069 2826 Dihedral : 5.182 49.324 2157 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 1.24 % Allowed : 10.09 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 1956 helix: 1.89 (0.17), residues: 946 sheet: -1.86 (0.32), residues: 251 loop : -1.13 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 952 TYR 0.014 0.001 TYR A 702 PHE 0.021 0.001 PHE A 272 TRP 0.010 0.001 TRP C 111 HIS 0.005 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00393 (16380) covalent geometry : angle 0.54169 (22136) SS BOND : bond 0.00540 ( 1) SS BOND : angle 2.21976 ( 2) hydrogen bonds : bond 0.04043 ( 881) hydrogen bonds : angle 4.58182 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7238 (tm-30) REVERT: D 317 LEU cc_start: 0.8395 (mt) cc_final: 0.8095 (mt) REVERT: A 108 ASP cc_start: 0.8041 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1025 MET cc_start: 0.7497 (mmt) cc_final: 0.7041 (mmt) outliers start: 22 outliers final: 21 residues processed: 176 average time/residue: 0.3124 time to fit residues: 81.3508 Evaluate side-chains 178 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 150 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 169 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097540 restraints weight = 88412.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097664 restraints weight = 99701.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098280 restraints weight = 85413.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098448 restraints weight = 69644.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098554 restraints weight = 62639.234| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16381 Z= 0.161 Angle : 0.546 9.076 22138 Z= 0.284 Chirality : 0.040 0.371 2455 Planarity : 0.004 0.052 2826 Dihedral : 5.148 48.805 2157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.24 % Allowed : 10.20 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.19), residues: 1956 helix: 1.94 (0.17), residues: 946 sheet: -1.85 (0.32), residues: 250 loop : -1.10 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 952 TYR 0.014 0.001 TYR A 702 PHE 0.020 0.001 PHE A 272 TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00361 (16380) covalent geometry : angle 0.54287 (22136) SS BOND : bond 0.01906 ( 1) SS BOND : angle 6.49409 ( 2) hydrogen bonds : bond 0.03985 ( 881) hydrogen bonds : angle 4.54773 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7230 (tm-30) REVERT: D 317 LEU cc_start: 0.8410 (mt) cc_final: 0.8121 (mt) outliers start: 22 outliers final: 20 residues processed: 177 average time/residue: 0.3273 time to fit residues: 85.4081 Evaluate side-chains 176 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 82 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097364 restraints weight = 89292.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097410 restraints weight = 103995.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097991 restraints weight = 90365.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098296 restraints weight = 70182.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098332 restraints weight = 64434.506| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16381 Z= 0.174 Angle : 0.552 7.876 22138 Z= 0.288 Chirality : 0.041 0.371 2455 Planarity : 0.004 0.049 2826 Dihedral : 5.145 48.830 2157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 1.13 % Allowed : 10.48 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 1956 helix: 1.93 (0.17), residues: 946 sheet: -1.88 (0.32), residues: 250 loop : -1.12 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 952 TYR 0.014 0.001 TYR A 702 PHE 0.020 0.001 PHE A 272 TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00394 (16380) covalent geometry : angle 0.54892 (22136) SS BOND : bond 0.01182 ( 1) SS BOND : angle 5.64677 ( 2) hydrogen bonds : bond 0.04001 ( 881) hydrogen bonds : angle 4.56026 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7202 (tm-30) REVERT: D 317 LEU cc_start: 0.8413 (mt) cc_final: 0.8121 (mt) outliers start: 20 outliers final: 20 residues processed: 173 average time/residue: 0.3153 time to fit residues: 80.4318 Evaluate side-chains 176 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 11 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097360 restraints weight = 89309.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097403 restraints weight = 105953.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097689 restraints weight = 92904.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098300 restraints weight = 78433.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098384 restraints weight = 68005.615| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 16381 Z= 0.196 Angle : 0.744 59.200 22138 Z= 0.442 Chirality : 0.041 0.372 2455 Planarity : 0.004 0.046 2826 Dihedral : 5.151 48.823 2157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 1.18 % Allowed : 10.54 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 1956 helix: 1.93 (0.17), residues: 946 sheet: -1.88 (0.32), residues: 250 loop : -1.11 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 952 TYR 0.014 0.001 TYR A 702 PHE 0.018 0.001 PHE A 272 TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A1137 Details of bonding type rmsd covalent geometry : bond 0.00431 (16380) covalent geometry : angle 0.74188 (22136) SS BOND : bond 0.01129 ( 1) SS BOND : angle 5.51102 ( 2) hydrogen bonds : bond 0.04005 ( 881) hydrogen bonds : angle 4.56263 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.44 seconds wall clock time: 71 minutes 2.84 seconds (4262.84 seconds total)