Starting phenix.real_space_refine on Fri Jun 27 20:52:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sor_40669/06_2025/8sor_40669_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sor_40669/06_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_40669/06_2025/8sor_40669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sor_40669/06_2025/8sor_40669.map" model { file = "/net/cci-nas-00/data/ceres_data/8sor_40669/06_2025/8sor_40669_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sor_40669/06_2025/8sor_40669_trim.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.74, per 1000 atoms: 0.43 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: 7.52 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.56 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: 12.77 Time building geometry restraints manager: 9.26 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.490 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 62.970 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.630 ------------------------------------------------------------------------------- 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 : 7.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (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 TRP 0.013 0.001 TRP C 111 HIS 0.008 0.001 HIS B 271 PHE 0.014 0.001 PHE A 38 TYR 0.015 0.002 TYR A 702 ARG 0.004 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.14319 ( 881) hydrogen bonds : angle 6.48300 ( 2514) SS BOND : bond 0.01420 ( 1) SS BOND : angle 4.05669 ( 2) covalent geometry : bond 0.00387 (16380) covalent geometry : angle 0.61498 (22136) *********************** 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 : 2.628 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 outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.6393 time to fit residues: 147.1543 Evaluate side-chains 149 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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 166 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 271 ASN A 777 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.112960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097415 restraints weight = 88782.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097425 restraints weight = 105888.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097978 restraints weight = 93493.877| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16381 Z= 0.211 Angle : 0.600 6.947 22138 Z= 0.322 Chirality : 0.042 0.388 2455 Planarity : 0.004 0.046 2826 Dihedral : 5.734 64.436 2160 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 0.51 % Allowed : 8.40 % Favored : 91.09 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 1956 helix: 1.39 (0.16), residues: 945 sheet: -1.58 (0.32), residues: 242 loop : -1.09 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.006 0.001 HIS B 271 PHE 0.015 0.001 PHE A1008 TYR 0.017 0.002 TYR A 702 ARG 0.004 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 881) hydrogen bonds : angle 5.23749 ( 2514) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.70932 ( 2) covalent geometry : bond 0.00470 (16380) covalent geometry : angle 0.59980 (22136) *********************** 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 173 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 7.357 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: A 108 ASP cc_start: 0.8316 (m-30) cc_final: 0.8054 (m-30) outliers start: 9 outliers final: 9 residues processed: 169 average time/residue: 1.1570 time to fit residues: 306.0241 Evaluate side-chains 164 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.0170 chunk 76 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.0026 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.113898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098014 restraints weight = 88759.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097990 restraints weight = 103706.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098459 restraints weight = 87903.994| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16381 Z= 0.151 Angle : 0.551 7.202 22138 Z= 0.291 Chirality : 0.041 0.379 2455 Planarity : 0.004 0.045 2826 Dihedral : 5.528 59.095 2157 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 0.85 % Allowed : 8.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 1956 helix: 1.62 (0.16), residues: 945 sheet: -1.58 (0.32), residues: 245 loop : -1.10 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.009 0.001 HIS C 388 PHE 0.015 0.001 PHE A1008 TYR 0.015 0.001 TYR A 702 ARG 0.004 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 881) hydrogen bonds : angle 4.91026 ( 2514) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.99853 ( 2) covalent geometry : bond 0.00334 (16380) covalent geometry : angle 0.55113 (22136) *********************** 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 176 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 2.588 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: 0.6491 (OUTLIER) cc_final: 0.5738 (mm-30) REVERT: A 108 ASP cc_start: 0.8117 (m-30) cc_final: 0.7847 (m-30) REVERT: A 1025 MET cc_start: 0.7543 (mmt) cc_final: 0.7216 (mmt) outliers start: 15 outliers final: 9 residues processed: 168 average time/residue: 0.6939 time to fit residues: 173.2169 Evaluate side-chains 163 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU 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 984 LEU Chi-restraints excluded: chain A residue 1122 VAL 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 120 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 191 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.114258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098866 restraints weight = 88320.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098789 restraints weight = 104007.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099474 restraints weight = 86364.842| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16381 Z= 0.141 Angle : 0.530 7.260 22138 Z= 0.278 Chirality : 0.040 0.376 2455 Planarity : 0.004 0.044 2826 Dihedral : 5.326 54.266 2157 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.96 % Allowed : 8.46 % Favored : 90.59 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1956 helix: 1.78 (0.17), residues: 952 sheet: -1.51 (0.32), residues: 246 loop : -1.06 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A1008 TYR 0.014 0.001 TYR A 702 ARG 0.003 0.000 ARG A1044 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 881) hydrogen bonds : angle 4.70151 ( 2514) SS BOND : bond 0.00402 ( 1) SS BOND : angle 2.06044 ( 2) covalent geometry : bond 0.00311 (16380) covalent geometry : angle 0.52926 (22136) *********************** 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 183 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 2.412 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: 0.6440 (OUTLIER) cc_final: 0.5706 (mm-30) REVERT: D 317 LEU cc_start: 0.8427 (mt) cc_final: 0.8145 (mt) REVERT: A 108 ASP cc_start: 0.8123 (m-30) cc_final: 0.7843 (m-30) REVERT: A 1025 MET cc_start: 0.7525 (mmt) cc_final: 0.7156 (mmt) outliers start: 17 outliers final: 12 residues processed: 176 average time/residue: 0.7332 time to fit residues: 192.2122 Evaluate side-chains 168 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 3.916 ------------------------------------------------------------------------------- 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 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 691 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 A1005 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098522 restraints weight = 88311.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098381 restraints weight = 102075.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098932 restraints weight = 88778.703| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16381 Z= 0.143 Angle : 0.527 7.238 22138 Z= 0.275 Chirality : 0.040 0.375 2455 Planarity : 0.004 0.042 2826 Dihedral : 5.191 49.445 2157 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 1.07 % Allowed : 8.85 % Favored : 90.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1956 helix: 1.92 (0.17), residues: 945 sheet: -1.66 (0.32), residues: 250 loop : -1.00 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.005 0.001 HIS A 146 PHE 0.014 0.001 PHE A1008 TYR 0.015 0.001 TYR A 702 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 881) hydrogen bonds : angle 4.57215 ( 2514) SS BOND : bond 0.00910 ( 1) SS BOND : angle 4.65020 ( 2) covalent geometry : bond 0.00319 (16380) covalent geometry : angle 0.52521 (22136) *********************** 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 178 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 2.612 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: D 317 LEU cc_start: 0.8414 (mt) cc_final: 0.8151 (mt) REVERT: A 108 ASP cc_start: 0.8050 (m-30) cc_final: 0.7797 (m-30) REVERT: A 1025 MET cc_start: 0.7500 (mmt) cc_final: 0.7052 (mmt) outliers start: 19 outliers final: 17 residues processed: 171 average time/residue: 0.7229 time to fit residues: 185.1855 Evaluate side-chains 172 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 335 CYS 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 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 99 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.112877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097425 restraints weight = 89419.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097246 restraints weight = 109199.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098427 restraints weight = 83874.960| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16381 Z= 0.218 Angle : 0.565 7.504 22138 Z= 0.298 Chirality : 0.041 0.377 2455 Planarity : 0.004 0.044 2826 Dihedral : 5.274 49.710 2157 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 1.24 % Allowed : 9.53 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1956 helix: 1.86 (0.17), residues: 938 sheet: -1.78 (0.32), residues: 250 loop : -1.10 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 442 HIS 0.005 0.001 HIS A 146 PHE 0.017 0.002 PHE A1008 TYR 0.017 0.002 TYR A 702 ARG 0.003 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 881) hydrogen bonds : angle 4.68598 ( 2514) SS BOND : bond 0.01039 ( 1) SS BOND : angle 4.12253 ( 2) covalent geometry : bond 0.00496 (16380) covalent geometry : angle 0.56345 (22136) *********************** 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 182 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.605 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: B 27 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5697 (mm-30) REVERT: A 108 ASP cc_start: 0.8105 (m-30) cc_final: 0.7854 (m-30) REVERT: A 1025 MET cc_start: 0.7497 (mmt) cc_final: 0.7102 (mmt) outliers start: 22 outliers final: 21 residues processed: 174 average time/residue: 0.6713 time to fit residues: 172.9365 Evaluate side-chains 179 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 335 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 141 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.114154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098606 restraints weight = 88558.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098752 restraints weight = 97482.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099266 restraints weight = 83263.620| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16381 Z= 0.130 Angle : 0.524 7.618 22138 Z= 0.272 Chirality : 0.040 0.373 2455 Planarity : 0.003 0.041 2826 Dihedral : 5.149 48.829 2157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 1.30 % Allowed : 9.75 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1956 helix: 1.99 (0.17), residues: 946 sheet: -1.76 (0.32), residues: 250 loop : -1.01 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 PHE 0.014 0.001 PHE A1008 TYR 0.014 0.001 TYR A 702 ARG 0.003 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 881) hydrogen bonds : angle 4.50510 ( 2514) SS BOND : bond 0.00515 ( 1) SS BOND : angle 3.04627 ( 2) covalent geometry : bond 0.00291 (16380) covalent geometry : angle 0.52326 (22136) *********************** 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 188 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 2.663 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: 0.7540 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 108 ASP cc_start: 0.7995 (m-30) cc_final: 0.7745 (m-30) REVERT: A 1025 MET cc_start: 0.7450 (mmt) cc_final: 0.6993 (mmt) outliers start: 23 outliers final: 18 residues processed: 180 average time/residue: 0.6971 time to fit residues: 184.4483 Evaluate side-chains 179 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.113530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098168 restraints weight = 88864.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098230 restraints weight = 101955.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098506 restraints weight = 86037.792| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1434 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= 0.169 Angle : 0.537 7.929 22138 Z= 0.281 Chirality : 0.040 0.372 2455 Planarity : 0.004 0.045 2826 Dihedral : 5.118 48.367 2157 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 1.18 % Allowed : 9.81 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 1956 helix: 1.98 (0.17), residues: 945 sheet: -1.75 (0.32), residues: 250 loop : -1.08 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 PHE 0.015 0.001 PHE A1008 TYR 0.015 0.001 TYR A 702 ARG 0.009 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 881) hydrogen bonds : angle 4.52889 ( 2514) SS BOND : bond 0.00463 ( 1) SS BOND : angle 2.78604 ( 2) covalent geometry : bond 0.00382 (16380) covalent geometry : angle 0.53605 (22136) *********************** 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 182 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 3.227 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: C 387 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 1025 MET cc_start: 0.7357 (mmt) cc_final: 0.6931 (mmt) outliers start: 21 outliers final: 19 residues processed: 175 average time/residue: 0.7814 time to fit residues: 204.4576 Evaluate side-chains 177 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL 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 965 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.113349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097946 restraints weight = 88867.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097681 restraints weight = 98322.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098576 restraints weight = 81513.545| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1492 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= 0.175 Angle : 0.543 8.032 22138 Z= 0.284 Chirality : 0.040 0.372 2455 Planarity : 0.004 0.050 2826 Dihedral : 5.127 49.022 2157 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % Rotamer: Outliers : 1.24 % Allowed : 10.03 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1956 helix: 1.98 (0.17), residues: 945 sheet: -1.79 (0.32), residues: 250 loop : -1.09 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.005 0.001 HIS A 146 PHE 0.016 0.001 PHE A1008 TYR 0.015 0.001 TYR A 702 ARG 0.008 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 881) hydrogen bonds : angle 4.53789 ( 2514) SS BOND : bond 0.00376 ( 1) SS BOND : angle 2.66740 ( 2) covalent geometry : bond 0.00395 (16380) covalent geometry : angle 0.54268 (22136) *********************** 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 183 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 2.346 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: 0.7581 (tm-30) cc_final: 0.7270 (tm-30) REVERT: A 1025 MET cc_start: 0.7340 (mmt) cc_final: 0.6863 (mmt) outliers start: 22 outliers final: 20 residues processed: 176 average time/residue: 0.6707 time to fit residues: 173.6194 Evaluate side-chains 181 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL 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 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 60 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 146 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.114135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098651 restraints weight = 88294.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098094 restraints weight = 78721.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098521 restraints weight = 76704.879| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16381 Z= 0.126 Angle : 0.523 8.168 22138 Z= 0.271 Chirality : 0.040 0.369 2455 Planarity : 0.004 0.054 2826 Dihedral : 5.027 47.217 2157 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.96 % Favored : 94.99 % Rotamer: Outliers : 0.90 % Allowed : 10.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1956 helix: 2.10 (0.17), residues: 946 sheet: -1.72 (0.32), residues: 249 loop : -1.00 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 PHE 0.015 0.001 PHE A1008 TYR 0.013 0.001 TYR A 702 ARG 0.007 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 881) hydrogen bonds : angle 4.42691 ( 2514) SS BOND : bond 0.00347 ( 1) SS BOND : angle 2.52624 ( 2) covalent geometry : bond 0.00283 (16380) covalent geometry : angle 0.52269 (22136) ********************** 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 179 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 2.611 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: symmetry clash REVERT: C 387 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7314 (tm-30) outliers start: 16 outliers final: 15 residues processed: 174 average time/residue: 0.7229 time to fit residues: 185.6789 Evaluate side-chains 173 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL 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 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 681 VAL Chi-restraints excluded: chain A residue 702 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 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 = 0.3566 r_free = 0.3566 target = 0.113420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097810 restraints weight = 88740.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097810 restraints weight = 104219.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098309 restraints weight = 93161.615| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1620 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= 0.168 Angle : 0.540 8.214 22138 Z= 0.282 Chirality : 0.040 0.370 2455 Planarity : 0.004 0.054 2826 Dihedral : 5.048 47.241 2157 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 1.01 % Allowed : 10.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1956 helix: 2.05 (0.17), residues: 945 sheet: -1.81 (0.32), residues: 249 loop : -1.05 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.004 0.001 HIS A 146 PHE 0.016 0.001 PHE A1008 TYR 0.015 0.001 TYR A 702 ARG 0.008 0.000 ARG A1292 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 881) hydrogen bonds : angle 4.47810 ( 2514) SS BOND : bond 0.00336 ( 1) SS BOND : angle 2.48105 ( 2) covalent geometry : bond 0.00379 (16380) covalent geometry : angle 0.53979 (22136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9044.01 seconds wall clock time: 159 minutes 50.34 seconds (9590.34 seconds total)