Starting phenix.real_space_refine on Sat Feb 7 12:49:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q0y_72110/02_2026/9q0y_72110_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q0y_72110/02_2026/9q0y_72110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q0y_72110/02_2026/9q0y_72110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q0y_72110/02_2026/9q0y_72110.map" model { file = "/net/cci-nas-00/data/ceres_data/9q0y_72110/02_2026/9q0y_72110_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q0y_72110/02_2026/9q0y_72110_trim.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 3 5.49 5 S 82 5.16 5 C 10349 2.51 5 N 2768 2.21 5 O 3001 1.98 5 H 15690 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31895 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 9775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 9775 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 33, 'TRANS': 569} Chain breaks: 2 Chain: "A" Number of atoms: 21950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 21950 Classifications: {'peptide': 1386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1316} Chain breaks: 3 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17743 SG CYS A 539 45.245 88.760 101.429 1.00119.97 S Time building chain proxies: 5.68, per 1000 atoms: 0.18 Number of scatterers: 31895 At special positions: 0 Unit cell: (97.06, 124.912, 167.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 82 16.00 P 3 15.00 O 3001 8.00 N 2768 7.00 C 10349 6.00 H 15690 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 72 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.0 seconds 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 18 sheets defined 56.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 180 through 195 removed outlier: 4.014A pdb=" N ILE B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 211 Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 220 through 223 removed outlier: 4.007A pdb=" N GLU B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.901A pdb=" N LYS B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 340 through 355 removed outlier: 4.125A pdb=" N GLN B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.668A pdb=" N GLU B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 384 through 404 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 430 through 447 removed outlier: 3.945A pdb=" N VAL B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 443 " --> pdb=" O MET B 439 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 495 Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'B' and resid 521 through 535 Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.433A pdb=" N ILE B 543 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 546 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 575 Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 623 through 634 Processing helix chain 'B' and resid 679 through 686 Processing helix chain 'B' and resid 717 through 727 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 747 through 750 Processing helix chain 'B' and resid 751 through 772 Processing helix chain 'B' and resid 777 through 783 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.029A pdb=" N ALA A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TRP A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.518A pdb=" N GLY A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.782A pdb=" N TRP A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 374 through 381 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.718A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.948A pdb=" N SER A 395 " --> pdb=" O HIS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.463A pdb=" N ILE A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 495 removed outlier: 3.818A pdb=" N VAL A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 540 through 545 removed outlier: 4.335A pdb=" N ILE A 543 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 624 through 633 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.624A pdb=" N ILE A 669 " --> pdb=" O PRO A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 removed outlier: 3.529A pdb=" N PHE A 682 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 683 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 685 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.557A pdb=" N ILE A 721 " --> pdb=" O MET A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 747 through 750 removed outlier: 3.636A pdb=" N THR A 750 " --> pdb=" O SER A 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 747 through 750' Processing helix chain 'A' and resid 751 through 772 Processing helix chain 'A' and resid 777 through 783 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.901A pdb=" N GLN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 922 through 924 No H-bonds generated for 'chain 'A' and resid 922 through 924' Processing helix chain 'A' and resid 925 through 935 removed outlier: 3.615A pdb=" N GLN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 973 Processing helix chain 'A' and resid 989 through 1005 Processing helix chain 'A' and resid 1024 through 1041 removed outlier: 3.766A pdb=" N SER A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A1041 " --> pdb=" O GLU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1089 through 1101 Processing helix chain 'A' and resid 1132 through 1139 Processing helix chain 'A' and resid 1148 through 1158 Processing helix chain 'A' and resid 1161 through 1176 Processing helix chain 'A' and resid 1181 through 1195 Processing helix chain 'A' and resid 1197 through 1205 Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 3.623A pdb=" N LEU A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing helix chain 'A' and resid 1298 through 1301 Processing helix chain 'A' and resid 1302 through 1319 Processing helix chain 'A' and resid 1339 through 1350 Processing helix chain 'A' and resid 1368 through 1376 removed outlier: 3.519A pdb=" N ASN A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1386 removed outlier: 3.818A pdb=" N HIS A1386 " --> pdb=" O GLN A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1414 Processing helix chain 'A' and resid 1418 through 1432 Processing helix chain 'A' and resid 1448 through 1458 removed outlier: 3.828A pdb=" N GLN A1452 " --> pdb=" O GLN A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1468 Processing sheet with id=AA1, first strand: chain 'B' and resid 582 through 583 removed outlier: 4.076A pdb=" N VAL B 582 " --> pdb=" O ASN B 713 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 598 through 599 Processing sheet with id=AA3, first strand: chain 'B' and resid 671 through 673 Processing sheet with id=AA4, first strand: chain 'B' and resid 705 through 707 removed outlier: 3.704A pdb=" N MET B 700 " --> pdb=" O TYR B 707 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 68 removed outlier: 3.778A pdb=" N VAL A 21 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 66 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 19 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG A 129 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 23 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN A 127 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA A 25 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET A 125 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 57 removed outlier: 3.931A pdb=" N ALA A 38 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 56 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR A 36 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 37 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 73 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE A 74 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS A 96 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 76 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 94 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 78 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.016A pdb=" N VAL A 582 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 598 through 599 Processing sheet with id=AA9, first strand: chain 'A' and resid 609 through 611 Processing sheet with id=AB1, first strand: chain 'A' and resid 671 through 673 Processing sheet with id=AB2, first strand: chain 'A' and resid 705 through 707 removed outlier: 3.526A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 860 through 864 removed outlier: 5.159A pdb=" N GLU A 906 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG A 862 " --> pdb=" O GLU A 906 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 908 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 944 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 867 through 868 removed outlier: 3.750A pdb=" N ASN A 944 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1017 through 1018 Processing sheet with id=AB6, first strand: chain 'A' and resid 1225 through 1228 removed outlier: 7.160A pdb=" N LEU A1066 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN A1048 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A1064 " --> pdb=" O ASN A1048 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU A1050 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR A1062 " --> pdb=" O GLU A1050 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1107 through 1108 Processing sheet with id=AB8, first strand: chain 'A' and resid 1248 through 1250 Processing sheet with id=AB9, first strand: chain 'A' and resid 1354 through 1359 removed outlier: 6.352A pdb=" N ALA A1325 " --> pdb=" O ASP A1354 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLN A1356 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A1327 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA A1358 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A1329 " --> pdb=" O ALA A1358 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A1294 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N CYS A1394 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1296 " --> pdb=" O CYS A1394 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR A1391 " --> pdb=" O SER A1436 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASP A1438 " --> pdb=" O TYR A1391 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A1393 " --> pdb=" O ASP A1438 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2379 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: 9.16 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 15668 1.09 - 1.35: 5356 1.35 - 1.60: 11146 1.60 - 1.85: 140 1.85 - 2.11: 8 Bond restraints: 32318 Sorted by residual: bond pdb=" N ASP B 777 " pdb=" H ASP B 777 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" N GLN A 783 " pdb=" H GLN A 783 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" N GLN A 779 " pdb=" H GLN A 779 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" N GLN B 783 " pdb=" H GLN B 783 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" N ALA B 782 " pdb=" H ALA B 782 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 32313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.35: 58298 7.35 - 14.70: 2 14.70 - 22.05: 4 22.05 - 29.40: 0 29.40 - 36.75: 1 Bond angle restraints: 58305 Sorted by residual: angle pdb=" N PHE B 825 " pdb=" CA PHE B 825 " pdb=" CB PHE B 825 " ideal model delta sigma weight residual 110.50 147.25 -36.75 1.70e+00 3.46e-01 4.67e+02 angle pdb=" N PHE A 825 " pdb=" CA PHE A 825 " pdb=" CB PHE A 825 " ideal model delta sigma weight residual 110.50 125.53 -15.03 1.70e+00 3.46e-01 7.82e+01 angle pdb=" N PHE A 825 " pdb=" CA PHE A 825 " pdb=" HA PHE A 825 " ideal model delta sigma weight residual 110.00 88.03 21.97 3.00e+00 1.11e-01 5.36e+01 angle pdb=" N PHE B 825 " pdb=" CA PHE B 825 " pdb=" HA PHE B 825 " ideal model delta sigma weight residual 110.00 88.09 21.91 3.00e+00 1.11e-01 5.33e+01 angle pdb=" N PHE B 825 " pdb=" CA PHE B 825 " pdb=" C PHE B 825 " ideal model delta sigma weight residual 111.00 91.19 19.81 2.80e+00 1.28e-01 5.01e+01 ... (remaining 58300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 13313 18.16 - 36.33: 1319 36.33 - 54.49: 444 54.49 - 72.65: 101 72.65 - 90.81: 48 Dihedral angle restraints: 15225 sinusoidal: 8244 harmonic: 6981 Sorted by residual: dihedral pdb=" N PHE B 825 " pdb=" C PHE B 825 " pdb=" CA PHE B 825 " pdb=" CB PHE B 825 " ideal model delta harmonic sigma weight residual 122.80 154.09 -31.29 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" N PHE A 825 " pdb=" C PHE A 825 " pdb=" CA PHE A 825 " pdb=" CB PHE A 825 " ideal model delta harmonic sigma weight residual 122.80 146.39 -23.59 0 2.50e+00 1.60e-01 8.91e+01 dihedral pdb=" C PHE A 825 " pdb=" N PHE A 825 " pdb=" CA PHE A 825 " pdb=" CB PHE A 825 " ideal model delta harmonic sigma weight residual -122.60 -140.37 17.77 0 2.50e+00 1.60e-01 5.05e+01 ... (remaining 15222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 2417 0.223 - 0.445: 0 0.445 - 0.667: 0 0.667 - 0.890: 1 0.890 - 1.112: 1 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CA PHE B 825 " pdb=" N PHE B 825 " pdb=" C PHE B 825 " pdb=" CB PHE B 825 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" CA PHE A 825 " pdb=" N PHE A 825 " pdb=" C PHE A 825 " pdb=" CB PHE A 825 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C3' FAD A1503 " pdb=" C2' FAD A1503 " pdb=" C4' FAD A1503 " pdb=" O3' FAD A1503 " both_signs ideal model delta sigma weight residual False -2.55 -2.41 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 2416 not shown) Planarity restraints: 4792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 779 " 0.325 2.00e-02 2.50e+03 4.48e-01 3.02e+03 pdb=" CD GLN A 779 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 779 " -0.316 2.00e-02 2.50e+03 pdb=" NE2 GLN A 779 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 779 " 0.715 2.00e-02 2.50e+03 pdb="HE22 GLN A 779 " -0.700 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 779 " -0.342 2.00e-02 2.50e+03 3.92e-01 2.30e+03 pdb=" CD GLN B 779 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN B 779 " 0.327 2.00e-02 2.50e+03 pdb=" NE2 GLN B 779 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 779 " -0.597 2.00e-02 2.50e+03 pdb="HE22 GLN B 779 " 0.583 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A1501 " -0.156 2.00e-02 2.50e+03 1.94e-01 8.50e+02 pdb=" C1B HEM A1501 " -0.026 2.00e-02 2.50e+03 pdb=" C2B HEM A1501 " -0.141 2.00e-02 2.50e+03 pdb=" C3B HEM A1501 " -0.048 2.00e-02 2.50e+03 pdb=" C4B HEM A1501 " -0.130 2.00e-02 2.50e+03 pdb=" CAB HEM A1501 " 0.323 2.00e-02 2.50e+03 pdb=" CHB HEM A1501 " 0.359 2.00e-02 2.50e+03 pdb=" CHC HEM A1501 " 0.023 2.00e-02 2.50e+03 pdb=" CMB HEM A1501 " -0.204 2.00e-02 2.50e+03 ... (remaining 4789 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 12985 2.39 - 2.95: 73021 2.95 - 3.50: 84931 3.50 - 4.05: 110107 4.05 - 4.60: 163247 Nonbonded interactions: 444291 Sorted by model distance: nonbonded pdb=" HG1 THR A1131 " pdb=" H GLN A1134 " model vdw 1.843 2.100 nonbonded pdb=" HG SER A 643 " pdb=" H TYR A 645 " model vdw 1.855 2.100 nonbonded pdb=" HD1 HIS A 520 " pdb=" HH TYR A 707 " model vdw 1.859 2.100 nonbonded pdb=" H GLN A1448 " pdb=" H ALA A1449 " model vdw 1.880 2.100 nonbonded pdb=" HG1 THR A 517 " pdb=" H TYR A 518 " model vdw 1.885 2.100 ... (remaining 444286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.040 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: 0.200 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.380 Find NCS groups from input model: 0.140 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.005 0.219 16631 Z= 0.194 Angle : 0.634 36.749 22613 Z= 0.324 Chirality : 0.047 1.112 2419 Planarity : 0.006 0.194 2912 Dihedral : 18.115 90.812 6148 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 1.81 % Allowed : 20.13 % Favored : 78.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1975 helix: 2.11 (0.16), residues: 1009 sheet: -2.02 (0.31), residues: 289 loop : -0.53 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.011 0.001 TYR B 335 PHE 0.009 0.001 PHE A 222 TRP 0.008 0.001 TRP A1381 HIS 0.004 0.001 HIS B 778 Details of bonding type rmsd covalent geometry : bond 0.00463 (16628) covalent geometry : angle 0.63444 (22611) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.45168 ( 2) hydrogen bonds : bond 0.15256 ( 822) hydrogen bonds : angle 5.83114 ( 2379) Misc. bond : bond 0.05846 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.056 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 MET cc_start: 0.8590 (tmm) cc_final: 0.8117 (tmm) REVERT: B 411 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5357 (pp) REVERT: B 439 MET cc_start: 0.5154 (mmp) cc_final: 0.4810 (mmm) outliers start: 31 outliers final: 19 residues processed: 131 average time/residue: 0.2902 time to fit residues: 58.0943 Evaluate side-chains 103 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1331 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.113785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065833 restraints weight = 119769.899| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.36 r_work: 0.2945 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16631 Z= 0.123 Angle : 0.496 7.727 22613 Z= 0.254 Chirality : 0.037 0.142 2419 Planarity : 0.003 0.037 2912 Dihedral : 7.374 84.260 2279 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.90 % Rotamer: Outliers : 1.69 % Allowed : 20.01 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1975 helix: 2.16 (0.16), residues: 1013 sheet: -1.90 (0.31), residues: 283 loop : -0.55 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.016 0.001 TYR A1064 PHE 0.009 0.001 PHE A 74 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00289 (16628) covalent geometry : angle 0.49610 (22611) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.32537 ( 2) hydrogen bonds : bond 0.04681 ( 822) hydrogen bonds : angle 4.70091 ( 2379) Misc. bond : bond 0.02891 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.898 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: B 293 MET cc_start: 0.8695 (tmm) cc_final: 0.8405 (tpt) REVERT: B 411 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5548 (pp) REVERT: B 412 MET cc_start: 0.8879 (mmm) cc_final: 0.8672 (mmm) REVERT: B 562 MET cc_start: 0.8747 (mtt) cc_final: 0.8528 (mtt) REVERT: A 618 MET cc_start: 0.8625 (ttp) cc_final: 0.8255 (ttt) outliers start: 29 outliers final: 20 residues processed: 106 average time/residue: 0.2761 time to fit residues: 45.8974 Evaluate side-chains 100 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1431 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 110 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 GLN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.112129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063904 restraints weight = 120044.645| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.36 r_work: 0.2912 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 16631 Z= 0.199 Angle : 0.518 6.602 22613 Z= 0.264 Chirality : 0.038 0.144 2419 Planarity : 0.004 0.035 2912 Dihedral : 6.484 87.144 2261 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 2.45 % Allowed : 19.66 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1975 helix: 2.05 (0.16), residues: 1016 sheet: -1.90 (0.30), residues: 271 loop : -0.67 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 334 TYR 0.017 0.001 TYR B 645 PHE 0.012 0.001 PHE B 365 TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00470 (16628) covalent geometry : angle 0.51804 (22611) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.46516 ( 2) hydrogen bonds : bond 0.04645 ( 822) hydrogen bonds : angle 4.53617 ( 2379) Misc. bond : bond 0.04750 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.905 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: B 293 MET cc_start: 0.8721 (tmm) cc_final: 0.8463 (tpt) REVERT: B 411 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5616 (pp) REVERT: B 412 MET cc_start: 0.8936 (mmm) cc_final: 0.8729 (mmm) REVERT: B 562 MET cc_start: 0.8801 (mtt) cc_final: 0.8528 (mtt) REVERT: B 734 MET cc_start: 0.8520 (ppp) cc_final: 0.7893 (pmm) outliers start: 42 outliers final: 29 residues processed: 115 average time/residue: 0.2945 time to fit residues: 51.8294 Evaluate side-chains 108 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 700 MET Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 154 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.112636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064346 restraints weight = 119427.601| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.43 r_work: 0.2922 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16631 Z= 0.143 Angle : 0.481 7.501 22613 Z= 0.244 Chirality : 0.037 0.143 2419 Planarity : 0.003 0.035 2912 Dihedral : 6.290 89.748 2261 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 2.16 % Allowed : 20.07 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1975 helix: 2.22 (0.16), residues: 1016 sheet: -1.81 (0.30), residues: 278 loop : -0.61 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.013 0.001 TYR A1064 PHE 0.019 0.001 PHE B 682 TRP 0.011 0.001 TRP B 290 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00342 (16628) covalent geometry : angle 0.48082 (22611) SS BOND : bond 0.00129 ( 1) SS BOND : angle 0.41688 ( 2) hydrogen bonds : bond 0.04069 ( 822) hydrogen bonds : angle 4.28506 ( 2379) Misc. bond : bond 0.03689 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.908 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: B 293 MET cc_start: 0.8741 (tmm) cc_final: 0.8469 (tpt) REVERT: B 411 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5650 (pp) REVERT: B 562 MET cc_start: 0.8840 (mtt) cc_final: 0.8544 (mtt) REVERT: A 1222 GLU cc_start: 0.7004 (pp20) cc_final: 0.6769 (pp20) outliers start: 37 outliers final: 29 residues processed: 112 average time/residue: 0.2960 time to fit residues: 50.8266 Evaluate side-chains 107 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 182 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.112155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.064080 restraints weight = 119260.882| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.36 r_work: 0.2915 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16631 Z= 0.153 Angle : 0.480 6.029 22613 Z= 0.243 Chirality : 0.037 0.143 2419 Planarity : 0.004 0.075 2912 Dihedral : 5.941 81.666 2259 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 1.93 % Allowed : 20.36 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1975 helix: 2.26 (0.16), residues: 1017 sheet: -1.78 (0.30), residues: 275 loop : -0.67 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1060 TYR 0.017 0.001 TYR B 645 PHE 0.012 0.001 PHE B 365 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00365 (16628) covalent geometry : angle 0.47981 (22611) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.42690 ( 2) hydrogen bonds : bond 0.04029 ( 822) hydrogen bonds : angle 4.20810 ( 2379) Misc. bond : bond 0.04342 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.835 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 293 MET cc_start: 0.8730 (tmm) cc_final: 0.8360 (tmm) REVERT: B 411 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5802 (pp) REVERT: B 562 MET cc_start: 0.8833 (mtt) cc_final: 0.8513 (mtt) REVERT: B 734 MET cc_start: 0.8558 (ppp) cc_final: 0.8284 (ppp) outliers start: 33 outliers final: 30 residues processed: 109 average time/residue: 0.2650 time to fit residues: 45.0190 Evaluate side-chains 107 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 105 optimal weight: 1.9990 chunk 183 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.111961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063969 restraints weight = 119176.841| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.39 r_work: 0.2915 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16631 Z= 0.155 Angle : 0.480 8.499 22613 Z= 0.241 Chirality : 0.037 0.143 2419 Planarity : 0.003 0.039 2912 Dihedral : 5.583 65.929 2256 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 2.39 % Allowed : 20.19 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1975 helix: 2.29 (0.16), residues: 1017 sheet: -1.78 (0.30), residues: 278 loop : -0.64 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1060 TYR 0.016 0.001 TYR B 645 PHE 0.010 0.001 PHE A 222 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00370 (16628) covalent geometry : angle 0.48015 (22611) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.47575 ( 2) hydrogen bonds : bond 0.03946 ( 822) hydrogen bonds : angle 4.15100 ( 2379) Misc. bond : bond 0.04066 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.843 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 293 MET cc_start: 0.8698 (tmm) cc_final: 0.8341 (tmm) REVERT: B 411 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5987 (pp) REVERT: B 562 MET cc_start: 0.8847 (mtt) cc_final: 0.8525 (mtt) REVERT: B 734 MET cc_start: 0.8552 (ppp) cc_final: 0.8286 (ppp) REVERT: A 653 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8659 (tp30) outliers start: 41 outliers final: 35 residues processed: 117 average time/residue: 0.2572 time to fit residues: 47.3053 Evaluate side-chains 115 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 184 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 19 optimal weight: 20.0000 chunk 103 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.112951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064935 restraints weight = 119476.716| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.44 r_work: 0.2931 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 16631 Z= 0.095 Angle : 0.453 6.813 22613 Z= 0.227 Chirality : 0.036 0.142 2419 Planarity : 0.003 0.046 2912 Dihedral : 5.347 58.251 2256 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.35 % Rotamer: Outliers : 1.98 % Allowed : 20.48 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1975 helix: 2.48 (0.16), residues: 1017 sheet: -1.73 (0.30), residues: 283 loop : -0.54 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1060 TYR 0.015 0.001 TYR B 645 PHE 0.008 0.001 PHE B 365 TRP 0.011 0.001 TRP B 290 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00229 (16628) covalent geometry : angle 0.45307 (22611) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.29176 ( 2) hydrogen bonds : bond 0.03565 ( 822) hydrogen bonds : angle 3.96455 ( 2379) Misc. bond : bond 0.04085 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.855 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: B 293 MET cc_start: 0.8688 (tmm) cc_final: 0.8332 (tmm) REVERT: B 411 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6071 (pp) REVERT: B 562 MET cc_start: 0.8846 (mtt) cc_final: 0.8529 (mtt) REVERT: B 734 MET cc_start: 0.8536 (ppp) cc_final: 0.8265 (ppp) REVERT: A 710 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9245 (pp) REVERT: A 1222 GLU cc_start: 0.6702 (pp20) cc_final: 0.6409 (pp20) outliers start: 34 outliers final: 29 residues processed: 110 average time/residue: 0.2860 time to fit residues: 48.6902 Evaluate side-chains 110 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.111325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063312 restraints weight = 120078.579| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.40 r_work: 0.2894 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16631 Z= 0.199 Angle : 0.507 7.004 22613 Z= 0.256 Chirality : 0.037 0.165 2419 Planarity : 0.004 0.036 2912 Dihedral : 5.364 59.265 2254 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 2.57 % Allowed : 20.01 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1975 helix: 2.28 (0.16), residues: 1023 sheet: -1.75 (0.30), residues: 271 loop : -0.70 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1060 TYR 0.017 0.001 TYR B 645 PHE 0.011 0.001 PHE A 222 TRP 0.011 0.001 TRP A 290 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00470 (16628) covalent geometry : angle 0.50661 (22611) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.52617 ( 2) hydrogen bonds : bond 0.04092 ( 822) hydrogen bonds : angle 4.16508 ( 2379) Misc. bond : bond 0.04309 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 78 time to evaluate : 0.926 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 293 MET cc_start: 0.8695 (tmm) cc_final: 0.8455 (tpt) REVERT: B 411 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6042 (pp) REVERT: B 562 MET cc_start: 0.8873 (mtt) cc_final: 0.8522 (mtt) REVERT: B 734 MET cc_start: 0.8586 (ppp) cc_final: 0.8274 (ppp) REVERT: A 1222 GLU cc_start: 0.6983 (pp20) cc_final: 0.6655 (pp20) outliers start: 44 outliers final: 38 residues processed: 119 average time/residue: 0.2826 time to fit residues: 52.3460 Evaluate side-chains 117 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 147 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 713 ASN ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.112242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064316 restraints weight = 119177.382| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.40 r_work: 0.2919 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16631 Z= 0.121 Angle : 0.469 6.350 22613 Z= 0.234 Chirality : 0.037 0.192 2419 Planarity : 0.003 0.037 2912 Dihedral : 5.286 57.461 2254 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 2.10 % Allowed : 20.01 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1975 helix: 2.43 (0.16), residues: 1017 sheet: -1.81 (0.30), residues: 285 loop : -0.56 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1060 TYR 0.016 0.001 TYR B 645 PHE 0.010 0.001 PHE B 273 TRP 0.010 0.001 TRP B 290 HIS 0.003 0.000 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00290 (16628) covalent geometry : angle 0.46942 (22611) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.38246 ( 2) hydrogen bonds : bond 0.03739 ( 822) hydrogen bonds : angle 4.01524 ( 2379) Misc. bond : bond 0.04591 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.895 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 293 MET cc_start: 0.8687 (tmm) cc_final: 0.8385 (tpt) REVERT: B 411 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6012 (pp) REVERT: B 562 MET cc_start: 0.8875 (mtt) cc_final: 0.8536 (mtt) REVERT: B 734 MET cc_start: 0.8607 (ppp) cc_final: 0.8292 (ppp) REVERT: A 1222 GLU cc_start: 0.6938 (pp20) cc_final: 0.6651 (pp20) outliers start: 36 outliers final: 31 residues processed: 112 average time/residue: 0.2787 time to fit residues: 48.2102 Evaluate side-chains 111 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 125 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.112693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064663 restraints weight = 119574.194| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.39 r_work: 0.2927 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 16631 Z= 0.097 Angle : 0.469 6.796 22613 Z= 0.233 Chirality : 0.037 0.148 2419 Planarity : 0.003 0.037 2912 Dihedral : 5.232 57.229 2254 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 1.87 % Allowed : 20.30 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1975 helix: 2.50 (0.16), residues: 1017 sheet: -1.82 (0.29), residues: 285 loop : -0.50 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1060 TYR 0.016 0.001 TYR B 645 PHE 0.012 0.001 PHE B 273 TRP 0.010 0.001 TRP B 290 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00229 (16628) covalent geometry : angle 0.46898 (22611) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.26384 ( 2) hydrogen bonds : bond 0.03601 ( 822) hydrogen bonds : angle 3.96446 ( 2379) Misc. bond : bond 0.04971 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 782 is missing expected H atoms. Skipping. Residue ALA 782 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 1.100 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: B 293 MET cc_start: 0.8627 (tmm) cc_final: 0.8393 (tpt) REVERT: B 411 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6089 (pp) REVERT: B 562 MET cc_start: 0.8876 (mtt) cc_final: 0.8527 (mtt) REVERT: B 734 MET cc_start: 0.8580 (ppp) cc_final: 0.8260 (ppp) REVERT: A 618 MET cc_start: 0.8595 (ttp) cc_final: 0.8223 (ttt) REVERT: A 1222 GLU cc_start: 0.6909 (pp20) cc_final: 0.6625 (pp20) outliers start: 32 outliers final: 30 residues processed: 109 average time/residue: 0.2946 time to fit residues: 49.8928 Evaluate side-chains 111 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1232 CYS Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1431 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 934 GLN ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.112524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064491 restraints weight = 119701.805| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.40 r_work: 0.2921 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16631 Z= 0.113 Angle : 0.466 6.522 22613 Z= 0.231 Chirality : 0.036 0.142 2419 Planarity : 0.003 0.038 2912 Dihedral : 5.171 56.968 2254 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 1.93 % Allowed : 20.36 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1975 helix: 2.52 (0.16), residues: 1017 sheet: -1.78 (0.30), residues: 285 loop : -0.48 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1060 TYR 0.016 0.001 TYR B 645 PHE 0.010 0.001 PHE B 273 TRP 0.009 0.001 TRP B 290 HIS 0.003 0.000 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00270 (16628) covalent geometry : angle 0.46615 (22611) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.28801 ( 2) hydrogen bonds : bond 0.03535 ( 822) hydrogen bonds : angle 3.93280 ( 2379) Misc. bond : bond 0.05179 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9505.75 seconds wall clock time: 161 minutes 44.96 seconds (9704.96 seconds total)