Starting phenix.real_space_refine on Sat Feb 7 13:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q15_72116/02_2026/9q15_72116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q15_72116/02_2026/9q15_72116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q15_72116/02_2026/9q15_72116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q15_72116/02_2026/9q15_72116.map" model { file = "/net/cci-nas-00/data/ceres_data/9q15_72116/02_2026/9q15_72116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q15_72116/02_2026/9q15_72116_trim.cif" } resolution = 3.08 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= 0.002 sd= 0.009 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 4 7.16 5 P 3 5.49 5 S 82 5.16 5 C 10425 2.51 5 N 2786 2.21 5 O 3007 1.98 5 H 15733 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 32040 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 9804 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 33, 'TRANS': 569} Chain breaks: 2 Chain: "A" Number of atoms: 21980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 21980 Classifications: {'peptide': 1386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1316} Chain breaks: 3 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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 17772 SG CYS A 539 45.278 88.776 101.423 1.00103.46 S Time building chain proxies: 4.96, per 1000 atoms: 0.15 Number of scatterers: 32040 At special positions: 0 Unit cell: (97.06, 124.912, 163.736, 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 4 26.01 S 82 16.00 P 3 15.00 O 3007 8.00 N 2786 7.00 C 10425 6.00 H 15733 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 944.8 milliseconds 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: 93 helices and 18 sheets defined 56.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.977A pdb=" N ILE B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.567A 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: 4.020A 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 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.905A 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: 4.145A pdb=" N GLN B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.662A pdb=" N GLU B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 4.233A pdb=" N ARG B 382 " --> pdb=" O PRO B 378 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) 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: 3.943A pdb=" N VAL B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 443 " --> pdb=" O MET B 439 " (cutoff:3.500A) removed outlier: 3.705A 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 removed outlier: 3.556A pdb=" N ASN B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 548 removed outlier: 3.829A pdb=" N GLN B 544 " --> pdb=" O GLY B 541 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 546 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 548 " --> pdb=" O TRP B 545 " (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 782 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: 4.359A 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: 3.519A 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: 3.778A pdb=" N TRP A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.865A 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: 3.731A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.949A 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: 4.446A pdb=" N ILE A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 495 removed outlier: 3.828A 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: 4.391A 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: 3.627A pdb=" N ILE A 669 " --> pdb=" O PRO A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 removed outlier: 3.511A pdb=" N PHE A 682 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 683 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 685 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.533A 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: 3.586A 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: 3.914A 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: 3.620A 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: 3.761A pdb=" N SER A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 3.981A 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: 3.630A 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: 3.587A pdb=" N ASN A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1386 removed outlier: 3.830A 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: 3.806A 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: 4.163A pdb=" N VAL B 582 " --> pdb=" O ASN B 713 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 713 " --> pdb=" O VAL B 582 " (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: 3.694A 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: 3.792A pdb=" N VAL A 21 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 66 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 19 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A 129 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 23 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 6.788A 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: 6.808A 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: 6.287A pdb=" N TYR A 36 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 37 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.645A 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: 4.399A pdb=" N LYS A 96 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 76 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 94 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.459A 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: 4.035A 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: 3.515A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 863 through 864 Processing sheet with id=AB4, first strand: chain 'A' and resid 867 through 868 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: 4.272A pdb=" N ASN A1048 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A1064 " --> pdb=" O ASN A1048 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU A1050 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 7.532A 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: 6.355A pdb=" N ALA A1325 " --> pdb=" O ASP A1354 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLN A1356 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A1327 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA A1358 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A1329 " --> pdb=" O ALA A1358 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU A1294 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N CYS A1394 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1296 " --> pdb=" O CYS A1394 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP A1438 " --> pdb=" O TYR A1391 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A1393 " --> pdb=" O ASP A1438 " (cutoff:3.500A) 826 hydrogen bonds defined for protein. 2376 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: 7.76 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.08: 15712 1.08 - 1.34: 5374 1.34 - 1.60: 11231 1.60 - 1.85: 144 1.85 - 2.11: 16 Bond restraints: 32477 Sorted by residual: bond pdb=" C4 FMN A1504 " pdb=" C4A FMN A1504 " ideal model delta sigma weight residual 1.485 1.383 0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" N SER B 180 " pdb=" H SER B 180 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C4A FMN A1504 " pdb=" N5 FMN A1504 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C2C HEM B1501 " pdb=" C3C HEM B1501 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O5' FMN A1504 " pdb=" P FMN A1504 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 32472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 58194 2.12 - 4.25: 334 4.25 - 6.37: 42 6.37 - 8.50: 7 8.50 - 10.62: 1 Bond angle restraints: 58578 Sorted by residual: angle pdb=" C TRP B 533 " pdb=" N ARG B 534 " pdb=" CA ARG B 534 " ideal model delta sigma weight residual 121.54 114.09 7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C3B HEM B1502 " pdb=" CAB HEM B1502 " pdb=" CBB HEM B1502 " ideal model delta sigma weight residual 120.00 130.62 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C ARG B 542 " pdb=" N ILE B 543 " pdb=" CA ILE B 543 " ideal model delta sigma weight residual 120.53 124.70 -4.17 1.41e+00 5.03e-01 8.74e+00 angle pdb=" C3B HEM A1502 " pdb=" CAB HEM A1502 " pdb=" CBB HEM A1502 " ideal model delta sigma weight residual 120.00 128.36 -8.36 3.00e+00 1.11e-01 7.76e+00 angle pdb=" O3P FMN A1504 " pdb=" P FMN A1504 " pdb=" O5' FMN A1504 " ideal model delta sigma weight residual 102.33 110.65 -8.32 3.00e+00 1.11e-01 7.69e+00 ... (remaining 58573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13294 17.98 - 35.96: 1339 35.96 - 53.95: 455 53.95 - 71.93: 119 71.93 - 89.91: 51 Dihedral angle restraints: 15258 sinusoidal: 8277 harmonic: 6981 Sorted by residual: dihedral pdb=" C2B HEM A1501 " pdb=" C3B HEM A1501 " pdb=" CAB HEM A1501 " pdb=" CBB HEM A1501 " ideal model delta sinusoidal sigma weight residual -0.00 -47.42 47.42 2 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" C2B HEM B1501 " pdb=" C3B HEM B1501 " pdb=" CAB HEM B1501 " pdb=" CBB HEM B1501 " ideal model delta sinusoidal sigma weight residual 0.00 -39.32 39.32 2 1.00e+01 1.00e-02 1.93e+01 dihedral pdb=" C2B HEM A1502 " pdb=" C3B HEM A1502 " pdb=" CAB HEM A1502 " pdb=" CBB HEM A1502 " ideal model delta sinusoidal sigma weight residual 180.00 149.78 30.22 2 1.00e+01 1.00e-02 1.22e+01 ... (remaining 15255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1632 0.028 - 0.056: 520 0.056 - 0.084: 129 0.084 - 0.113: 115 0.113 - 0.141: 23 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL B 447 " pdb=" N VAL B 447 " pdb=" C VAL B 447 " pdb=" CB VAL B 447 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 599 " pdb=" N ILE A 599 " pdb=" C ILE A 599 " pdb=" CB ILE A 599 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 2416 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEM B1501 " -0.036 2.00e-02 2.50e+03 1.21e-01 3.27e+02 pdb=" C2C HEM B1501 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEM B1501 " 0.164 2.00e-02 2.50e+03 pdb=" C4C HEM B1501 " 0.003 2.00e-02 2.50e+03 pdb=" CAC HEM B1501 " 0.068 2.00e-02 2.50e+03 pdb=" CHC HEM B1501 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEM B1501 " -0.198 2.00e-02 2.50e+03 pdb=" CMC HEM B1501 " -0.207 2.00e-02 2.50e+03 pdb=" NC HEM B1501 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM A1502 " -0.031 2.00e-02 2.50e+03 7.70e-02 1.33e+02 pdb=" C2C HEM A1502 " 0.006 2.00e-02 2.50e+03 pdb=" C3C HEM A1502 " 0.097 2.00e-02 2.50e+03 pdb=" C4C HEM A1502 " -0.030 2.00e-02 2.50e+03 pdb=" CAC HEM A1502 " -0.120 2.00e-02 2.50e+03 pdb=" CHC HEM A1502 " -0.104 2.00e-02 2.50e+03 pdb=" CHD HEM A1502 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEM A1502 " 0.076 2.00e-02 2.50e+03 pdb=" NC HEM A1502 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM B1502 " -0.125 2.00e-02 2.50e+03 7.67e-02 1.32e+02 pdb=" C2C HEM B1502 " 0.043 2.00e-02 2.50e+03 pdb=" C3C HEM B1502 " -0.053 2.00e-02 2.50e+03 pdb=" C4C HEM B1502 " 0.118 2.00e-02 2.50e+03 pdb=" CAC HEM B1502 " -0.081 2.00e-02 2.50e+03 pdb=" CHC HEM B1502 " -0.039 2.00e-02 2.50e+03 pdb=" CHD HEM B1502 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEM B1502 " 0.092 2.00e-02 2.50e+03 pdb=" NC HEM B1502 " 0.049 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 13047 2.39 - 2.94: 73443 2.94 - 3.50: 85372 3.50 - 4.05: 111061 4.05 - 4.60: 164660 Nonbonded interactions: 447583 Sorted by model distance: nonbonded pdb=" HG1 THR A1131 " pdb=" H GLN A1134 " model vdw 1.841 2.100 nonbonded pdb=" HD1 HIS A 520 " pdb=" HH TYR A 707 " model vdw 1.848 2.100 nonbonded pdb=" H SER A1303 " pdb=" HG SER A1303 " model vdw 1.853 2.100 nonbonded pdb=" HG SER A 643 " pdb=" H TYR A 645 " model vdw 1.857 2.100 nonbonded pdb=" H GLN A1448 " pdb=" H ALA A1449 " model vdw 1.875 2.100 ... (remaining 447578 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: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.470 Find NCS groups from input model: 0.090 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.007 0.352 16748 Z= 0.230 Angle : 0.576 10.622 22795 Z= 0.257 Chirality : 0.036 0.141 2419 Planarity : 0.005 0.121 2926 Dihedral : 18.349 89.908 6178 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 1.69 % Allowed : 20.22 % Favored : 78.09 % 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: 0.83 (0.20), residues: 1975 helix: 2.08 (0.16), residues: 1013 sheet: -2.01 (0.30), residues: 289 loop : -0.55 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.011 0.001 TYR B 335 PHE 0.017 0.001 PHE B 380 TRP 0.026 0.001 TRP B 458 HIS 0.003 0.000 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00602 (16744) covalent geometry : angle 0.57640 (22793) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.44981 ( 2) hydrogen bonds : bond 0.15254 ( 820) hydrogen bonds : angle 5.86849 ( 2376) Misc. bond : bond 0.21015 ( 3) *********************** 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 **************************** Evaluate side-chains 107 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.791 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 232 MET cc_start: 0.7377 (ttp) cc_final: 0.7164 (ttp) REVERT: B 299 TYR cc_start: 0.8322 (m-80) cc_final: 0.8031 (m-10) REVERT: B 548 MET cc_start: 0.8350 (ttp) cc_final: 0.8075 (ttp) REVERT: B 562 MET cc_start: 0.8872 (mmm) cc_final: 0.8485 (mmt) REVERT: B 583 MET cc_start: 0.7130 (ptm) cc_final: 0.6699 (ptm) REVERT: B 673 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: B 675 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: B 716 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6891 (t80) REVERT: A 200 MET cc_start: 0.8506 (mmm) cc_final: 0.8050 (mmt) REVERT: A 302 GLU cc_start: 0.7780 (tp30) cc_final: 0.7560 (tp30) outliers start: 29 outliers final: 19 residues processed: 104 average time/residue: 0.2643 time to fit residues: 41.7306 Evaluate side-chains 99 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 675 GLU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 460 VAL 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 1002 ARG Chi-restraints excluded: chain A residue 1028 SER 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 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 475 ASN A 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.061844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.047553 restraints weight = 246206.570| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.37 r_work: 0.3084 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 16748 Z= 0.131 Angle : 0.493 8.247 22795 Z= 0.251 Chirality : 0.037 0.142 2419 Planarity : 0.003 0.035 2926 Dihedral : 8.166 82.286 2307 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.05 % Favored : 95.80 % Rotamer: Outliers : 2.04 % Allowed : 19.70 % Favored : 78.26 % 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: 0.82 (0.20), residues: 1975 helix: 2.07 (0.16), residues: 1021 sheet: -1.87 (0.30), residues: 289 loop : -0.67 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.017 0.001 TYR A1064 PHE 0.009 0.001 PHE A 222 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00321 (16744) covalent geometry : angle 0.49342 (22793) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.26438 ( 2) hydrogen bonds : bond 0.04554 ( 820) hydrogen bonds : angle 4.68054 ( 2376) Misc. bond : bond 0.13822 ( 3) *********************** 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 **************************** Evaluate side-chains 111 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.892 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 299 TYR cc_start: 0.8292 (m-80) cc_final: 0.8013 (m-10) REVERT: B 511 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: B 548 MET cc_start: 0.8380 (ttp) cc_final: 0.7878 (ttp) REVERT: B 562 MET cc_start: 0.8861 (mmm) cc_final: 0.8450 (mmt) REVERT: B 583 MET cc_start: 0.7089 (ptm) cc_final: 0.6510 (ptm) REVERT: B 673 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: B 675 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: B 716 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6750 (t80) REVERT: A 200 MET cc_start: 0.8575 (mmm) cc_final: 0.8081 (mmt) REVERT: A 847 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7986 (pp20) REVERT: A 966 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8781 (t0) outliers start: 35 outliers final: 19 residues processed: 106 average time/residue: 0.2760 time to fit residues: 44.9983 Evaluate side-chains 99 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 643 SER 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 B residue 828 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 734 MET 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 1028 SER Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1331 CYS Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 54 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3699 r_free = 0.3699 target = 0.061142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.046838 restraints weight = 246838.537| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.32 r_work: 0.3054 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.353 16748 Z= 0.216 Angle : 0.528 13.696 22795 Z= 0.262 Chirality : 0.037 0.139 2419 Planarity : 0.004 0.040 2926 Dihedral : 7.291 72.511 2292 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.01 % Favored : 94.84 % Rotamer: Outliers : 2.51 % Allowed : 19.52 % Favored : 77.97 % 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: 0.71 (0.20), residues: 1975 helix: 1.95 (0.16), residues: 1027 sheet: -1.84 (0.31), residues: 273 loop : -0.79 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 554 TYR 0.015 0.001 TYR A1064 PHE 0.009 0.001 PHE A 222 TRP 0.010 0.001 TRP B 290 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00516 (16744) covalent geometry : angle 0.52779 (22793) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.38809 ( 2) hydrogen bonds : bond 0.04670 ( 820) hydrogen bonds : angle 4.56346 ( 2376) Misc. bond : bond 0.20401 ( 3) *********************** 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 **************************** Evaluate side-chains 115 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 72 time to evaluate : 0.781 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 299 TYR cc_start: 0.8277 (m-80) cc_final: 0.8028 (m-10) REVERT: B 343 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7446 (tp) REVERT: B 511 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 548 MET cc_start: 0.8411 (ttp) cc_final: 0.8156 (ttp) REVERT: B 562 MET cc_start: 0.8856 (mmm) cc_final: 0.8409 (mmt) REVERT: B 583 MET cc_start: 0.7118 (ptm) cc_final: 0.6718 (ptm) REVERT: B 673 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 675 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6346 (pm20) REVERT: A 200 MET cc_start: 0.8565 (mmm) cc_final: 0.8120 (mmt) REVERT: A 227 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7720 (t70) REVERT: A 847 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7968 (pp20) REVERT: A 966 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8888 (t0) outliers start: 43 outliers final: 29 residues processed: 111 average time/residue: 0.2565 time to fit residues: 44.8376 Evaluate side-chains 108 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3701 r_free = 0.3701 target = 0.061185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046911 restraints weight = 245718.075| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.33 r_work: 0.3057 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.293 16748 Z= 0.183 Angle : 0.502 12.275 22795 Z= 0.251 Chirality : 0.037 0.140 2419 Planarity : 0.004 0.040 2926 Dihedral : 6.967 75.302 2289 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 2.45 % Allowed : 19.64 % Favored : 77.91 % 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: 0.76 (0.20), residues: 1975 helix: 1.99 (0.16), residues: 1027 sheet: -1.76 (0.30), residues: 278 loop : -0.78 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 305 TYR 0.015 0.001 TYR A1064 PHE 0.010 0.001 PHE A 222 TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00439 (16744) covalent geometry : angle 0.50216 (22793) SS BOND : bond 0.00102 ( 1) SS BOND : angle 0.39377 ( 2) hydrogen bonds : bond 0.04278 ( 820) hydrogen bonds : angle 4.41482 ( 2376) Misc. bond : bond 0.16947 ( 3) *********************** 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 **************************** Evaluate side-chains 114 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 72 time to evaluate : 0.821 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: B 232 MET cc_start: 0.7480 (ttp) cc_final: 0.7254 (ttp) REVERT: B 299 TYR cc_start: 0.8310 (m-80) cc_final: 0.8062 (m-10) REVERT: B 343 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 511 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: B 548 MET cc_start: 0.8415 (ttp) cc_final: 0.8134 (ttp) REVERT: B 583 MET cc_start: 0.7123 (ptm) cc_final: 0.6719 (ptm) REVERT: B 673 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: B 675 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: B 828 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: A 200 MET cc_start: 0.8575 (mmm) cc_final: 0.8102 (mmt) REVERT: A 227 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7727 (t70) REVERT: A 847 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7985 (pp20) REVERT: A 966 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8913 (t0) outliers start: 42 outliers final: 29 residues processed: 110 average time/residue: 0.2452 time to fit residues: 42.4709 Evaluate side-chains 109 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 643 SER 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 B residue 828 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 436 SER 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 734 MET 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 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 133 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.061338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.047077 restraints weight = 245153.207| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.32 r_work: 0.3066 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.219 16748 Z= 0.142 Angle : 0.480 9.914 22795 Z= 0.238 Chirality : 0.037 0.141 2419 Planarity : 0.003 0.038 2926 Dihedral : 6.699 75.299 2289 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 2.39 % Allowed : 19.70 % Favored : 77.91 % 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: 2.15 (0.16), residues: 1027 sheet: -1.76 (0.30), residues: 278 loop : -0.70 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 554 TYR 0.013 0.001 TYR B 335 PHE 0.008 0.001 PHE A 222 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00349 (16744) covalent geometry : angle 0.47957 (22793) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.33324 ( 2) hydrogen bonds : bond 0.03936 ( 820) hydrogen bonds : angle 4.22332 ( 2376) Misc. bond : bond 0.12688 ( 3) *********************** 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 **************************** Evaluate side-chains 111 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 0.635 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: B 232 MET cc_start: 0.7468 (ttp) cc_final: 0.7219 (ttp) REVERT: B 299 TYR cc_start: 0.8296 (m-80) cc_final: 0.8084 (m-10) REVERT: B 343 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7493 (tp) REVERT: B 442 MET cc_start: 0.7879 (mmp) cc_final: 0.7541 (mmm) REVERT: B 511 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: B 548 MET cc_start: 0.8451 (ttp) cc_final: 0.8150 (ttp) REVERT: B 583 MET cc_start: 0.7146 (ptm) cc_final: 0.6785 (ptm) REVERT: B 673 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: B 675 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6313 (pm20) REVERT: B 828 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: A 200 MET cc_start: 0.8571 (mmm) cc_final: 0.7952 (mmt) REVERT: A 227 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7715 (t70) REVERT: A 847 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: A 966 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8904 (t0) outliers start: 41 outliers final: 29 residues processed: 107 average time/residue: 0.2581 time to fit residues: 43.7070 Evaluate side-chains 105 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 643 SER 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 B residue 828 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 34 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** 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 = 0.3696 r_free = 0.3696 target = 0.061013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046743 restraints weight = 245119.928| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.32 r_work: 0.3056 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 16748 Z= 0.169 Angle : 0.493 10.126 22795 Z= 0.244 Chirality : 0.037 0.141 2419 Planarity : 0.003 0.038 2926 Dihedral : 6.641 77.350 2289 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.19 % Rotamer: Outliers : 2.62 % Allowed : 19.58 % Favored : 77.80 % 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: 0.94 (0.20), residues: 1975 helix: 2.13 (0.16), residues: 1029 sheet: -1.73 (0.30), residues: 277 loop : -0.67 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 554 TYR 0.013 0.001 TYR B 335 PHE 0.009 0.001 PHE A 222 TRP 0.010 0.001 TRP B 290 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00408 (16744) covalent geometry : angle 0.49328 (22793) SS BOND : bond 0.00102 ( 1) SS BOND : angle 0.36650 ( 2) hydrogen bonds : bond 0.03970 ( 820) hydrogen bonds : angle 4.19302 ( 2376) Misc. bond : bond 0.13159 ( 3) *********************** 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 **************************** Evaluate side-chains 114 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 69 time to evaluate : 0.825 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: B 232 MET cc_start: 0.7459 (ttp) cc_final: 0.7220 (ttp) REVERT: B 299 TYR cc_start: 0.8315 (m-80) cc_final: 0.8101 (m-10) REVERT: B 343 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7567 (tp) REVERT: B 511 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: B 548 MET cc_start: 0.8455 (ttp) cc_final: 0.8175 (ttp) REVERT: B 583 MET cc_start: 0.7206 (ptm) cc_final: 0.6840 (ptm) REVERT: B 673 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: B 697 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8609 (t0) REVERT: A 200 MET cc_start: 0.8645 (mmm) cc_final: 0.8011 (mmt) REVERT: A 227 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7675 (t70) REVERT: A 847 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7968 (pp20) REVERT: A 966 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8926 (t0) outliers start: 45 outliers final: 33 residues processed: 111 average time/residue: 0.2566 time to fit residues: 45.2475 Evaluate side-chains 108 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 335 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 697 ASN 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 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 154 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.061436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047416 restraints weight = 246386.804| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.33 r_work: 0.3089 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 16748 Z= 0.119 Angle : 0.469 8.673 22795 Z= 0.231 Chirality : 0.036 0.141 2419 Planarity : 0.003 0.036 2926 Dihedral : 6.350 77.161 2283 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 2.27 % Allowed : 20.05 % Favored : 77.68 % 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: 1.11 (0.20), residues: 1975 helix: 2.30 (0.16), residues: 1023 sheet: -1.69 (0.31), residues: 275 loop : -0.59 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 305 TYR 0.013 0.001 TYR B 335 PHE 0.008 0.001 PHE A 222 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.000 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00296 (16744) covalent geometry : angle 0.46888 (22793) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.34574 ( 2) hydrogen bonds : bond 0.03712 ( 820) hydrogen bonds : angle 4.04876 ( 2376) Misc. bond : bond 0.10673 ( 3) *********************** 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 **************************** Evaluate side-chains 108 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 69 time to evaluate : 0.869 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: B 232 MET cc_start: 0.7462 (ttp) cc_final: 0.7194 (ttp) REVERT: B 299 TYR cc_start: 0.8345 (m-80) cc_final: 0.8128 (m-10) REVERT: B 511 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: B 548 MET cc_start: 0.8434 (ttp) cc_final: 0.8141 (ttp) REVERT: B 583 MET cc_start: 0.7189 (ptm) cc_final: 0.6785 (ptm) REVERT: B 673 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: B 697 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8570 (t0) REVERT: A 227 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7747 (t70) REVERT: A 847 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: A 966 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8903 (t0) outliers start: 39 outliers final: 30 residues processed: 104 average time/residue: 0.2528 time to fit residues: 41.4235 Evaluate side-chains 105 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 THR 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 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 603 GLN ** A1248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3687 r_free = 0.3687 target = 0.060473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046476 restraints weight = 247940.880| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.30 r_work: 0.3052 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.223 16748 Z= 0.261 Angle : 0.533 9.673 22795 Z= 0.268 Chirality : 0.038 0.140 2419 Planarity : 0.004 0.038 2926 Dihedral : 6.554 79.241 2283 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.38 % Rotamer: Outliers : 2.68 % Allowed : 19.70 % Favored : 77.62 % 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: 0.82 (0.20), residues: 1975 helix: 2.03 (0.16), residues: 1029 sheet: -1.78 (0.31), residues: 272 loop : -0.73 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1225 TYR 0.013 0.001 TYR B 335 PHE 0.012 0.001 PHE A 222 TRP 0.012 0.001 TRP A 290 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00620 (16744) covalent geometry : angle 0.53331 (22793) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.46872 ( 2) hydrogen bonds : bond 0.04255 ( 820) hydrogen bonds : angle 4.30933 ( 2376) Misc. bond : bond 0.13100 ( 3) *********************** 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 **************************** Evaluate side-chains 115 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 69 time to evaluate : 0.928 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: B 299 TYR cc_start: 0.8366 (m-80) cc_final: 0.8165 (m-10) REVERT: B 347 MET cc_start: 0.6241 (mmt) cc_final: 0.6014 (mmt) REVERT: B 511 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: B 548 MET cc_start: 0.8506 (ttp) cc_final: 0.8242 (ttp) REVERT: B 562 MET cc_start: 0.8882 (mmm) cc_final: 0.8144 (mmm) REVERT: B 583 MET cc_start: 0.7273 (ptm) cc_final: 0.6876 (ptm) REVERT: B 618 MET cc_start: 0.7460 (ttt) cc_final: 0.7233 (ttt) REVERT: B 673 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: B 675 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6171 (pm20) REVERT: B 697 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8534 (t0) REVERT: A 200 MET cc_start: 0.8641 (mmm) cc_final: 0.8079 (mmt) REVERT: A 227 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7704 (t70) REVERT: A 847 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7980 (pp20) REVERT: A 966 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8972 (t0) outliers start: 46 outliers final: 36 residues processed: 111 average time/residue: 0.2679 time to fit residues: 46.8971 Evaluate side-chains 112 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU 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 697 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.061271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047273 restraints weight = 243696.999| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.33 r_work: 0.3085 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 16748 Z= 0.109 Angle : 0.473 7.727 22795 Z= 0.233 Chirality : 0.036 0.141 2419 Planarity : 0.003 0.036 2926 Dihedral : 6.369 78.802 2283 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.39 % Favored : 96.46 % Rotamer: Outliers : 2.16 % Allowed : 20.16 % Favored : 77.68 % 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: 1.11 (0.20), residues: 1975 helix: 2.30 (0.16), residues: 1022 sheet: -1.73 (0.31), residues: 275 loop : -0.58 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 334 TYR 0.021 0.001 TYR B 335 PHE 0.008 0.001 PHE A 222 TRP 0.010 0.001 TRP B 290 HIS 0.002 0.000 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00273 (16744) covalent geometry : angle 0.47338 (22793) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.34977 ( 2) hydrogen bonds : bond 0.03705 ( 820) hydrogen bonds : angle 4.01998 ( 2376) Misc. bond : bond 0.09383 ( 3) *********************** 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 **************************** Evaluate side-chains 109 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.903 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: B 232 MET cc_start: 0.7473 (ttp) cc_final: 0.7234 (ttp) REVERT: B 299 TYR cc_start: 0.8341 (m-80) cc_final: 0.8134 (m-10) REVERT: B 347 MET cc_start: 0.6266 (mmt) cc_final: 0.6023 (mmt) REVERT: B 511 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: B 548 MET cc_start: 0.8464 (ttp) cc_final: 0.8210 (ttp) REVERT: B 562 MET cc_start: 0.8875 (mmm) cc_final: 0.8122 (mmm) REVERT: B 583 MET cc_start: 0.7262 (ptm) cc_final: 0.6847 (ptm) REVERT: B 618 MET cc_start: 0.7466 (ttt) cc_final: 0.7232 (ttt) REVERT: B 673 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: B 697 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8577 (t0) REVERT: A 33 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 227 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7764 (t70) REVERT: A 847 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: A 966 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8913 (t0) outliers start: 37 outliers final: 30 residues processed: 105 average time/residue: 0.2783 time to fit residues: 46.1702 Evaluate side-chains 107 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER 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 Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 193 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 118 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.061273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.047128 restraints weight = 247394.970| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.38 r_work: 0.3084 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 16748 Z= 0.110 Angle : 0.468 7.126 22795 Z= 0.230 Chirality : 0.036 0.140 2419 Planarity : 0.003 0.037 2926 Dihedral : 6.271 78.238 2283 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.41 % Rotamer: Outliers : 2.33 % Allowed : 19.99 % Favored : 77.68 % 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: 1.17 (0.20), residues: 1975 helix: 2.34 (0.16), residues: 1022 sheet: -1.69 (0.31), residues: 275 loop : -0.54 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 753 TYR 0.018 0.001 TYR B 335 PHE 0.008 0.001 PHE A 222 TRP 0.010 0.001 TRP B 290 HIS 0.003 0.000 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00273 (16744) covalent geometry : angle 0.46799 (22793) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.29960 ( 2) hydrogen bonds : bond 0.03609 ( 820) hydrogen bonds : angle 3.97928 ( 2376) Misc. bond : bond 0.09044 ( 3) ********************** 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 **************************** Evaluate side-chains 110 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 0.983 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: B 232 MET cc_start: 0.7496 (ttp) cc_final: 0.7259 (ttp) REVERT: B 299 TYR cc_start: 0.8337 (m-80) cc_final: 0.8135 (m-10) REVERT: B 347 MET cc_start: 0.6266 (mmt) cc_final: 0.6023 (mmt) REVERT: B 511 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: B 548 MET cc_start: 0.8465 (ttp) cc_final: 0.8219 (ttp) REVERT: B 562 MET cc_start: 0.8868 (mmm) cc_final: 0.8123 (mmm) REVERT: B 583 MET cc_start: 0.7305 (ptm) cc_final: 0.6886 (ptm) REVERT: B 618 MET cc_start: 0.7540 (ttt) cc_final: 0.7301 (ttt) REVERT: B 675 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: B 697 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8593 (t0) REVERT: A 33 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: A 227 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7757 (t70) REVERT: A 847 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: A 966 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8904 (t0) outliers start: 40 outliers final: 31 residues processed: 106 average time/residue: 0.2436 time to fit residues: 40.2928 Evaluate side-chains 107 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 657 HIS Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1230 SER 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 Chi-restraints excluded: chain A residue 1442 VAL 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 45 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 152 optimal weight: 0.0060 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.060956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.046985 restraints weight = 245670.865| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.32 r_work: 0.3077 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 16748 Z= 0.145 Angle : 0.480 7.219 22795 Z= 0.236 Chirality : 0.036 0.141 2419 Planarity : 0.003 0.038 2926 Dihedral : 6.200 78.168 2280 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.90 % Favored : 95.95 % Rotamer: Outliers : 2.27 % Allowed : 19.87 % Favored : 77.86 % 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: 1.15 (0.20), residues: 1975 helix: 2.31 (0.16), residues: 1029 sheet: -1.66 (0.31), residues: 271 loop : -0.57 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 334 TYR 0.017 0.001 TYR B 335 PHE 0.009 0.001 PHE A 222 TRP 0.009 0.001 TRP B 290 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00354 (16744) covalent geometry : angle 0.47984 (22793) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.34498 ( 2) hydrogen bonds : bond 0.03710 ( 820) hydrogen bonds : angle 4.01647 ( 2376) Misc. bond : bond 0.09619 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7115.94 seconds wall clock time: 121 minutes 28.93 seconds (7288.93 seconds total)