Starting phenix.real_space_refine on Thu Mar 5 04:26:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zju_74342/03_2026/9zju_74342.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zju_74342/03_2026/9zju_74342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zju_74342/03_2026/9zju_74342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zju_74342/03_2026/9zju_74342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zju_74342/03_2026/9zju_74342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zju_74342/03_2026/9zju_74342.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 11872 2.51 5 N 3048 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9181 Classifications: {'peptide': 1121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1081} Chain breaks: 11 Chain: "B" Number of atoms: 9181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9181 Classifications: {'peptide': 1121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1081} Chain breaks: 11 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.23 Number of scatterers: 18426 At special positions: 0 Unit cell: (110.88, 128.04, 182.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 82 16.00 P 6 15.00 Mg 2 11.99 O 3416 8.00 N 3048 7.00 C 11872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 831.2 milliseconds 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4288 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 12 sheets defined 61.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 389 through 400 removed outlier: 4.068A pdb=" N LYS A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.735A pdb=" N LYS A 426 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 428 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP A 429 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 430 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 431 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 432 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.584A pdb=" N ALA A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.596A pdb=" N GLU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.603A pdb=" N GLY A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.720A pdb=" N PHE A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 804 through 821 removed outlier: 4.355A pdb=" N TYR A 808 " --> pdb=" O GLN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 858 through 876 removed outlier: 3.805A pdb=" N GLU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 881 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 893 through 906 removed outlier: 3.540A pdb=" N ILE A 897 " --> pdb=" O ASN A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 928 Processing helix chain 'A' and resid 935 through 942 Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 962 through 965 removed outlier: 3.677A pdb=" N THR A 965 " --> pdb=" O THR A 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 985 through 1001 Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1014 through 1018 removed outlier: 3.716A pdb=" N PHE A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1036 Processing helix chain 'A' and resid 1052 through 1062 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 4.035A pdb=" N VAL A1067 " --> pdb=" O GLY A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 removed outlier: 3.696A pdb=" N CYS A1085 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1113 Processing helix chain 'A' and resid 1116 through 1139 removed outlier: 3.559A pdb=" N SER A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A1130 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1142 No H-bonds generated for 'chain 'A' and resid 1140 through 1142' Processing helix chain 'A' and resid 1145 through 1173 Processing helix chain 'A' and resid 1194 through 1212 removed outlier: 3.601A pdb=" N GLN A1198 " --> pdb=" O ILE A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 6.209A pdb=" N PHE A1216 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A1218 " --> pdb=" O PRO A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1244 through 1253 removed outlier: 3.730A pdb=" N TYR A1253 " --> pdb=" O ALA A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1259 Processing helix chain 'A' and resid 1260 through 1277 Processing helix chain 'A' and resid 1286 through 1308 Processing helix chain 'A' and resid 1325 through 1339 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1373 removed outlier: 3.950A pdb=" N ASN A1367 " --> pdb=" O LYS A1363 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A1368 " --> pdb=" O CYS A1364 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A1369 " --> pdb=" O ILE A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1399 Processing helix chain 'A' and resid 1407 through 1423 Proline residue: A1421 - end of helix Processing helix chain 'A' and resid 1429 through 1439 Processing helix chain 'A' and resid 1448 through 1451 removed outlier: 3.701A pdb=" N GLU A1451 " --> pdb=" O GLN A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1448 through 1451' Processing helix chain 'A' and resid 1452 through 1468 Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1495 through 1502 removed outlier: 3.838A pdb=" N PHE A1502 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1525 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.667A pdb=" N LYS B 426 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 428 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 465 through 470 removed outlier: 4.265A pdb=" N TYR B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 470 " --> pdb=" O PRO B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 470' Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.553A pdb=" N GLU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 610 through 620 Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 668 through 686 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.825A pdb=" N PHE B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 804 through 821 removed outlier: 4.265A pdb=" N TYR B 808 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 809 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 858 through 876 removed outlier: 3.592A pdb=" N GLU B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 881 Processing helix chain 'B' and resid 882 through 890 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 912 through 928 Processing helix chain 'B' and resid 935 through 943 Processing helix chain 'B' and resid 956 through 961 removed outlier: 3.559A pdb=" N GLY B 961 " --> pdb=" O GLU B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 removed outlier: 3.509A pdb=" N THR B 965 " --> pdb=" O THR B 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 985 through 1001 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1014 through 1018 removed outlier: 3.593A pdb=" N PHE B1017 " --> pdb=" O GLU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1036 Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1063 through 1078 removed outlier: 3.965A pdb=" N VAL B1067 " --> pdb=" O GLY B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1095 removed outlier: 3.638A pdb=" N CYS B1085 " --> pdb=" O ASN B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1113 Processing helix chain 'B' and resid 1116 through 1139 removed outlier: 3.598A pdb=" N LYS B1130 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B1131 " --> pdb=" O TYR B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1173 removed outlier: 3.551A pdb=" N ARG B1173 " --> pdb=" O GLN B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1212 Processing helix chain 'B' and resid 1213 through 1218 removed outlier: 6.216A pdb=" N PHE B1216 " --> pdb=" O LEU B1213 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B1218 " --> pdb=" O PRO B1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1233 Processing helix chain 'B' and resid 1244 through 1253 removed outlier: 3.667A pdb=" N LYS B1251 " --> pdb=" O LYS B1247 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B1252 " --> pdb=" O LEU B1248 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR B1253 " --> pdb=" O ALA B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1259 removed outlier: 3.682A pdb=" N THR B1258 " --> pdb=" O ILE B1254 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS B1259 " --> pdb=" O PRO B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1276 Processing helix chain 'B' and resid 1286 through 1308 removed outlier: 3.679A pdb=" N ASP B1305 " --> pdb=" O LYS B1301 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B1306 " --> pdb=" O LYS B1302 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1339 Processing helix chain 'B' and resid 1343 through 1348 Processing helix chain 'B' and resid 1349 through 1353 removed outlier: 3.615A pdb=" N ILE B1352 " --> pdb=" O GLU B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1354 through 1375 removed outlier: 3.684A pdb=" N CYS B1364 " --> pdb=" O SER B1360 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1399 removed outlier: 3.750A pdb=" N LYS B1385 " --> pdb=" O GLN B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1423 removed outlier: 3.612A pdb=" N LEU B1411 " --> pdb=" O PRO B1407 " (cutoff:3.500A) Proline residue: B1421 - end of helix Processing helix chain 'B' and resid 1429 through 1439 Processing helix chain 'B' and resid 1448 through 1451 Processing helix chain 'B' and resid 1452 through 1468 Processing helix chain 'B' and resid 1487 through 1490 Processing helix chain 'B' and resid 1495 through 1501 Processing helix chain 'B' and resid 1520 through 1525 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.153A pdb=" N ASN A 462 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE A 493 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N HIS A 464 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR A 413 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LEU A 440 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 415 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 412 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 542 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 414 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU A 544 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 416 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A 574 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 541 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 576 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 543 " --> pdb=" O ILE A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.012A pdb=" N ARG A 759 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU A 797 " --> pdb=" O ARG A 759 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 761 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASP A 799 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 763 " --> pdb=" O ASP A 799 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 794 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 833 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 796 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N CYS A 835 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 798 " --> pdb=" O CYS A 835 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ARG A 837 " --> pdb=" O VAL A 798 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS A 731 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN A 834 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 733 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N MET A 836 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A 735 " --> pdb=" O MET A 836 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE A 851 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS A 734 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 853 " --> pdb=" O HIS A 734 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR A 736 " --> pdb=" O VAL A 853 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 933 through 934 removed outlier: 3.550A pdb=" N TYR A 978 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1280 Processing sheet with id=AA6, first strand: chain 'A' and resid 1492 through 1494 removed outlier: 3.524A pdb=" N PHE A1481 " --> pdb=" O PHE A1576 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A1573 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP A1585 " --> pdb=" O TYR A1573 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A1575 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA A1583 " --> pdb=" O GLY A1575 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER A1577 " --> pdb=" O PRO A1581 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA A1583 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A1554 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASP A1585 " --> pdb=" O THR A1554 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1535 " --> pdb=" O CYS A1538 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU A1542 " --> pdb=" O GLN A1531 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLN A1531 " --> pdb=" O GLU A1542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 462 through 464 removed outlier: 3.534A pdb=" N SER B 490 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR B 413 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 439 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 415 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU B 441 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR B 417 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN B 412 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL B 542 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE B 414 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU B 544 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 416 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 574 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 541 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE B 576 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE B 543 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AA9, first strand: chain 'B' and resid 652 through 655 removed outlier: 4.152A pdb=" N CYS B 760 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG B 759 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU B 797 " --> pdb=" O ARG B 759 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 761 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ASP B 799 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU B 763 " --> pdb=" O ASP B 799 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 794 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU B 833 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 796 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N CYS B 835 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 798 " --> pdb=" O CYS B 835 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ARG B 837 " --> pdb=" O VAL B 798 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 731 " --> pdb=" O ILE B 832 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN B 834 " --> pdb=" O LYS B 731 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE B 733 " --> pdb=" O ASN B 834 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET B 836 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 735 " --> pdb=" O MET B 836 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N ILE B 851 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS B 734 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B 853 " --> pdb=" O HIS B 734 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR B 736 " --> pdb=" O VAL B 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 933 through 934 Processing sheet with id=AB2, first strand: chain 'B' and resid 1278 through 1280 Processing sheet with id=AB3, first strand: chain 'B' and resid 1492 through 1494 removed outlier: 5.854A pdb=" N LEU B1574 " --> pdb=" O LEU B1483 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR B1573 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP B1585 " --> pdb=" O TYR B1573 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B1575 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA B1583 " --> pdb=" O GLY B1575 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER B1577 " --> pdb=" O PRO B1581 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B1554 " --> pdb=" O PRO B1581 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1583 " --> pdb=" O THR B1554 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B1541 " --> pdb=" O ILE B1551 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU B1542 " --> pdb=" O GLN B1531 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLN B1531 " --> pdb=" O GLU B1542 " (cutoff:3.500A) 934 hydrogen bonds defined for protein. 2718 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: 3.50 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5821 1.34 - 1.46: 2930 1.46 - 1.57: 9935 1.57 - 1.69: 10 1.69 - 1.81: 118 Bond restraints: 18814 Sorted by residual: bond pdb=" N ILE A1238 " pdb=" CA ILE A1238 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.69e+01 bond pdb=" N ILE A1365 " pdb=" CA ILE A1365 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.21e-02 6.83e+03 1.15e+01 bond pdb=" N VAL A1366 " pdb=" CA VAL A1366 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.06e+01 bond pdb=" N VAL B1232 " pdb=" CA VAL B1232 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.06e-02 8.90e+03 1.03e+01 bond pdb=" N TYR A1253 " pdb=" CA TYR A1253 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.10e-02 8.26e+03 9.18e+00 ... (remaining 18809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 24759 1.52 - 3.03: 496 3.03 - 4.55: 77 4.55 - 6.06: 27 6.06 - 7.58: 5 Bond angle restraints: 25364 Sorted by residual: angle pdb=" CA GLY B1240 " pdb=" C GLY B1240 " pdb=" O GLY B1240 " ideal model delta sigma weight residual 122.29 118.38 3.91 8.10e-01 1.52e+00 2.33e+01 angle pdb=" N TYR A1369 " pdb=" CA TYR A1369 " pdb=" CB TYR A1369 " ideal model delta sigma weight residual 110.30 117.19 -6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" N GLU A1374 " pdb=" CA GLU A1374 " pdb=" C GLU A1374 " ideal model delta sigma weight residual 112.68 106.82 5.86 1.33e+00 5.65e-01 1.94e+01 angle pdb=" C GLU A1374 " pdb=" N GLN A1375 " pdb=" CA GLN A1375 " ideal model delta sigma weight residual 120.95 113.42 7.53 1.78e+00 3.16e-01 1.79e+01 angle pdb=" CA LEU B 485 " pdb=" C LEU B 485 " pdb=" O LEU B 485 " ideal model delta sigma weight residual 121.56 117.23 4.33 1.09e+00 8.42e-01 1.58e+01 ... (remaining 25359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9687 17.82 - 35.63: 1235 35.63 - 53.45: 377 53.45 - 71.27: 98 71.27 - 89.09: 27 Dihedral angle restraints: 11424 sinusoidal: 4818 harmonic: 6606 Sorted by residual: dihedral pdb=" CG ARG A 846 " pdb=" CD ARG A 846 " pdb=" NE ARG A 846 " pdb=" CZ ARG A 846 " ideal model delta sinusoidal sigma weight residual 90.00 41.03 48.97 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA ASN A1392 " pdb=" CB ASN A1392 " pdb=" CG ASN A1392 " pdb=" OD1 ASN A1392 " ideal model delta sinusoidal sigma weight residual 120.00 -165.94 -74.06 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU B1289 " pdb=" CG GLU B1289 " pdb=" CD GLU B1289 " pdb=" OE1 GLU B1289 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 11421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2067 0.042 - 0.083: 507 0.083 - 0.125: 187 0.125 - 0.166: 14 0.166 - 0.208: 5 Chirality restraints: 2780 Sorted by residual: chirality pdb=" CB ILE A1394 " pdb=" CA ILE A1394 " pdb=" CG1 ILE A1394 " pdb=" CG2 ILE A1394 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A1238 " pdb=" N ILE A1238 " pdb=" C ILE A1238 " pdb=" CB ILE A1238 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA ILE B1238 " pdb=" N ILE B1238 " pdb=" C ILE B1238 " pdb=" CB ILE B1238 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 2777 not shown) Planarity restraints: 3200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A1364 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C CYS A1364 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS A1364 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A1365 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1420 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A1421 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1421 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1421 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1214 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A1215 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A1215 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1215 " -0.022 5.00e-02 4.00e+02 ... (remaining 3197 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 128 2.60 - 3.17: 14495 3.17 - 3.75: 27922 3.75 - 4.32: 40581 4.32 - 4.90: 66814 Nonbonded interactions: 149940 Sorted by model distance: nonbonded pdb=" OG1 THR B 744 " pdb="MG MG B1602 " model vdw 2.024 2.170 nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1602 " model vdw 2.085 2.170 nonbonded pdb=" O2B ATP B1601 " pdb="MG MG B1602 " model vdw 2.208 2.170 nonbonded pdb=" OH TYR A 486 " pdb=" O ILE A 533 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP B1154 " pdb=" OH TYR B1253 " model vdw 2.237 3.040 ... (remaining 149935 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 12.690 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.010 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.003 0.068 18814 Z= 0.215 Angle : 0.540 7.577 25364 Z= 0.341 Chirality : 0.042 0.208 2780 Planarity : 0.004 0.054 3200 Dihedral : 18.061 89.087 7136 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.18 % Rotamer: Outliers : 1.91 % Allowed : 22.90 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2194 helix: 1.25 (0.15), residues: 1182 sheet: 0.95 (0.35), residues: 212 loop : 0.18 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 788 TYR 0.020 0.001 TYR A1468 PHE 0.017 0.001 PHE B1216 TRP 0.012 0.001 TRP A 586 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00336 (18814) covalent geometry : angle 0.54031 (25364) hydrogen bonds : bond 0.20289 ( 934) hydrogen bonds : angle 6.38086 ( 2718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 419 LYS cc_start: 0.7559 (tptt) cc_final: 0.6749 (mttp) REVERT: A 499 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6680 (p0) REVERT: A 516 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 536 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7764 (ptt-90) REVERT: A 558 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: A 712 GLU cc_start: 0.7905 (pt0) cc_final: 0.7567 (tt0) REVERT: A 728 THR cc_start: 0.6581 (p) cc_final: 0.6293 (t) REVERT: A 866 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8149 (tp30) REVERT: A 998 LYS cc_start: 0.7992 (tttt) cc_final: 0.7397 (mttt) REVERT: A 1461 LYS cc_start: 0.6246 (mmmt) cc_final: 0.5629 (mptt) REVERT: A 1524 GLN cc_start: 0.6929 (mt0) cc_final: 0.6004 (tp-100) REVERT: B 603 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 728 THR cc_start: 0.6233 (OUTLIER) cc_final: 0.6013 (p) REVERT: B 788 ARG cc_start: 0.6983 (ttm110) cc_final: 0.6228 (mtp180) REVERT: B 842 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7686 (mp0) REVERT: B 1288 GLU cc_start: 0.4585 (mm-30) cc_final: 0.4179 (mm-30) REVERT: B 1293 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6156 (ttt-90) outliers start: 39 outliers final: 20 residues processed: 192 average time/residue: 0.6858 time to fit residues: 146.1328 Evaluate side-chains 174 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1293 ARG Chi-restraints excluded: chain B residue 1375 GLN Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1436 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0050 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.9554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1049 ASN A1252 ASN B 449 ASN B 484 ASN B1076 HIS B1212 GLN B1219 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122858 restraints weight = 23140.022| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.31 r_work: 0.3332 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18814 Z= 0.118 Angle : 0.467 7.842 25364 Z= 0.250 Chirality : 0.041 0.212 2780 Planarity : 0.004 0.040 3200 Dihedral : 7.729 76.392 2526 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.42 % Allowed : 20.40 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.18), residues: 2194 helix: 1.84 (0.15), residues: 1240 sheet: 0.61 (0.35), residues: 240 loop : 0.06 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 788 TYR 0.018 0.001 TYR B1093 PHE 0.017 0.001 PHE B1216 TRP 0.011 0.001 TRP B 586 HIS 0.008 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00263 (18814) covalent geometry : angle 0.46720 (25364) hydrogen bonds : bond 0.04647 ( 934) hydrogen bonds : angle 4.55460 ( 2718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 166 time to evaluate : 0.723 Fit side-chains REVERT: A 419 LYS cc_start: 0.7463 (tptt) cc_final: 0.6686 (mttp) REVERT: A 516 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: A 522 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7274 (tmt170) REVERT: A 536 ARG cc_start: 0.8346 (ttp-170) cc_final: 0.7848 (ptt-90) REVERT: A 551 ASP cc_start: 0.8026 (t0) cc_final: 0.7792 (t0) REVERT: A 634 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7213 (m) REVERT: A 712 GLU cc_start: 0.7902 (pt0) cc_final: 0.7541 (tt0) REVERT: A 728 THR cc_start: 0.6600 (OUTLIER) cc_final: 0.6308 (t) REVERT: A 866 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8134 (tp30) REVERT: A 998 LYS cc_start: 0.7936 (tttt) cc_final: 0.7361 (mttt) REVERT: A 1349 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: A 1453 MET cc_start: 0.3997 (OUTLIER) cc_final: 0.3702 (tpt) REVERT: A 1461 LYS cc_start: 0.6217 (mmmt) cc_final: 0.5599 (mptt) REVERT: A 1490 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4642 (mt-10) REVERT: A 1521 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5857 (pm20) REVERT: A 1524 GLN cc_start: 0.6768 (mt0) cc_final: 0.6192 (mm-40) REVERT: B 453 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6916 (tmtp) REVERT: B 522 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8249 (tpt90) REVERT: B 612 GLU cc_start: 0.7055 (mp0) cc_final: 0.6810 (mp0) REVERT: B 613 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7451 (mt-10) REVERT: B 728 THR cc_start: 0.6179 (OUTLIER) cc_final: 0.5976 (p) REVERT: B 827 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7417 (mtpp) REVERT: B 842 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7703 (mp0) REVERT: B 955 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6212 (mtmt) REVERT: B 1168 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6736 (tp40) REVERT: B 1215 PRO cc_start: 0.7121 (Cg_exo) cc_final: 0.6909 (Cg_endo) REVERT: B 1302 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.5686 (mptt) REVERT: B 1453 MET cc_start: 0.4405 (mmm) cc_final: 0.4122 (mmm) outliers start: 70 outliers final: 25 residues processed: 222 average time/residue: 0.6062 time to fit residues: 150.2565 Evaluate side-chains 189 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1453 MET Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1521 GLU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 955 LYS Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1302 LYS Chi-restraints excluded: chain B residue 1437 LEU Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 116 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 chunk 206 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1049 ASN B 449 ASN B1076 HIS B1167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119856 restraints weight = 23831.966| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.06 r_work: 0.3359 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18814 Z= 0.102 Angle : 0.436 8.020 25364 Z= 0.230 Chirality : 0.041 0.196 2780 Planarity : 0.003 0.041 3200 Dihedral : 6.904 75.589 2493 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.28 % Allowed : 21.09 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.18), residues: 2194 helix: 2.17 (0.15), residues: 1238 sheet: 0.54 (0.35), residues: 236 loop : 0.10 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1173 TYR 0.016 0.001 TYR B1093 PHE 0.014 0.001 PHE B1216 TRP 0.009 0.001 TRP A 586 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00225 (18814) covalent geometry : angle 0.43620 (25364) hydrogen bonds : bond 0.03783 ( 934) hydrogen bonds : angle 4.24552 ( 2718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 169 time to evaluate : 0.574 Fit side-chains REVERT: A 419 LYS cc_start: 0.7457 (tptt) cc_final: 0.6684 (mttp) REVERT: A 514 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6060 (mp10) REVERT: A 536 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.7897 (ptt-90) REVERT: A 551 ASP cc_start: 0.7955 (t0) cc_final: 0.7692 (t0) REVERT: A 634 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.7224 (m) REVERT: A 712 GLU cc_start: 0.7930 (pt0) cc_final: 0.7572 (tt0) REVERT: A 728 THR cc_start: 0.6558 (p) cc_final: 0.6262 (t) REVERT: A 772 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: A 788 ARG cc_start: 0.6565 (mtt90) cc_final: 0.5857 (mpt-90) REVERT: A 826 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6880 (pt0) REVERT: A 866 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8147 (tp30) REVERT: A 911 PHE cc_start: 0.7786 (m-80) cc_final: 0.7177 (m-80) REVERT: A 998 LYS cc_start: 0.7924 (tttt) cc_final: 0.7362 (mttt) REVERT: A 1349 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 1453 MET cc_start: 0.4033 (OUTLIER) cc_final: 0.3770 (tpt) REVERT: A 1461 LYS cc_start: 0.6174 (mmmt) cc_final: 0.5640 (mptt) REVERT: A 1490 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4670 (mt-10) REVERT: A 1524 GLN cc_start: 0.6701 (mt0) cc_final: 0.6064 (tp-100) REVERT: B 453 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6969 (tmtp) REVERT: B 522 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8223 (tpt90) REVERT: B 603 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 612 GLU cc_start: 0.7051 (mp0) cc_final: 0.6779 (mp0) REVERT: B 613 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 827 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7505 (mtpp) REVERT: B 842 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7678 (mp0) REVERT: B 955 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.6227 (mtmt) REVERT: B 1168 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6780 (tp40) REVERT: B 1173 ARG cc_start: 0.6456 (ttt-90) cc_final: 0.5908 (ttp80) REVERT: B 1254 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7544 (mp) REVERT: B 1302 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.5792 (mptt) REVERT: B 1406 LYS cc_start: 0.4274 (OUTLIER) cc_final: 0.3797 (mtpt) REVERT: B 1476 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6206 (pp30) outliers start: 67 outliers final: 28 residues processed: 222 average time/residue: 0.6501 time to fit residues: 160.2625 Evaluate side-chains 187 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1453 MET Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1478 ILE Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 955 LYS Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1302 LYS Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN B1076 HIS B1230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.169274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119522 restraints weight = 23868.927| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.05 r_work: 0.3355 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18814 Z= 0.105 Angle : 0.436 8.173 25364 Z= 0.230 Chirality : 0.041 0.195 2780 Planarity : 0.003 0.048 3200 Dihedral : 6.751 75.502 2488 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.57 % Allowed : 20.84 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.18), residues: 2194 helix: 2.25 (0.15), residues: 1240 sheet: 0.51 (0.35), residues: 236 loop : 0.12 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 788 TYR 0.017 0.001 TYR B1093 PHE 0.017 0.001 PHE B1216 TRP 0.009 0.001 TRP A 586 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00237 (18814) covalent geometry : angle 0.43624 (25364) hydrogen bonds : bond 0.03694 ( 934) hydrogen bonds : angle 4.17442 ( 2718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 166 time to evaluate : 0.530 Fit side-chains REVERT: A 419 LYS cc_start: 0.7431 (tptt) cc_final: 0.6679 (mttp) REVERT: A 522 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7164 (tmt170) REVERT: A 536 ARG cc_start: 0.8382 (ttp-170) cc_final: 0.7901 (ptt-90) REVERT: A 712 GLU cc_start: 0.7922 (pt0) cc_final: 0.7563 (tt0) REVERT: A 728 THR cc_start: 0.6527 (p) cc_final: 0.6217 (t) REVERT: A 772 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 788 ARG cc_start: 0.6557 (mtt90) cc_final: 0.5885 (mpt-90) REVERT: A 866 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8182 (tp30) REVERT: A 906 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7001 (pttp) REVERT: A 998 LYS cc_start: 0.7937 (tttt) cc_final: 0.7375 (mttt) REVERT: A 1349 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: A 1448 GLN cc_start: 0.3571 (OUTLIER) cc_final: 0.3299 (tm-30) REVERT: A 1453 MET cc_start: 0.4047 (OUTLIER) cc_final: 0.3803 (tpt) REVERT: A 1461 LYS cc_start: 0.6189 (mmmt) cc_final: 0.5664 (mptt) REVERT: A 1490 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.4711 (mt-10) REVERT: A 1524 GLN cc_start: 0.6717 (mt0) cc_final: 0.6037 (tp-100) REVERT: B 453 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6980 (tmtp) REVERT: B 522 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8236 (tpt90) REVERT: B 603 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 842 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7690 (mp0) REVERT: B 1168 GLN cc_start: 0.7307 (tm-30) cc_final: 0.6796 (tp-100) REVERT: B 1173 ARG cc_start: 0.6386 (ttt-90) cc_final: 0.5854 (ttp80) REVERT: B 1190 ASP cc_start: 0.7035 (m-30) cc_final: 0.6772 (m-30) REVERT: B 1302 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.5737 (mptt) REVERT: B 1343 LYS cc_start: 0.6393 (pttt) cc_final: 0.6093 (pttp) REVERT: B 1406 LYS cc_start: 0.4380 (OUTLIER) cc_final: 0.3859 (mtpt) REVERT: B 1476 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6160 (pp30) outliers start: 73 outliers final: 30 residues processed: 224 average time/residue: 0.6591 time to fit residues: 163.1151 Evaluate side-chains 193 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1448 GLN Chi-restraints excluded: chain A residue 1453 MET Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1478 ILE Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1302 LYS Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN B1076 HIS ** B1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1470 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.169332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119632 restraints weight = 23769.410| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.04 r_work: 0.3347 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18814 Z= 0.104 Angle : 0.433 8.107 25364 Z= 0.227 Chirality : 0.040 0.203 2780 Planarity : 0.003 0.041 3200 Dihedral : 6.449 76.418 2483 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.47 % Allowed : 20.69 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.18), residues: 2194 helix: 2.29 (0.15), residues: 1240 sheet: 0.51 (0.35), residues: 236 loop : 0.14 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 788 TYR 0.017 0.001 TYR B1093 PHE 0.014 0.001 PHE B1216 TRP 0.010 0.001 TRP A 586 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00237 (18814) covalent geometry : angle 0.43296 (25364) hydrogen bonds : bond 0.03582 ( 934) hydrogen bonds : angle 4.11715 ( 2718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 0.771 Fit side-chains REVERT: A 419 LYS cc_start: 0.7416 (tptt) cc_final: 0.6656 (mttp) REVERT: A 522 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7156 (tmt170) REVERT: A 536 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.7890 (ptt-90) REVERT: A 551 ASP cc_start: 0.7974 (t0) cc_final: 0.7645 (t0) REVERT: A 558 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: A 634 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7240 (m) REVERT: A 712 GLU cc_start: 0.7920 (pt0) cc_final: 0.7565 (tt0) REVERT: A 728 THR cc_start: 0.6505 (p) cc_final: 0.6187 (t) REVERT: A 772 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 788 ARG cc_start: 0.6573 (mtt90) cc_final: 0.5774 (mpt-90) REVERT: A 866 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8166 (tp30) REVERT: A 998 LYS cc_start: 0.7920 (tttt) cc_final: 0.7354 (mttt) REVERT: A 1172 ASP cc_start: 0.6152 (m-30) cc_final: 0.5934 (m-30) REVERT: A 1349 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: A 1427 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: A 1448 GLN cc_start: 0.3578 (OUTLIER) cc_final: 0.3307 (tm-30) REVERT: A 1453 MET cc_start: 0.3959 (OUTLIER) cc_final: 0.3745 (tpt) REVERT: A 1461 LYS cc_start: 0.6144 (mmmt) cc_final: 0.5608 (mptt) REVERT: A 1490 GLU cc_start: 0.5040 (OUTLIER) cc_final: 0.4692 (mt-10) REVERT: A 1524 GLN cc_start: 0.6705 (mt0) cc_final: 0.6034 (tp-100) REVERT: A 1530 LEU cc_start: 0.3747 (OUTLIER) cc_final: 0.3312 (mm) REVERT: B 453 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6974 (tmtp) REVERT: B 522 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8259 (tpt90) REVERT: B 603 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 789 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7217 (mm110) REVERT: B 842 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7680 (mp0) REVERT: B 1168 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6803 (tp-100) REVERT: B 1302 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.5833 (mptt) REVERT: B 1406 LYS cc_start: 0.4606 (OUTLIER) cc_final: 0.4002 (mtpt) REVERT: B 1416 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5229 (ptm160) REVERT: B 1476 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6202 (pp30) outliers start: 71 outliers final: 33 residues processed: 222 average time/residue: 0.6814 time to fit residues: 167.5273 Evaluate side-chains 195 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1427 GLN Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1448 GLN Chi-restraints excluded: chain A residue 1453 MET Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1478 ILE Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1302 LYS Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1416 ARG Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 210 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 123 optimal weight: 0.0170 chunk 195 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN B 449 ASN B1076 HIS ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1470 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.167995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118222 restraints weight = 23653.628| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.03 r_work: 0.3337 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18814 Z= 0.130 Angle : 0.456 8.306 25364 Z= 0.240 Chirality : 0.042 0.243 2780 Planarity : 0.003 0.042 3200 Dihedral : 6.630 74.542 2483 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.82 % Allowed : 20.50 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.18), residues: 2194 helix: 2.22 (0.15), residues: 1240 sheet: 0.43 (0.34), residues: 250 loop : 0.14 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 788 TYR 0.017 0.001 TYR B1093 PHE 0.016 0.001 PHE B1216 TRP 0.011 0.001 TRP A 586 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00308 (18814) covalent geometry : angle 0.45578 (25364) hydrogen bonds : bond 0.03959 ( 934) hydrogen bonds : angle 4.16710 ( 2718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 0.820 Fit side-chains REVERT: A 419 LYS cc_start: 0.7486 (tptt) cc_final: 0.6713 (mttp) REVERT: A 522 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7164 (tmt170) REVERT: A 536 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7901 (ptt-90) REVERT: A 551 ASP cc_start: 0.7982 (t0) cc_final: 0.7634 (t0) REVERT: A 558 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 634 SER cc_start: 0.7618 (OUTLIER) cc_final: 0.7310 (m) REVERT: A 712 GLU cc_start: 0.7962 (pt0) cc_final: 0.7601 (tt0) REVERT: A 772 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 788 ARG cc_start: 0.6658 (mtt90) cc_final: 0.5960 (mpt-90) REVERT: A 866 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8197 (tp30) REVERT: A 906 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7056 (pttp) REVERT: A 998 LYS cc_start: 0.7928 (tttt) cc_final: 0.7386 (mttt) REVERT: A 1172 ASP cc_start: 0.6204 (m-30) cc_final: 0.5951 (m-30) REVERT: A 1427 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6958 (pt0) REVERT: A 1448 GLN cc_start: 0.3511 (OUTLIER) cc_final: 0.3244 (tm-30) REVERT: A 1461 LYS cc_start: 0.6244 (mmmt) cc_final: 0.5666 (mptt) REVERT: A 1490 GLU cc_start: 0.5096 (OUTLIER) cc_final: 0.4785 (mt-10) REVERT: A 1524 GLN cc_start: 0.6692 (mt0) cc_final: 0.6011 (tp-100) REVERT: A 1530 LEU cc_start: 0.3767 (OUTLIER) cc_final: 0.3283 (mm) REVERT: B 453 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7068 (tmtp) REVERT: B 522 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8257 (tpt90) REVERT: B 775 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6491 (tm-30) REVERT: B 789 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7202 (mm110) REVERT: B 827 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7432 (mtpp) REVERT: B 842 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7700 (mp0) REVERT: B 1168 GLN cc_start: 0.7444 (tm-30) cc_final: 0.6881 (tp-100) REVERT: B 1173 ARG cc_start: 0.6513 (ttt180) cc_final: 0.5913 (ttp80) REVERT: B 1302 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.5830 (mptt) REVERT: B 1406 LYS cc_start: 0.4805 (OUTLIER) cc_final: 0.4014 (mtpt) REVERT: B 1416 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5248 (ptm160) REVERT: B 1476 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.6190 (pp30) outliers start: 78 outliers final: 42 residues processed: 224 average time/residue: 0.6313 time to fit residues: 157.2588 Evaluate side-chains 209 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1427 GLN Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1448 GLN Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1210 ILE Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1302 LYS Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1416 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 160 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 113 optimal weight: 0.0870 chunk 200 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 182 optimal weight: 4.9990 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN B1076 HIS ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1470 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116558 restraints weight = 23868.727| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.04 r_work: 0.3307 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18814 Z= 0.166 Angle : 0.495 8.383 25364 Z= 0.261 Chirality : 0.043 0.236 2780 Planarity : 0.004 0.041 3200 Dihedral : 6.892 71.532 2483 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.91 % Allowed : 20.89 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.18), residues: 2194 helix: 2.03 (0.15), residues: 1240 sheet: 0.40 (0.34), residues: 250 loop : 0.01 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 846 TYR 0.017 0.002 TYR A1093 PHE 0.017 0.002 PHE B1083 TRP 0.014 0.001 TRP B1134 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00402 (18814) covalent geometry : angle 0.49467 (25364) hydrogen bonds : bond 0.04451 ( 934) hydrogen bonds : angle 4.26772 ( 2718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 155 time to evaluate : 0.745 Fit side-chains REVERT: A 419 LYS cc_start: 0.7535 (tptt) cc_final: 0.6743 (mttp) REVERT: A 522 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7236 (tmt170) REVERT: A 536 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.7931 (ptt-90) REVERT: A 634 SER cc_start: 0.7641 (OUTLIER) cc_final: 0.7327 (m) REVERT: A 712 GLU cc_start: 0.7965 (pt0) cc_final: 0.7612 (tt0) REVERT: A 772 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: A 788 ARG cc_start: 0.6654 (mtt90) cc_final: 0.5801 (mpt-90) REVERT: A 866 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8245 (tp30) REVERT: A 998 LYS cc_start: 0.7931 (tttt) cc_final: 0.7391 (mttt) REVERT: A 1172 ASP cc_start: 0.6218 (m-30) cc_final: 0.5958 (m-30) REVERT: A 1448 GLN cc_start: 0.3552 (OUTLIER) cc_final: 0.3282 (tm-30) REVERT: A 1461 LYS cc_start: 0.6168 (mmmt) cc_final: 0.5510 (mptt) REVERT: A 1490 GLU cc_start: 0.5073 (OUTLIER) cc_final: 0.4822 (mt-10) REVERT: A 1524 GLN cc_start: 0.6602 (mt0) cc_final: 0.5877 (tp-100) REVERT: A 1530 LEU cc_start: 0.3681 (OUTLIER) cc_final: 0.3204 (mm) REVERT: B 453 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7122 (tmtp) REVERT: B 522 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8256 (tpt90) REVERT: B 789 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7199 (mm110) REVERT: B 842 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7699 (mp0) REVERT: B 1168 GLN cc_start: 0.7507 (tm-30) cc_final: 0.6929 (tp-100) REVERT: B 1173 ARG cc_start: 0.6513 (ttt180) cc_final: 0.5881 (ttp80) REVERT: B 1406 LYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4249 (mtpt) REVERT: B 1416 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5214 (ptm160) REVERT: B 1465 LYS cc_start: 0.7295 (mptp) cc_final: 0.7052 (mtmm) REVERT: B 1469 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5367 (ptmt) REVERT: B 1476 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6260 (pp30) outliers start: 80 outliers final: 42 residues processed: 218 average time/residue: 0.6601 time to fit residues: 159.7565 Evaluate side-chains 203 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1448 GLN Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1210 ILE Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1416 ARG Chi-restraints excluded: chain B residue 1469 LYS Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 99 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN A 804 GLN B1076 HIS ** B1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1399 GLN B1470 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.167684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118865 restraints weight = 23645.034| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.01 r_work: 0.3344 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18814 Z= 0.115 Angle : 0.445 8.220 25364 Z= 0.235 Chirality : 0.041 0.222 2780 Planarity : 0.003 0.041 3200 Dihedral : 6.652 74.625 2483 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.42 % Allowed : 21.18 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.18), residues: 2194 helix: 2.18 (0.15), residues: 1242 sheet: 0.42 (0.35), residues: 250 loop : 0.07 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1294 TYR 0.016 0.001 TYR B1093 PHE 0.015 0.001 PHE B 801 TRP 0.012 0.001 TRP B1134 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00266 (18814) covalent geometry : angle 0.44547 (25364) hydrogen bonds : bond 0.03723 ( 934) hydrogen bonds : angle 4.11747 ( 2718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 0.717 Fit side-chains REVERT: A 419 LYS cc_start: 0.7483 (tptt) cc_final: 0.6698 (mttp) REVERT: A 522 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7126 (tmt170) REVERT: A 536 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7926 (ptt-90) REVERT: A 551 ASP cc_start: 0.7963 (t0) cc_final: 0.7525 (t0) REVERT: A 634 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.7324 (m) REVERT: A 712 GLU cc_start: 0.7907 (pt0) cc_final: 0.7544 (tt0) REVERT: A 772 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 788 ARG cc_start: 0.6613 (mtt90) cc_final: 0.5866 (mpt-90) REVERT: A 866 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8211 (tp30) REVERT: A 906 LYS cc_start: 0.7778 (ptmm) cc_final: 0.7093 (pttp) REVERT: A 998 LYS cc_start: 0.7938 (tttt) cc_final: 0.7393 (mttt) REVERT: A 1172 ASP cc_start: 0.6169 (m-30) cc_final: 0.5841 (m-30) REVERT: A 1448 GLN cc_start: 0.3541 (OUTLIER) cc_final: 0.3270 (tm-30) REVERT: A 1461 LYS cc_start: 0.6180 (mmmt) cc_final: 0.5595 (mptt) REVERT: A 1490 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4872 (mt-10) REVERT: A 1524 GLN cc_start: 0.6606 (mt0) cc_final: 0.5885 (tp-100) REVERT: B 453 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7096 (tmtp) REVERT: B 522 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8258 (tpt90) REVERT: B 789 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7151 (mm110) REVERT: B 842 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7695 (mp0) REVERT: B 1168 GLN cc_start: 0.7489 (tm-30) cc_final: 0.6896 (tp40) REVERT: B 1173 ARG cc_start: 0.6436 (ttt180) cc_final: 0.5863 (ttp80) REVERT: B 1406 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4290 (mtpt) REVERT: B 1416 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5165 (ptm160) REVERT: B 1469 LYS cc_start: 0.5742 (OUTLIER) cc_final: 0.5310 (ptmt) REVERT: B 1476 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6194 (pp30) outliers start: 70 outliers final: 40 residues processed: 216 average time/residue: 0.6569 time to fit residues: 157.7702 Evaluate side-chains 205 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1448 GLN Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1210 ILE Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1373 LEU Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1416 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1469 LYS Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 12 optimal weight: 0.4980 chunk 218 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 0.0980 chunk 164 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN A 804 GLN B1076 HIS ** B1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1470 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118047 restraints weight = 23629.554| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.01 r_work: 0.3338 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18814 Z= 0.133 Angle : 0.470 9.353 25364 Z= 0.247 Chirality : 0.042 0.252 2780 Planarity : 0.003 0.041 3200 Dihedral : 6.716 74.004 2483 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.33 % Allowed : 21.28 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.18), residues: 2194 helix: 2.13 (0.15), residues: 1242 sheet: 0.41 (0.35), residues: 250 loop : 0.03 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1294 TYR 0.017 0.001 TYR B1093 PHE 0.017 0.001 PHE B 801 TRP 0.015 0.001 TRP B1134 HIS 0.008 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00316 (18814) covalent geometry : angle 0.46961 (25364) hydrogen bonds : bond 0.03943 ( 934) hydrogen bonds : angle 4.15943 ( 2718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 159 time to evaluate : 0.744 Fit side-chains REVERT: A 419 LYS cc_start: 0.7477 (tptt) cc_final: 0.6680 (mttp) REVERT: A 522 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7217 (tmt170) REVERT: A 536 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7911 (ptt-90) REVERT: A 551 ASP cc_start: 0.7958 (t0) cc_final: 0.7580 (t0) REVERT: A 634 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.7318 (m) REVERT: A 712 GLU cc_start: 0.7924 (pt0) cc_final: 0.7574 (tt0) REVERT: A 772 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 788 ARG cc_start: 0.6602 (mtt90) cc_final: 0.5869 (mpt-90) REVERT: A 866 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8215 (tp30) REVERT: A 998 LYS cc_start: 0.7931 (tttt) cc_final: 0.7392 (mttt) REVERT: A 1172 ASP cc_start: 0.6174 (m-30) cc_final: 0.5837 (m-30) REVERT: A 1448 GLN cc_start: 0.3556 (OUTLIER) cc_final: 0.3291 (tm-30) REVERT: A 1461 LYS cc_start: 0.6186 (mmmt) cc_final: 0.5599 (mptt) REVERT: A 1490 GLU cc_start: 0.5122 (OUTLIER) cc_final: 0.4886 (mt-10) REVERT: A 1524 GLN cc_start: 0.6606 (mt0) cc_final: 0.5888 (tp-100) REVERT: A 1530 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3239 (mm) REVERT: B 453 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7097 (tmtp) REVERT: B 522 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8251 (tpt90) REVERT: B 789 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7148 (mm110) REVERT: B 842 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7698 (mp0) REVERT: B 1088 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7727 (tt) REVERT: B 1168 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6876 (tp40) REVERT: B 1173 ARG cc_start: 0.6443 (ttt180) cc_final: 0.5852 (ttp80) REVERT: B 1251 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7122 (mmtt) REVERT: B 1406 LYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4332 (mtpt) REVERT: B 1416 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5186 (ptm160) REVERT: B 1469 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5340 (ptmt) REVERT: B 1476 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.6220 (pp30) outliers start: 68 outliers final: 40 residues processed: 210 average time/residue: 0.6982 time to fit residues: 162.7854 Evaluate side-chains 207 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1448 GLN Chi-restraints excluded: chain A residue 1474 THR Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain B residue 1210 ILE Chi-restraints excluded: chain B residue 1251 LYS Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1373 LEU Chi-restraints excluded: chain B residue 1406 LYS Chi-restraints excluded: chain B residue 1416 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1469 LYS Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 191 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 148 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN A 804 GLN B 856 GLN B1076 HIS B1212 GLN B1219 ASN B1470 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120614 restraints weight = 23640.882| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.00 r_work: 0.3359 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18814 Z= 0.092 Angle : 0.432 7.897 25364 Z= 0.228 Chirality : 0.040 0.200 2780 Planarity : 0.003 0.040 3200 Dihedral : 6.467 77.046 2483 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.64 % Allowed : 22.02 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.12 (0.19), residues: 2194 helix: 2.33 (0.15), residues: 1242 sheet: 0.47 (0.35), residues: 250 loop : 0.14 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1294 TYR 0.016 0.001 TYR B1093 PHE 0.019 0.001 PHE B 801 TRP 0.015 0.001 TRP B1134 HIS 0.008 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00202 (18814) covalent geometry : angle 0.43238 (25364) hydrogen bonds : bond 0.03274 ( 934) hydrogen bonds : angle 4.02874 ( 2718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.698 Fit side-chains REVERT: A 419 LYS cc_start: 0.7427 (tptt) cc_final: 0.6626 (mttp) REVERT: A 522 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7120 (tmt170) REVERT: A 536 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.7882 (ptt-90) REVERT: A 551 ASP cc_start: 0.7957 (t0) cc_final: 0.7569 (t0) REVERT: A 634 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.7241 (m) REVERT: A 712 GLU cc_start: 0.7863 (pt0) cc_final: 0.7496 (tt0) REVERT: A 728 THR cc_start: 0.6509 (p) cc_final: 0.6194 (t) REVERT: A 772 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 788 ARG cc_start: 0.6531 (mtt90) cc_final: 0.5731 (mpt-90) REVERT: A 866 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8124 (tp30) REVERT: A 998 LYS cc_start: 0.7929 (tttt) cc_final: 0.7380 (mttt) REVERT: A 1402 SER cc_start: 0.4331 (OUTLIER) cc_final: 0.3928 (m) REVERT: A 1461 LYS cc_start: 0.6094 (mmmt) cc_final: 0.5521 (mptt) REVERT: A 1490 GLU cc_start: 0.5108 (OUTLIER) cc_final: 0.4885 (mt-10) REVERT: A 1524 GLN cc_start: 0.6593 (mt0) cc_final: 0.5900 (tp-100) REVERT: B 453 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6836 (tmtp) REVERT: B 522 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8222 (tpt90) REVERT: B 603 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 789 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7087 (mm110) REVERT: B 842 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7658 (mp0) REVERT: B 1088 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 1168 GLN cc_start: 0.7423 (tm-30) cc_final: 0.6827 (tp40) REVERT: B 1173 ARG cc_start: 0.6370 (ttt180) cc_final: 0.5915 (ttp80) REVERT: B 1251 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7089 (mmtt) REVERT: B 1416 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5120 (ptm160) REVERT: B 1469 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.5190 (ptmt) REVERT: B 1476 GLN cc_start: 0.6326 (OUTLIER) cc_final: 0.5999 (pp30) outliers start: 54 outliers final: 27 residues processed: 205 average time/residue: 0.6738 time to fit residues: 153.2920 Evaluate side-chains 191 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1261 LYS Chi-restraints excluded: chain A residue 1282 ASN Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1251 LYS Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1373 LEU Chi-restraints excluded: chain B residue 1416 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1469 LYS Chi-restraints excluded: chain B residue 1476 GLN Chi-restraints excluded: chain B residue 1570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1076 HIS ** B1470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.167987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119499 restraints weight = 23531.823| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.95 r_work: 0.3332 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18814 Z= 0.137 Angle : 0.481 8.041 25364 Z= 0.253 Chirality : 0.042 0.225 2780 Planarity : 0.004 0.061 3200 Dihedral : 6.692 74.781 2483 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.40 % Allowed : 22.31 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.18), residues: 2194 helix: 2.22 (0.15), residues: 1242 sheet: 0.44 (0.35), residues: 250 loop : 0.09 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1294 TYR 0.017 0.001 TYR B1093 PHE 0.022 0.001 PHE B 801 TRP 0.021 0.001 TRP B1134 HIS 0.007 0.001 HIS B1076 Details of bonding type rmsd covalent geometry : bond 0.00326 (18814) covalent geometry : angle 0.48052 (25364) hydrogen bonds : bond 0.03902 ( 934) hydrogen bonds : angle 4.12568 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8826.82 seconds wall clock time: 150 minutes 45.38 seconds (9045.38 seconds total)