Starting phenix.real_space_refine on Wed Mar 4 18:23:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zjv_74343/03_2026/9zjv_74343.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zjv_74343/03_2026/9zjv_74343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zjv_74343/03_2026/9zjv_74343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zjv_74343/03_2026/9zjv_74343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zjv_74343/03_2026/9zjv_74343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zjv_74343/03_2026/9zjv_74343.map" } resolution = 3.13 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= 0.024 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 3 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 9538 2.51 5 N 2449 2.21 5 O 2735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 14786 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 9101 Classifications: {'peptide': 1112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1072} Chain breaks: 12 Chain: "B" Number of atoms: 5653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5653 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 661} Chain breaks: 3 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} Time building chain proxies: 3.16, per 1000 atoms: 0.21 Number of scatterers: 14786 At special positions: 0 Unit cell: (100.98, 127.38, 137.28, 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 60 16.00 P 3 15.00 Mg 1 11.99 O 2735 8.00 N 2449 7.00 C 9538 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: 1.36 Conformation dependent library (CDL) restraints added in 553.4 milliseconds 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 9 sheets defined 62.1% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.997A pdb=" N LYS A 426 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.747A pdb=" N LYS A 432 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.679A pdb=" N ARG A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 removed outlier: 3.543A pdb=" N VAL A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.654A pdb=" N GLU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 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 620 removed outlier: 3.530A pdb=" N LYS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.570A pdb=" N PHE A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.982A pdb=" N PHE A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.780A 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 803 through 821 removed outlier: 4.371A pdb=" N VAL A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.155A 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: 3.595A pdb=" N GLU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.655A 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 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: 3.693A 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 1000 removed outlier: 3.547A pdb=" N GLU A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1014 Processing helix chain 'A' and resid 1014 through 1019 removed outlier: 4.356A pdb=" N PHE A1018 " --> 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: 3.826A pdb=" N VAL A1067 " --> pdb=" O GLY A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1096 Processing helix chain 'A' and resid 1098 through 1113 Processing helix chain 'A' and resid 1116 through 1139 removed outlier: 3.729A pdb=" N LYS A1130 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1174 removed outlier: 3.673A pdb=" N GLU A1174 " --> pdb=" O SER A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1212 Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 6.191A pdb=" N PHE A1216 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 4.044A 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 1251 Processing helix chain 'A' and resid 1253 through 1258 Processing helix chain 'A' and resid 1259 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 1350 removed outlier: 3.885A pdb=" N TYR A1350 " --> pdb=" O GLY A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1375 removed outlier: 3.589A pdb=" N SER A1360 " --> pdb=" O GLU A1356 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A1367 " --> pdb=" O LYS A1363 " (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 removed outlier: 3.587A pdb=" N LEU A1437 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1438 " --> pdb=" O LEU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1468 removed outlier: 3.696A pdb=" N GLN A1458 " --> pdb=" O LYS A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1472 removed outlier: 3.726A pdb=" N HIS A1472 " --> pdb=" O LYS A1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1469 through 1472' Processing helix chain 'A' and resid 1495 through 1501 Processing helix chain 'A' and resid 1515 through 1519 removed outlier: 3.613A pdb=" N TRP A1518 " --> pdb=" O GLY A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1527 removed outlier: 3.854A pdb=" N GLN A1524 " --> pdb=" O GLU A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1561 removed outlier: 3.640A pdb=" N GLN A1560 " --> pdb=" O PHE A1557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1561 " --> pdb=" O LEU A1558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1557 through 1561' Processing helix chain 'B' and resid 391 through 400 Processing helix chain 'B' and resid 421 through 428 removed outlier: 3.928A pdb=" N LYS B 426 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.838A 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 459 removed outlier: 3.569A pdb=" N ALA B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.909A pdb=" N TYR B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 509 through 529 removed outlier: 4.357A pdb=" N ALA B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP B 520 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.559A 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 598 through 604 removed outlier: 3.511A pdb=" N SER B 602 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 620 Processing helix chain 'B' and resid 1100 through 1113 Processing helix chain 'B' and resid 1117 through 1142 removed outlier: 3.874A pdb=" N GLY B1140 " --> pdb=" O GLU B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1172 Processing helix chain 'B' and resid 1194 through 1214 removed outlier: 3.614A pdb=" N GLN B1198 " --> pdb=" O ILE B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1233 Processing helix chain 'B' and resid 1244 through 1253 removed outlier: 3.561A pdb=" N TYR B1253 " --> pdb=" O ALA B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1259 removed outlier: 3.909A 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 1307 Processing helix chain 'B' and resid 1325 through 1339 Processing helix chain 'B' and resid 1343 through 1349 removed outlier: 3.574A pdb=" N LEU B1347 " --> pdb=" O LYS B1343 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1352 No H-bonds generated for 'chain 'B' and resid 1350 through 1352' Processing helix chain 'B' and resid 1354 through 1375 removed outlier: 4.104A pdb=" N SER B1360 " --> pdb=" O GLU B1356 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B1375 " --> pdb=" O PHE B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1399 removed outlier: 3.691A pdb=" N LYS B1385 " --> pdb=" O GLN B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1423 Proline residue: B1421 - end of helix Processing helix chain 'B' and resid 1429 through 1440 removed outlier: 3.602A pdb=" N LEU B1434 " --> pdb=" O GLU B1430 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP B1440 " --> pdb=" O SER B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1451 Processing helix chain 'B' and resid 1452 through 1468 Processing helix chain 'B' and resid 1469 through 1472 removed outlier: 3.799A pdb=" N HIS B1472 " --> pdb=" O LYS B1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1469 through 1472' Processing helix chain 'B' and resid 1487 through 1490 Processing helix chain 'B' and resid 1495 through 1500 Processing helix chain 'B' and resid 1507 through 1515 removed outlier: 3.581A pdb=" N LEU B1511 " --> pdb=" O ASP B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1516 through 1519 Processing helix chain 'B' and resid 1520 through 1527 removed outlier: 3.530A pdb=" N LEU B1526 " --> pdb=" O LYS B1522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.097A pdb=" N VAL A 439 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 413 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LEU A 440 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 415 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN A 412 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A 542 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 414 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A 544 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 416 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 606 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS A 575 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 630 through 632 removed outlier: 4.251A pdb=" N ARG A 630 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 653 through 654 removed outlier: 6.696A pdb=" N ALA A 761 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASP A 799 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 731 " --> pdb=" O VAL A 830 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 832 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N VAL A 853 " --> pdb=" O HIS A 734 " (cutoff:3.500A) removed outlier: 6.499A 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 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: 5.632A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA A1583 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A1554 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1541 " --> pdb=" O ILE A1551 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A1540 " --> pdb=" O ARG A1533 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A1533 " --> pdb=" O TYR A1540 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLU A1542 " --> pdb=" O GLN A1531 " (cutoff:3.500A) removed outlier: 8.199A 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: 3.644A pdb=" N PHE B 493 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 439 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR B 413 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU B 440 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 415 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN B 412 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL B 542 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 414 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B 544 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL B 416 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1278 through 1280 Processing sheet with id=AA9, first strand: chain 'B' and resid 1492 through 1494 removed outlier: 3.751A pdb=" N LEU B1483 " --> pdb=" O LEU B1574 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B1574 " --> pdb=" O LEU B1483 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR B1573 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP B1585 " --> pdb=" O TYR B1573 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B1575 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA B1583 " --> pdb=" O GLY B1575 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER B1577 " --> pdb=" O PRO B1581 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ALA B1583 " --> pdb=" O PRO B1552 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR B1554 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASP B1585 " --> pdb=" O THR B1554 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B1541 " --> pdb=" O ILE B1551 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU B1542 " --> pdb=" O GLN B1531 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLN B1531 " --> pdb=" O GLU B1542 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2253 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: 2.97 Time building geometry restraints manager: 1.80 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: 4672 1.34 - 1.46: 2297 1.46 - 1.58: 8046 1.58 - 1.69: 5 1.69 - 1.81: 84 Bond restraints: 15104 Sorted by residual: bond pdb=" N ILE A 595 " pdb=" CA ILE A 595 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.39e+00 bond pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 7.96e+00 bond pdb=" N ILE A 973 " pdb=" CA ILE A 973 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.74e+00 bond pdb=" N ILE A 606 " pdb=" CA ILE A 606 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.68e+00 bond pdb=" N VAL A 981 " pdb=" CA VAL A 981 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.20e-02 6.94e+03 7.47e+00 ... (remaining 15099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 19698 1.56 - 3.12: 570 3.12 - 4.68: 85 4.68 - 6.23: 13 6.23 - 7.79: 6 Bond angle restraints: 20372 Sorted by residual: angle pdb=" C ARG B1488 " pdb=" CA ARG B1488 " pdb=" CB ARG B1488 " ideal model delta sigma weight residual 116.54 111.12 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" N ARG A 593 " pdb=" CA ARG A 593 " pdb=" C ARG A 593 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" CA GLY A 980 " pdb=" C GLY A 980 " pdb=" O GLY A 980 " ideal model delta sigma weight residual 121.57 118.11 3.46 8.70e-01 1.32e+00 1.58e+01 angle pdb=" N ILE A1284 " pdb=" CA ILE A1284 " pdb=" C ILE A1284 " ideal model delta sigma weight residual 111.56 108.34 3.22 8.60e-01 1.35e+00 1.40e+01 angle pdb=" CA LEU A 485 " pdb=" C LEU A 485 " pdb=" O LEU A 485 " ideal model delta sigma weight residual 121.56 117.61 3.95 1.09e+00 8.42e-01 1.31e+01 ... (remaining 20367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 7765 17.56 - 35.13: 1019 35.13 - 52.69: 287 52.69 - 70.25: 72 70.25 - 87.82: 19 Dihedral angle restraints: 9162 sinusoidal: 3853 harmonic: 5309 Sorted by residual: dihedral pdb=" CB GLU B1202 " pdb=" CG GLU B1202 " pdb=" CD GLU B1202 " pdb=" OE1 GLU B1202 " ideal model delta sinusoidal sigma weight residual 0.00 87.82 -87.82 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A1490 " pdb=" CG GLU A1490 " pdb=" CD GLU A1490 " pdb=" OE1 GLU A1490 " ideal model delta sinusoidal sigma weight residual 0.00 87.81 -87.81 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU B1330 " pdb=" CG GLU B1330 " pdb=" CD GLU B1330 " pdb=" OE1 GLU B1330 " ideal model delta sinusoidal sigma weight residual 0.00 87.50 -87.50 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 9159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1697 0.044 - 0.089: 385 0.089 - 0.133: 128 0.133 - 0.178: 13 0.178 - 0.222: 6 Chirality restraints: 2229 Sorted by residual: chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE A 480 " pdb=" N ILE A 480 " pdb=" C ILE A 480 " pdb=" CB ILE A 480 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 972 " pdb=" N VAL A 972 " pdb=" C VAL A 972 " pdb=" CB VAL A 972 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2226 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1388 " 0.014 2.00e-02 2.50e+03 2.04e-02 7.31e+00 pdb=" CG PHE B1388 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B1388 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B1388 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B1388 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1388 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B1388 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 788 " 0.229 9.50e-02 1.11e+02 1.03e-01 6.47e+00 pdb=" NE ARG A 788 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 788 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 788 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 788 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 968 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ILE A 968 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 968 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 969 " 0.011 2.00e-02 2.50e+03 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 80 2.54 - 3.13: 11021 3.13 - 3.72: 23263 3.72 - 4.31: 31497 4.31 - 4.90: 53015 Nonbonded interactions: 118876 Sorted by model distance: nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1602 " model vdw 1.950 2.170 nonbonded pdb=" OG1 THR A 744 " pdb="MG MG A1602 " model vdw 2.058 2.170 nonbonded pdb=" OG SER A1145 " pdb=" OD1 ASP A1148 " model vdw 2.214 3.040 nonbonded pdb=" O GLY B1100 " pdb=" ND2 ASN B1104 " model vdw 2.250 3.120 nonbonded pdb=" OG SER B1354 " pdb=" OD2 ASP B1357 " model vdw 2.251 3.040 ... (remaining 118871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15104 Z= 0.221 Angle : 0.621 7.793 20372 Z= 0.376 Chirality : 0.044 0.222 2229 Planarity : 0.004 0.103 2579 Dihedral : 17.455 87.816 5720 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 23.51 % Favored : 74.30 % 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: 0.85 (0.20), residues: 1769 helix: 1.13 (0.16), residues: 999 sheet: -0.01 (0.41), residues: 176 loop : -0.05 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 630 TYR 0.021 0.001 TYR A 409 PHE 0.046 0.001 PHE B1388 TRP 0.013 0.001 TRP B1105 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00364 (15104) covalent geometry : angle 0.62137 (20372) hydrogen bonds : bond 0.22315 ( 775) hydrogen bonds : angle 6.60125 ( 2253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 LYS cc_start: 0.8252 (pptt) cc_final: 0.8050 (mttp) REVERT: A 709 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 731 LYS cc_start: 0.7315 (ptmt) cc_final: 0.6472 (mttt) REVERT: A 860 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8288 (ptmt) REVERT: A 863 ARG cc_start: 0.8626 (mmp-170) cc_final: 0.8169 (mtm180) REVERT: A 871 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 930 ASP cc_start: 0.8322 (t70) cc_final: 0.7998 (t0) REVERT: A 994 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8048 (mt-10) REVERT: A 1056 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8199 (mm-30) REVERT: A 1135 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7566 (mp) REVERT: A 1221 ASN cc_start: 0.8832 (t0) cc_final: 0.8510 (t0) REVERT: A 1223 LEU cc_start: 0.7936 (tp) cc_final: 0.7547 (mt) REVERT: A 1422 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.6977 (mt) REVERT: A 1511 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5925 (mm) REVERT: A 1513 GLN cc_start: 0.5441 (pm20) cc_final: 0.5223 (pp30) REVERT: A 1528 LEU cc_start: 0.7870 (tt) cc_final: 0.7411 (mt) REVERT: A 1530 LEU cc_start: 0.8183 (mm) cc_final: 0.7976 (mp) REVERT: B 424 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 478 GLU cc_start: 0.8625 (tt0) cc_final: 0.8409 (tt0) REVERT: B 501 ASP cc_start: 0.7804 (t0) cc_final: 0.6994 (p0) REVERT: B 1227 TYR cc_start: 0.8062 (m-80) cc_final: 0.7621 (m-80) REVERT: B 1344 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 1425 THR cc_start: 0.8853 (m) cc_final: 0.8608 (p) REVERT: B 1473 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.6997 (ttp-170) REVERT: B 1490 GLU cc_start: 0.8474 (tp30) cc_final: 0.8165 (mp0) outliers start: 36 outliers final: 19 residues processed: 228 average time/residue: 0.1214 time to fit residues: 40.3023 Evaluate side-chains 180 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain A residue 934 SER Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1210 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1263 SER Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1424 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1563 SER Chi-restraints excluded: chain B residue 1568 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 427 HIS A 449 ASN A 530 HIS A 719 GLN A 834 ASN A 985 HIS A1167 GLN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1458 GLN A1462 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 ASN B1513 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.127552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096909 restraints weight = 27897.688| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.89 r_work: 0.3310 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15104 Z= 0.129 Angle : 0.527 8.073 20372 Z= 0.275 Chirality : 0.041 0.138 2229 Planarity : 0.004 0.044 2579 Dihedral : 6.384 60.007 2020 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.65 % Allowed : 20.58 % Favored : 75.76 % 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: 1.37 (0.20), residues: 1769 helix: 1.70 (0.16), residues: 1011 sheet: -0.22 (0.39), residues: 177 loop : 0.00 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 630 TYR 0.018 0.001 TYR B1127 PHE 0.026 0.001 PHE B1388 TRP 0.010 0.001 TRP B1134 HIS 0.007 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00289 (15104) covalent geometry : angle 0.52724 (20372) hydrogen bonds : bond 0.04629 ( 775) hydrogen bonds : angle 4.58934 ( 2253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7210 (pt0) cc_final: 0.6885 (pt0) REVERT: A 731 LYS cc_start: 0.7214 (ptmt) cc_final: 0.6431 (mttt) REVERT: A 863 ARG cc_start: 0.8628 (mmp-170) cc_final: 0.8146 (mtm180) REVERT: A 871 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 977 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7979 (m110) REVERT: A 994 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7929 (mt-10) REVERT: A 1068 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 1079 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7765 (t0) REVERT: A 1362 MET cc_start: 0.8316 (mpp) cc_final: 0.7934 (mpp) REVERT: A 1422 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.6962 (mt) REVERT: A 1528 LEU cc_start: 0.7803 (tt) cc_final: 0.7266 (mt) REVERT: A 1548 LYS cc_start: -0.0120 (OUTLIER) cc_final: -0.1454 (ptpt) REVERT: B 478 GLU cc_start: 0.8737 (tt0) cc_final: 0.8521 (tt0) REVERT: B 501 ASP cc_start: 0.7888 (t0) cc_final: 0.7023 (p0) REVERT: B 516 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 1271 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7343 (t80) REVERT: B 1327 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7595 (tp) REVERT: B 1425 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 1490 GLU cc_start: 0.8457 (tp30) cc_final: 0.8112 (mp0) outliers start: 60 outliers final: 24 residues processed: 216 average time/residue: 0.1081 time to fit residues: 35.4708 Evaluate side-chains 177 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 738 HIS Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 977 ASN Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1541 ILE Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1271 PHE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1434 LEU Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1561 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN A 738 HIS A1414 GLN A1513 GLN A1536 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1168 GLN B1392 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.123392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092513 restraints weight = 28394.483| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.93 r_work: 0.3235 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15104 Z= 0.159 Angle : 0.529 10.830 20372 Z= 0.275 Chirality : 0.042 0.232 2229 Planarity : 0.004 0.043 2579 Dihedral : 5.548 63.447 1983 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.96 % Allowed : 20.89 % Favored : 75.15 % 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: 1.31 (0.20), residues: 1769 helix: 1.74 (0.17), residues: 1013 sheet: -0.43 (0.39), residues: 178 loop : -0.15 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 846 TYR 0.015 0.001 TYR A1274 PHE 0.024 0.002 PHE A 801 TRP 0.011 0.001 TRP B1134 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00372 (15104) covalent geometry : angle 0.52876 (20372) hydrogen bonds : bond 0.04325 ( 775) hydrogen bonds : angle 4.31857 ( 2253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 153 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: A 478 GLU cc_start: 0.7300 (pt0) cc_final: 0.7054 (mt-10) REVERT: A 588 ASP cc_start: 0.8367 (m-30) cc_final: 0.8167 (t0) REVERT: A 664 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 731 LYS cc_start: 0.7598 (ptmt) cc_final: 0.6807 (mttt) REVERT: A 863 ARG cc_start: 0.8625 (mmp-170) cc_final: 0.8235 (mtm180) REVERT: A 871 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 994 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7890 (mt-10) REVERT: A 1079 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7942 (t0) REVERT: A 1422 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7026 (mt) REVERT: A 1495 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7678 (tttt) REVERT: A 1528 LEU cc_start: 0.7855 (tt) cc_final: 0.7294 (mt) REVERT: A 1548 LYS cc_start: 0.0225 (OUTLIER) cc_final: -0.1274 (ptpt) REVERT: B 478 GLU cc_start: 0.8831 (tt0) cc_final: 0.8554 (tt0) REVERT: B 501 ASP cc_start: 0.7986 (t0) cc_final: 0.7152 (p0) REVERT: B 606 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 1105 TRP cc_start: 0.6773 (m-90) cc_final: 0.4526 (t60) REVERT: B 1271 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7403 (t80) REVERT: B 1344 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7723 (t80) REVERT: B 1425 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8617 (p) REVERT: B 1490 GLU cc_start: 0.8466 (tp30) cc_final: 0.8122 (mp0) outliers start: 65 outliers final: 33 residues processed: 208 average time/residue: 0.1075 time to fit residues: 34.4186 Evaluate side-chains 184 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 738 HIS Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1541 ILE Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1254 ILE Chi-restraints excluded: chain B residue 1271 PHE Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1434 LEU Chi-restraints excluded: chain B residue 1561 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN A1086 GLN ** A1536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.123838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093146 restraints weight = 28407.997| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.93 r_work: 0.3245 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15104 Z= 0.125 Angle : 0.493 10.164 20372 Z= 0.255 Chirality : 0.041 0.241 2229 Planarity : 0.004 0.041 2579 Dihedral : 5.414 62.711 1981 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.78 % Allowed : 20.95 % Favored : 75.27 % 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: 1.43 (0.20), residues: 1769 helix: 1.87 (0.17), residues: 1005 sheet: -0.42 (0.40), residues: 172 loop : -0.16 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 459 TYR 0.014 0.001 TYR A1274 PHE 0.027 0.001 PHE A 801 TRP 0.010 0.001 TRP B1134 HIS 0.009 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00290 (15104) covalent geometry : angle 0.49329 (20372) hydrogen bonds : bond 0.03757 ( 775) hydrogen bonds : angle 4.15413 ( 2253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: A 449 ASN cc_start: 0.8135 (t0) cc_final: 0.7899 (p0) REVERT: A 478 GLU cc_start: 0.7282 (pt0) cc_final: 0.7055 (mt-10) REVERT: A 664 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8631 (mp) REVERT: A 731 LYS cc_start: 0.7555 (ptmt) cc_final: 0.6773 (mttt) REVERT: A 754 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 863 ARG cc_start: 0.8593 (mmp-170) cc_final: 0.8221 (mtm180) REVERT: A 871 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 930 ASP cc_start: 0.8258 (t70) cc_final: 0.7979 (t0) REVERT: A 994 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7845 (mt-10) REVERT: A 1079 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 1253 TYR cc_start: 0.7614 (m-80) cc_final: 0.7307 (m-10) REVERT: A 1362 MET cc_start: 0.8391 (mpp) cc_final: 0.8127 (mpp) REVERT: A 1422 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.6947 (mt) REVERT: A 1478 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8435 (tt) REVERT: A 1495 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7671 (tttt) REVERT: A 1528 LEU cc_start: 0.7848 (tt) cc_final: 0.7290 (mt) REVERT: A 1548 LYS cc_start: 0.0302 (OUTLIER) cc_final: -0.1241 (ptpt) REVERT: B 478 GLU cc_start: 0.8836 (tt0) cc_final: 0.8586 (tt0) REVERT: B 501 ASP cc_start: 0.7988 (t0) cc_final: 0.7156 (p0) REVERT: B 1105 TRP cc_start: 0.6772 (m-90) cc_final: 0.4537 (t60) REVERT: B 1127 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 1327 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 1344 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7573 (t80) REVERT: B 1425 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 1490 GLU cc_start: 0.8464 (tp30) cc_final: 0.8148 (mp0) outliers start: 62 outliers final: 34 residues processed: 208 average time/residue: 0.1105 time to fit residues: 34.3989 Evaluate side-chains 184 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1478 ILE Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1541 ILE Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1127 TYR Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1434 LEU Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN A1219 ASN ** A1536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.123005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092484 restraints weight = 28397.464| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.91 r_work: 0.3237 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15104 Z= 0.132 Angle : 0.492 8.880 20372 Z= 0.255 Chirality : 0.041 0.194 2229 Planarity : 0.004 0.040 2579 Dihedral : 5.425 62.586 1981 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.08 % Allowed : 20.83 % Favored : 75.09 % 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: 1.48 (0.20), residues: 1769 helix: 1.88 (0.17), residues: 1015 sheet: -0.45 (0.40), residues: 173 loop : -0.08 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 459 TYR 0.014 0.001 TYR A1274 PHE 0.021 0.001 PHE A 801 TRP 0.010 0.001 TRP B1134 HIS 0.009 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00311 (15104) covalent geometry : angle 0.49225 (20372) hydrogen bonds : bond 0.03700 ( 775) hydrogen bonds : angle 4.08387 ( 2253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ASN cc_start: 0.8115 (t0) cc_final: 0.7800 (p0) REVERT: A 478 GLU cc_start: 0.7295 (pt0) cc_final: 0.7053 (mt-10) REVERT: A 664 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8662 (mp) REVERT: A 731 LYS cc_start: 0.7597 (ptmt) cc_final: 0.6844 (mttt) REVERT: A 754 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 863 ARG cc_start: 0.8601 (mmp-170) cc_final: 0.8247 (mtm180) REVERT: A 871 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 930 ASP cc_start: 0.8217 (t70) cc_final: 0.7939 (t70) REVERT: A 994 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7848 (mt-10) REVERT: A 1074 SER cc_start: 0.9301 (t) cc_final: 0.9050 (p) REVERT: A 1079 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: A 1253 TYR cc_start: 0.7698 (m-80) cc_final: 0.7495 (m-80) REVERT: A 1282 ASN cc_start: 0.8570 (t0) cc_final: 0.8254 (t0) REVERT: A 1331 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7658 (ptt-90) REVERT: A 1362 MET cc_start: 0.8371 (mpp) cc_final: 0.8115 (mpp) REVERT: A 1422 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7172 (mm) REVERT: A 1478 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 1495 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7672 (tttt) REVERT: A 1528 LEU cc_start: 0.7916 (tt) cc_final: 0.7327 (mt) REVERT: A 1548 LYS cc_start: 0.0293 (OUTLIER) cc_final: -0.1260 (ptpt) REVERT: B 501 ASP cc_start: 0.8020 (t0) cc_final: 0.7184 (p0) REVERT: B 606 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 1105 TRP cc_start: 0.6855 (m-90) cc_final: 0.4628 (t60) REVERT: B 1127 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7283 (t80) REVERT: B 1271 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7294 (t80) REVERT: B 1327 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7714 (tp) REVERT: B 1344 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7616 (t80) REVERT: B 1425 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8688 (p) REVERT: B 1490 GLU cc_start: 0.8440 (tp30) cc_final: 0.8140 (mp0) outliers start: 67 outliers final: 38 residues processed: 201 average time/residue: 0.1043 time to fit residues: 32.2037 Evaluate side-chains 184 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1331 ARG Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1478 ILE Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1541 ILE Chi-restraints excluded: chain A residue 1548 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1127 TYR Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1238 ILE Chi-restraints excluded: chain B residue 1271 PHE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1434 LEU Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1538 CYS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN A1536 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091360 restraints weight = 28268.517| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.90 r_work: 0.3217 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15104 Z= 0.146 Angle : 0.508 9.158 20372 Z= 0.261 Chirality : 0.041 0.177 2229 Planarity : 0.004 0.039 2579 Dihedral : 5.525 64.089 1981 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.69 % Allowed : 20.52 % Favored : 74.79 % 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: 1.42 (0.20), residues: 1769 helix: 1.83 (0.17), residues: 1016 sheet: -0.51 (0.41), residues: 165 loop : -0.08 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 846 TYR 0.015 0.001 TYR A1274 PHE 0.019 0.001 PHE A 801 TRP 0.010 0.001 TRP B1134 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00347 (15104) covalent geometry : angle 0.50755 (20372) hydrogen bonds : bond 0.03796 ( 775) hydrogen bonds : angle 4.06041 ( 2253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 148 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: A 478 GLU cc_start: 0.7322 (pt0) cc_final: 0.7095 (mt-10) REVERT: A 553 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8615 (mtt90) REVERT: A 664 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 717 MET cc_start: 0.8694 (ttm) cc_final: 0.8409 (ttt) REVERT: A 731 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7023 (mttt) REVERT: A 754 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 863 ARG cc_start: 0.8615 (mmp-170) cc_final: 0.8261 (mtm180) REVERT: A 871 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8005 (tm-30) REVERT: A 930 ASP cc_start: 0.8210 (t70) cc_final: 0.7937 (t70) REVERT: A 994 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7835 (mt-10) REVERT: A 1074 SER cc_start: 0.9278 (t) cc_final: 0.9048 (p) REVERT: A 1079 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: A 1111 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 1253 TYR cc_start: 0.7727 (m-80) cc_final: 0.7401 (m-10) REVERT: A 1331 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7562 (ptt-90) REVERT: A 1422 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7223 (mm) REVERT: A 1495 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7670 (tttt) REVERT: A 1528 LEU cc_start: 0.7871 (tt) cc_final: 0.7234 (mt) REVERT: B 499 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8580 (p0) REVERT: B 501 ASP cc_start: 0.8135 (t0) cc_final: 0.7292 (p0) REVERT: B 606 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 1105 TRP cc_start: 0.6828 (m-90) cc_final: 0.4668 (t60) REVERT: B 1127 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 1327 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7648 (tp) REVERT: B 1344 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7664 (t80) REVERT: B 1348 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8390 (tt) REVERT: B 1425 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 1561 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7742 (tm) outliers start: 77 outliers final: 44 residues processed: 213 average time/residue: 0.1122 time to fit residues: 35.8613 Evaluate side-chains 193 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1331 ARG Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1541 ILE Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1127 TYR Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1210 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1238 ILE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1538 CYS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 159 optimal weight: 0.0060 chunk 147 optimal weight: 4.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091614 restraints weight = 28286.586| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.90 r_work: 0.3221 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15104 Z= 0.136 Angle : 0.499 10.759 20372 Z= 0.257 Chirality : 0.041 0.236 2229 Planarity : 0.004 0.042 2579 Dihedral : 5.483 64.415 1981 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.26 % Allowed : 21.19 % Favored : 74.54 % 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: 1.45 (0.20), residues: 1769 helix: 1.87 (0.17), residues: 1018 sheet: -0.55 (0.41), residues: 164 loop : -0.11 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 846 TYR 0.014 0.001 TYR A1274 PHE 0.031 0.001 PHE A 801 TRP 0.010 0.001 TRP B 586 HIS 0.009 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00322 (15104) covalent geometry : angle 0.49916 (20372) hydrogen bonds : bond 0.03640 ( 775) hydrogen bonds : angle 4.01865 ( 2253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 140 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: A 478 GLU cc_start: 0.7311 (pt0) cc_final: 0.7100 (mt-10) REVERT: A 553 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8598 (mtt90) REVERT: A 664 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 731 LYS cc_start: 0.7707 (ptmt) cc_final: 0.7004 (mttt) REVERT: A 754 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 863 ARG cc_start: 0.8614 (mmp-170) cc_final: 0.8263 (mtm180) REVERT: A 871 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 930 ASP cc_start: 0.8230 (t70) cc_final: 0.7950 (t70) REVERT: A 994 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7806 (mt-10) REVERT: A 1074 SER cc_start: 0.9282 (t) cc_final: 0.9048 (p) REVERT: A 1079 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: A 1111 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8784 (tp) REVERT: A 1253 TYR cc_start: 0.7761 (m-80) cc_final: 0.7436 (m-80) REVERT: A 1331 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7565 (ptt-90) REVERT: A 1422 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7235 (mm) REVERT: A 1495 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7666 (tttt) REVERT: A 1528 LEU cc_start: 0.7897 (tt) cc_final: 0.7264 (mt) REVERT: B 499 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8586 (p0) REVERT: B 501 ASP cc_start: 0.8166 (t0) cc_final: 0.7378 (p0) REVERT: B 570 MET cc_start: 0.7958 (ptp) cc_final: 0.7690 (mtp) REVERT: B 606 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8166 (mp) REVERT: B 1105 TRP cc_start: 0.6840 (m-90) cc_final: 0.4749 (t60) REVERT: B 1327 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7560 (tp) REVERT: B 1344 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 1425 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8753 (p) REVERT: B 1561 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7748 (tm) outliers start: 70 outliers final: 46 residues processed: 200 average time/residue: 0.1095 time to fit residues: 32.9389 Evaluate side-chains 190 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1079 ASN Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1331 ARG Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1541 ILE Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1238 ILE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1360 SER Chi-restraints excluded: chain B residue 1385 LYS Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1538 CYS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 719 GLN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.123248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093023 restraints weight = 28186.805| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.88 r_work: 0.3244 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15104 Z= 0.106 Angle : 0.477 9.992 20372 Z= 0.245 Chirality : 0.040 0.227 2229 Planarity : 0.003 0.041 2579 Dihedral : 5.316 61.652 1981 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.35 % Allowed : 22.47 % Favored : 74.18 % 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: 1.56 (0.20), residues: 1769 helix: 1.93 (0.17), residues: 1018 sheet: -0.47 (0.40), residues: 172 loop : -0.02 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 846 TYR 0.023 0.001 TYR B1127 PHE 0.027 0.001 PHE A 801 TRP 0.011 0.001 TRP B 586 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00243 (15104) covalent geometry : angle 0.47745 (20372) hydrogen bonds : bond 0.03290 ( 775) hydrogen bonds : angle 3.94705 ( 2253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7336 (pt0) cc_final: 0.7126 (mt-10) REVERT: A 553 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8568 (mtt90) REVERT: A 664 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8788 (mp) REVERT: A 717 MET cc_start: 0.8692 (ttm) cc_final: 0.8452 (ttt) REVERT: A 731 LYS cc_start: 0.7609 (ptmt) cc_final: 0.6931 (mttt) REVERT: A 754 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 863 ARG cc_start: 0.8576 (mmp-170) cc_final: 0.8263 (mtm180) REVERT: A 871 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8083 (tm-30) REVERT: A 930 ASP cc_start: 0.8187 (t70) cc_final: 0.7892 (t70) REVERT: A 1074 SER cc_start: 0.9277 (t) cc_final: 0.9005 (p) REVERT: A 1111 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8759 (tp) REVERT: A 1253 TYR cc_start: 0.7729 (m-80) cc_final: 0.7421 (m-80) REVERT: A 1331 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7545 (ptt-90) REVERT: A 1422 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7228 (mm) REVERT: A 1495 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7658 (tttt) REVERT: A 1528 LEU cc_start: 0.7857 (tt) cc_final: 0.7218 (mt) REVERT: B 501 ASP cc_start: 0.8131 (t0) cc_final: 0.7388 (p0) REVERT: B 570 MET cc_start: 0.7927 (ptp) cc_final: 0.7685 (mtp) REVERT: B 606 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 1105 TRP cc_start: 0.6828 (m-90) cc_final: 0.4778 (t60) REVERT: B 1227 TYR cc_start: 0.8300 (m-80) cc_final: 0.7970 (m-80) REVERT: B 1327 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7577 (tp) REVERT: B 1344 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7603 (t80) REVERT: B 1348 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8444 (tt) REVERT: B 1425 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 1561 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7751 (tm) outliers start: 55 outliers final: 36 residues processed: 191 average time/residue: 0.1160 time to fit residues: 33.2003 Evaluate side-chains 184 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1331 ARG Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1429 SER Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1385 LYS Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 49 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 719 GLN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.123365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093071 restraints weight = 28294.974| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.90 r_work: 0.3246 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15104 Z= 0.107 Angle : 0.483 9.619 20372 Z= 0.249 Chirality : 0.040 0.231 2229 Planarity : 0.003 0.042 2579 Dihedral : 5.279 61.021 1981 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 23.02 % Favored : 73.81 % 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: 1.61 (0.20), residues: 1769 helix: 1.96 (0.17), residues: 1019 sheet: -0.45 (0.40), residues: 172 loop : 0.02 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 846 TYR 0.020 0.001 TYR B1127 PHE 0.025 0.001 PHE A 801 TRP 0.011 0.001 TRP B 586 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00246 (15104) covalent geometry : angle 0.48341 (20372) hydrogen bonds : bond 0.03276 ( 775) hydrogen bonds : angle 3.91187 ( 2253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7408 (pt0) cc_final: 0.7033 (pt0) REVERT: A 553 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8546 (mtt90) REVERT: A 664 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8790 (mp) REVERT: A 717 MET cc_start: 0.8739 (ttm) cc_final: 0.8395 (ttt) REVERT: A 731 LYS cc_start: 0.7577 (ptmt) cc_final: 0.6905 (mttt) REVERT: A 863 ARG cc_start: 0.8570 (mmp-170) cc_final: 0.8265 (mtm180) REVERT: A 871 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 930 ASP cc_start: 0.8183 (t70) cc_final: 0.7895 (t70) REVERT: A 1056 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 1074 SER cc_start: 0.9243 (t) cc_final: 0.8974 (p) REVERT: A 1111 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8763 (tp) REVERT: A 1253 TYR cc_start: 0.7761 (m-80) cc_final: 0.7464 (m-80) REVERT: A 1331 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7513 (ptt-90) REVERT: A 1495 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7669 (tttt) REVERT: A 1528 LEU cc_start: 0.7808 (tt) cc_final: 0.7150 (mt) REVERT: B 501 ASP cc_start: 0.8134 (t0) cc_final: 0.7393 (p0) REVERT: B 570 MET cc_start: 0.7918 (ptp) cc_final: 0.7690 (mtp) REVERT: B 606 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8195 (mp) REVERT: B 1105 TRP cc_start: 0.6816 (m-90) cc_final: 0.4777 (t60) REVERT: B 1227 TYR cc_start: 0.8273 (m-80) cc_final: 0.7930 (m-80) REVERT: B 1327 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7587 (tp) REVERT: B 1344 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 1348 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 1425 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 1561 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7768 (tm) outliers start: 52 outliers final: 35 residues processed: 185 average time/residue: 0.1100 time to fit residues: 30.7986 Evaluate side-chains 182 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1331 ARG Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1385 LYS Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1538 CYS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 719 GLN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092503 restraints weight = 28239.275| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.88 r_work: 0.3237 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15104 Z= 0.120 Angle : 0.497 9.736 20372 Z= 0.255 Chirality : 0.041 0.231 2229 Planarity : 0.004 0.042 2579 Dihedral : 5.193 61.071 1977 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.11 % Allowed : 23.26 % Favored : 73.63 % 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: 1.59 (0.20), residues: 1769 helix: 1.95 (0.17), residues: 1019 sheet: -0.45 (0.40), residues: 172 loop : 0.00 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 846 TYR 0.024 0.001 TYR B1127 PHE 0.026 0.001 PHE A 801 TRP 0.010 0.001 TRP B 586 HIS 0.010 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00281 (15104) covalent geometry : angle 0.49750 (20372) hydrogen bonds : bond 0.03393 ( 775) hydrogen bonds : angle 3.92856 ( 2253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7419 (pt0) cc_final: 0.7045 (pt0) REVERT: A 553 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8558 (mtt90) REVERT: A 664 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (mp) REVERT: A 717 MET cc_start: 0.8750 (ttm) cc_final: 0.8469 (ttt) REVERT: A 731 LYS cc_start: 0.7619 (ptmt) cc_final: 0.6975 (mttt) REVERT: A 812 TYR cc_start: 0.8642 (t80) cc_final: 0.8336 (t80) REVERT: A 863 ARG cc_start: 0.8596 (mmp-170) cc_final: 0.8275 (mtm180) REVERT: A 871 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 930 ASP cc_start: 0.8205 (t70) cc_final: 0.7915 (t70) REVERT: A 1074 SER cc_start: 0.9247 (t) cc_final: 0.8994 (p) REVERT: A 1111 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8768 (tp) REVERT: A 1253 TYR cc_start: 0.7781 (m-80) cc_final: 0.7501 (m-80) REVERT: A 1331 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7529 (ptt-90) REVERT: A 1495 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (tttt) REVERT: A 1528 LEU cc_start: 0.7823 (tt) cc_final: 0.7150 (mt) REVERT: B 501 ASP cc_start: 0.8156 (t0) cc_final: 0.7438 (p0) REVERT: B 570 MET cc_start: 0.7902 (ptp) cc_final: 0.7671 (mtp) REVERT: B 606 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 1105 TRP cc_start: 0.6819 (m-90) cc_final: 0.4801 (t60) REVERT: B 1127 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6916 (t80) REVERT: B 1227 TYR cc_start: 0.8260 (m-80) cc_final: 0.7922 (m-80) REVERT: B 1327 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7542 (tp) REVERT: B 1344 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 1348 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 1425 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8783 (p) REVERT: B 1561 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7762 (tm) outliers start: 51 outliers final: 38 residues processed: 182 average time/residue: 0.1179 time to fit residues: 32.0622 Evaluate side-chains 186 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1331 ARG Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 1119 ILE Chi-restraints excluded: chain B residue 1127 TYR Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain B residue 1327 LEU Chi-restraints excluded: chain B residue 1344 PHE Chi-restraints excluded: chain B residue 1348 LEU Chi-restraints excluded: chain B residue 1385 LYS Chi-restraints excluded: chain B residue 1401 THR Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1425 THR Chi-restraints excluded: chain B residue 1436 SER Chi-restraints excluded: chain B residue 1538 CYS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1589 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 719 GLN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.122996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092787 restraints weight = 28099.875| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.87 r_work: 0.3244 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15104 Z= 0.116 Angle : 0.500 9.884 20372 Z= 0.255 Chirality : 0.040 0.230 2229 Planarity : 0.003 0.043 2579 Dihedral : 5.177 60.807 1977 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 23.14 % Favored : 73.69 % 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: 1.61 (0.20), residues: 1769 helix: 1.97 (0.17), residues: 1020 sheet: -0.43 (0.40), residues: 172 loop : 0.01 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 846 TYR 0.021 0.001 TYR B1127 PHE 0.025 0.001 PHE A 801 TRP 0.011 0.001 TRP B 586 HIS 0.010 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00271 (15104) covalent geometry : angle 0.50031 (20372) hydrogen bonds : bond 0.03353 ( 775) hydrogen bonds : angle 3.91355 ( 2253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3495.66 seconds wall clock time: 60 minutes 48.76 seconds (3648.76 seconds total)