Starting phenix.real_space_refine on Sat Sep 12 09:35:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oya_71012/09_2026/9oya_71012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oya_71012/09_2026/9oya_71012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oya_71012/09_2026/9oya_71012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oya_71012/09_2026/9oya_71012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oya_71012/09_2026/9oya_71012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oya_71012/09_2026/9oya_71012.map" } resolution = 3.44 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= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 90 5.16 5 C 9111 2.51 5 N 2444 2.21 5 O 2623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14270 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 14242 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1801, 14231 Classifications: {'peptide': 1801} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 77, 'TRANS': 1723} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 41 Conformer: "B" Number of residues, atoms: 1801, 14231 Classifications: {'peptide': 1801} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 77, 'TRANS': 1723} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 41 bond proxies already assigned to first conformer: 14482 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B1908 " occ=0.49 ... (20 atoms not shown) pdb=" CZ BPHE B1908 " occ=0.51 Time building chain proxies: 5.09, per 1000 atoms: 0.36 Number of scatterers: 14270 At special positions: 0 Unit cell: (127.16, 113.135, 144.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 2 15.00 O 2623 8.00 N 2444 7.00 C 9111 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: 1.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 15 sheets defined 33.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'B' and resid 543 through 555 removed outlier: 3.757A pdb=" N LEU B 547 " --> pdb=" O HIS B 543 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 4.576A pdb=" N LYS B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 596 Processing helix chain 'B' and resid 599 through 611 removed outlier: 3.925A pdb=" N GLY B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 644 through 659 removed outlier: 3.914A pdb=" N GLY B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 Processing helix chain 'B' and resid 670 through 680 removed outlier: 3.622A pdb=" N VAL B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 701 Processing helix chain 'B' and resid 705 through 719 Processing helix chain 'B' and resid 721 through 731 removed outlier: 3.777A pdb=" N VAL B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 754 through 764 removed outlier: 3.872A pdb=" N VAL B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 781 Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.710A pdb=" N LEU B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 853 removed outlier: 3.753A pdb=" N SER B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.546A pdb=" N SER B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B1002 " --> pdb=" O ASP B 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 997 through 1002' Processing helix chain 'B' and resid 1005 through 1011 removed outlier: 3.910A pdb=" N HIS B1009 " --> pdb=" O CYS B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1034 removed outlier: 3.748A pdb=" N CYS B1031 " --> pdb=" O PRO B1027 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B1032 " --> pdb=" O GLN B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1057 removed outlier: 3.561A pdb=" N MET B1057 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1191 through 1195 removed outlier: 3.504A pdb=" N ASN B1194 " --> pdb=" O ALA B1191 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1217 removed outlier: 3.742A pdb=" N TRP B1217 " --> pdb=" O PRO B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1240 through 1245 Processing helix chain 'B' and resid 1261 through 1267 Processing helix chain 'B' and resid 1285 through 1291 Processing helix chain 'B' and resid 1314 through 1328 Processing helix chain 'B' and resid 1348 through 1355 removed outlier: 3.633A pdb=" N MET B1355 " --> pdb=" O LEU B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1398 through 1402 Processing helix chain 'B' and resid 1404 through 1409 removed outlier: 3.584A pdb=" N MET B1409 " --> pdb=" O PRO B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1422 through 1424 No H-bonds generated for 'chain 'B' and resid 1422 through 1424' Processing helix chain 'B' and resid 1426 through 1442 Proline residue: B1433 - end of helix Processing helix chain 'B' and resid 1463 through 1468 Processing helix chain 'B' and resid 1469 through 1474 removed outlier: 3.614A pdb=" N LEU B1474 " --> pdb=" O THR B1470 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1509 Processing helix chain 'B' and resid 1517 through 1520 Processing helix chain 'B' and resid 1525 through 1541 removed outlier: 4.077A pdb=" N LYS B1539 " --> pdb=" O LEU B1535 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B1540 " --> pdb=" O SER B1536 " (cutoff:3.500A) Processing helix chain 'B' and resid 1550 through 1560 Processing helix chain 'B' and resid 1568 through 1579 removed outlier: 3.569A pdb=" N ALA B1572 " --> pdb=" O GLU B1568 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1593 removed outlier: 3.842A pdb=" N SER B1593 " --> pdb=" O LEU B1590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1590 through 1593' Processing helix chain 'B' and resid 1645 through 1653 removed outlier: 3.553A pdb=" N PHE B1650 " --> pdb=" O MET B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1703 through 1715 removed outlier: 3.921A pdb=" N ILE B1715 " --> pdb=" O ARG B1711 " (cutoff:3.500A) Processing helix chain 'B' and resid 1770 through 1792 Processing helix chain 'B' and resid 1829 through 1834 Processing helix chain 'B' and resid 1852 through 1856 Processing helix chain 'B' and resid 1913 through 1925 removed outlier: 3.640A pdb=" N VAL B1923 " --> pdb=" O GLN B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1961 removed outlier: 3.574A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1988 removed outlier: 3.531A pdb=" N HIS B1972 " --> pdb=" O ARG B1968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1996 through 1998 No H-bonds generated for 'chain 'B' and resid 1996 through 1998' Processing helix chain 'B' and resid 2040 through 2045 removed outlier: 3.635A pdb=" N ARG B2045 " --> pdb=" O PRO B2041 " (cutoff:3.500A) Processing helix chain 'B' and resid 2053 through 2068 removed outlier: 3.626A pdb=" N TYR B2057 " --> pdb=" O GLN B2053 " (cutoff:3.500A) Processing helix chain 'B' and resid 2074 through 2079 Processing helix chain 'B' and resid 2079 through 2090 removed outlier: 3.867A pdb=" N GLU B2085 " --> pdb=" O ASN B2081 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B2087 " --> pdb=" O PHE B2083 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2100 Processing helix chain 'B' and resid 2107 through 2115 Processing helix chain 'B' and resid 2126 through 2133 removed outlier: 3.525A pdb=" N ASP B2130 " --> pdb=" O ALA B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2134 through 2139 removed outlier: 4.164A pdb=" N VAL B2138 " --> pdb=" O SER B2134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B2139 " --> pdb=" O ALA B2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2134 through 2139' Processing helix chain 'B' and resid 2208 through 2211 Processing helix chain 'B' and resid 2389 through 2395 Processing helix chain 'B' and resid 2499 through 2524 removed outlier: 3.695A pdb=" N GLN B2505 " --> pdb=" O PRO B2501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 796 through 797 removed outlier: 6.618A pdb=" N ILE B 803 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 987 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B1016 " --> pdb=" O ASP B1041 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B1040 " --> pdb=" O ASP B1064 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B1063 " --> pdb=" O ASN B1089 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE B1158 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B1250 " --> pdb=" O ASP B1274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1329 through 1332 removed outlier: 4.125A pdb=" N GLN B1521 " --> pdb=" O TYR B1332 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1374 through 1379 removed outlier: 6.929A pdb=" N MET B1335 " --> pdb=" O ASN B1391 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N LEU B1414 " --> pdb=" O ARG B1334 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS B1336 " --> pdb=" O LEU B1414 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU B1416 " --> pdb=" O LYS B1336 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET B1338 " --> pdb=" O LEU B1416 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL B1418 " --> pdb=" O MET B1338 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B1340 " --> pdb=" O VAL B1418 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ASP B1420 " --> pdb=" O VAL B1340 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ILE B1448 " --> pdb=" O ALA B1413 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR B1415 " --> pdb=" O ILE B1448 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL B1450 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR B1452 " --> pdb=" O ALA B1417 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR B1419 " --> pdb=" O THR B1452 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B1447 " --> pdb=" O ILE B1482 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B1484 " --> pdb=" O VAL B1447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1547 through 1549 Processing sheet with id=AA5, first strand: chain 'B' and resid 1730 through 1731 removed outlier: 4.996A pdb=" N ASN B1741 " --> pdb=" O CYS B1748 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS B1748 " --> pdb=" O ASN B1741 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B1747 " --> pdb=" O PRO B1768 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B1762 " --> pdb=" O GLU B1753 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B1692 " --> pdb=" O LEU B1813 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AA7, first strand: chain 'B' and resid 1894 through 1897 removed outlier: 3.522A pdb=" N TYR B1894 " --> pdb=" O VAL B1905 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1904 " --> pdb=" O MET B1947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2000 through 2002 Processing sheet with id=AA9, first strand: chain 'B' and resid 2140 through 2145 removed outlier: 6.445A pdb=" N LEU B2140 " --> pdb=" O ASP B2497 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B2497 " --> pdb=" O LEU B2140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B2142 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS B2467 " --> pdb=" O LEU B2463 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B2463 " --> pdb=" O LYS B2467 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B2475 " --> pdb=" O VAL B2455 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL B2455 " --> pdb=" O TYR B2475 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 2156 through 2157 removed outlier: 6.516A pdb=" N GLY B2177 " --> pdb=" O VAL B2194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2199 through 2207 Processing sheet with id=AB3, first strand: chain 'B' and resid 2245 through 2250 removed outlier: 6.223A pdb=" N GLY B2266 " --> pdb=" O THR B2246 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B2248 " --> pdb=" O LEU B2264 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B2264 " --> pdb=" O LEU B2248 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B2250 " --> pdb=" O PHE B2262 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B2262 " --> pdb=" O CYS B2250 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B2267 " --> pdb=" O LYS B2271 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS B2271 " --> pdb=" O THR B2267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2300 through 2305 removed outlier: 3.850A pdb=" N CYS B2302 " --> pdb=" O GLY B2318 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B2325 " --> pdb=" O LYS B2334 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B2334 " --> pdb=" O SER B2325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2354 through 2358 removed outlier: 7.170A pdb=" N ALA B2366 " --> pdb=" O ILE B2355 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL B2357 " --> pdb=" O TYR B2364 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B2364 " --> pdb=" O VAL B2357 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS B2367 " --> pdb=" O VAL B2372 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL B2372 " --> pdb=" O LYS B2367 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B2377 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B2383 " --> pdb=" O ASP B2377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2414 through 2419 removed outlier: 3.506A pdb=" N THR B2416 " --> pdb=" O GLY B2428 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B2446 " --> pdb=" O LEU B2436 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4122 1.33 - 1.46: 2291 1.46 - 1.58: 7988 1.58 - 1.70: 3 1.70 - 1.82: 134 Bond restraints: 14538 Sorted by residual: bond pdb=" C5 GDP B2601 " pdb=" C4 GDP B2601 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C5 GDP B2601 " pdb=" C6 GDP B2601 " ideal model delta sigma weight residual 1.490 1.414 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C6 GDP B2601 " pdb=" N1 GDP B2601 " ideal model delta sigma weight residual 1.337 1.394 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" N THR B1343 " pdb=" CA THR B1343 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.70e+00 bond pdb=" N GLU B1878 " pdb=" CA GLU B1878 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.26e-02 6.30e+03 5.70e+00 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 19152 2.29 - 4.58: 424 4.58 - 6.87: 67 6.87 - 9.16: 21 9.16 - 11.45: 6 Bond angle restraints: 19670 Sorted by residual: angle pdb=" C THR B1849 " pdb=" N ILE B1850 " pdb=" CA ILE B1850 " ideal model delta sigma weight residual 123.33 119.06 4.27 8.70e-01 1.32e+00 2.41e+01 angle pdb=" N LYS B1347 " pdb=" CA LYS B1347 " pdb=" C LYS B1347 " ideal model delta sigma weight residual 114.04 108.33 5.71 1.24e+00 6.50e-01 2.12e+01 angle pdb=" C ASN B1644 " pdb=" N TYR B1645 " pdb=" CA TYR B1645 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C ASP B1756 " pdb=" N ASN B1757 " pdb=" CA ASN B1757 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C3' GDP B2601 " pdb=" C2' GDP B2601 " pdb=" C1' GDP B2601 " ideal model delta sigma weight residual 111.00 99.68 11.32 3.00e+00 1.11e-01 1.42e+01 ... (remaining 19665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.38: 8312 20.38 - 40.76: 505 40.76 - 61.14: 54 61.14 - 81.52: 22 81.52 - 101.90: 5 Dihedral angle restraints: 8898 sinusoidal: 3630 harmonic: 5268 Sorted by residual: dihedral pdb=" CA PHE B1306 " pdb=" C PHE B1306 " pdb=" N ASP B1307 " pdb=" CA ASP B1307 " ideal model delta harmonic sigma weight residual -180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" O2B GDP B2601 " pdb=" O3A GDP B2601 " pdb=" PB GDP B2601 " pdb=" PA GDP B2601 " ideal model delta sinusoidal sigma weight residual -180.00 -78.10 -101.90 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" C4' GDP B2601 " pdb=" O5' GDP B2601 " pdb=" C5' GDP B2601 " pdb=" PA GDP B2601 " ideal model delta sinusoidal sigma weight residual 180.02 89.48 90.54 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 8895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1693 0.052 - 0.105: 471 0.105 - 0.157: 106 0.157 - 0.209: 8 0.209 - 0.262: 3 Chirality restraints: 2281 Sorted by residual: chirality pdb=" CB VAL B 632 " pdb=" CA VAL B 632 " pdb=" CG1 VAL B 632 " pdb=" CG2 VAL B 632 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB THR B2223 " pdb=" CA THR B2223 " pdb=" OG1 THR B2223 " pdb=" CG2 THR B2223 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU B 673 " pdb=" CB LEU B 673 " pdb=" CD1 LEU B 673 " pdb=" CD2 LEU B 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2278 not shown) Planarity restraints: 2489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 676 " -0.023 2.00e-02 2.50e+03 3.12e-02 1.70e+01 pdb=" CG PHE B 676 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE B 676 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 676 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE B 676 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 676 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 676 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B2168 " 0.025 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP B2168 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B2168 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B2168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B2168 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B2168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B2168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B2168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B2168 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B2168 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1845 " 0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO B1846 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B1846 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B1846 " 0.042 5.00e-02 4.00e+02 ... (remaining 2486 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1267 2.75 - 3.29: 14023 3.29 - 3.82: 22398 3.82 - 4.36: 27289 4.36 - 4.90: 46547 Nonbonded interactions: 111524 Sorted by model distance: nonbonded pdb=" OG1 THR B2267 " pdb=" OD1 ASP B2269 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU B1544 " pdb=" OG SER B1636 " model vdw 2.277 3.040 nonbonded pdb=" O VAL B2152 " pdb=" OH TYR B2475 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B1992 " pdb=" OD1 ASN B1999 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASP B1484 " pdb=" N TYR B1485 " model vdw 2.290 3.120 ... (remaining 111519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.49 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 0.114 14538 Z= 0.194 Angle : 0.841 11.453 19670 Z= 0.433 Chirality : 0.050 0.262 2281 Planarity : 0.007 0.077 2489 Dihedral : 13.509 101.899 5466 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.84 % Favored : 90.05 % Rotamer: Outliers : 0.12 % Allowed : 0.19 % Favored : 99.69 % 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: -2.03 (0.19), residues: 1782 helix: -0.85 (0.22), residues: 525 sheet: -0.80 (0.31), residues: 291 loop : -1.83 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1941 TYR 0.016 0.002 TYR B1898 PHE 0.070 0.002 PHE B 676 TRP 0.064 0.002 TRP B2168 HIS 0.010 0.001 HIS B1758 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (14538) covalent geometry : angle 0.84122 / 0.43 (19670) hydrogen bonds : bond 0.14980 / 9.79 ( 482) hydrogen bonds : angle 6.73544 / 4.82 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.488 Fit side-chains REVERT: B 1062 ASN cc_start: 0.8176 (t0) cc_final: 0.7924 (t0) REVERT: B 1317 ASP cc_start: 0.7658 (m-30) cc_final: 0.7246 (m-30) REVERT: B 1719 MET cc_start: 0.7075 (ppp) cc_final: 0.6181 (ppp) REVERT: B 2167 ILE cc_start: 0.7741 (mm) cc_final: 0.7494 (mm) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.0986 time to fit residues: 32.7068 Evaluate side-chains 168 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 690 GLN B1039 HIS B1437 ASN B1741 ASN B1998 HIS B2391 HIS B2502 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.173906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125555 restraints weight = 37802.359| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 4.19 r_work: 0.3395 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14538 Z= 0.193 Angle : 0.691 11.144 19670 Z= 0.351 Chirality : 0.046 0.161 2281 Planarity : 0.005 0.062 2489 Dihedral : 5.880 81.804 1929 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.23 % Favored : 89.71 % Rotamer: Outliers : 0.87 % Allowed : 6.37 % Favored : 92.75 % 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: -1.60 (0.20), residues: 1782 helix: -0.14 (0.23), residues: 534 sheet: -0.75 (0.30), residues: 312 loop : -1.74 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1941 TYR 0.012 0.001 TYR B1332 PHE 0.029 0.002 PHE B 676 TRP 0.030 0.002 TRP B2168 HIS 0.007 0.001 HIS B 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (14538) covalent geometry : angle 0.69056 / 0.35 (19670) hydrogen bonds : bond 0.04346 / 3.02 ( 482) hydrogen bonds : angle 5.20511 / 3.71 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.592 Fit side-chains REVERT: B 1314 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6777 (ttpt) REVERT: B 1317 ASP cc_start: 0.7937 (m-30) cc_final: 0.7455 (m-30) REVERT: B 1606 ILE cc_start: 0.6832 (tp) cc_final: 0.6343 (tp) REVERT: B 1687 ASN cc_start: 0.8190 (t0) cc_final: 0.7678 (t0) REVERT: B 2167 ILE cc_start: 0.8159 (mm) cc_final: 0.7776 (mm) outliers start: 14 outliers final: 11 residues processed: 185 average time/residue: 0.1053 time to fit residues: 30.8881 Evaluate side-chains 174 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1232 ILE Chi-restraints excluded: chain B residue 1306 PHE Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1776 LEU Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 2358 VAL Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 132 optimal weight: 0.0270 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1117 ASN B1998 HIS B2391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.176352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127295 restraints weight = 58854.872| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 5.95 r_work: 0.3382 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14538 Z= 0.120 Angle : 0.620 12.846 19670 Z= 0.312 Chirality : 0.044 0.148 2281 Planarity : 0.005 0.053 2489 Dihedral : 5.434 74.252 1929 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.16 % Favored : 90.78 % Rotamer: Outliers : 0.87 % Allowed : 8.18 % Favored : 90.94 % 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: -1.50 (0.20), residues: 1782 helix: 0.12 (0.23), residues: 539 sheet: -0.79 (0.30), residues: 312 loop : -1.77 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1941 TYR 0.010 0.001 TYR B1332 PHE 0.021 0.001 PHE B 676 TRP 0.022 0.001 TRP B1742 HIS 0.006 0.001 HIS B1039 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14538) covalent geometry : angle 0.61972 / 0.31 (19670) hydrogen bonds : bond 0.03717 / 2.58 ( 482) hydrogen bonds : angle 4.92333 / 3.50 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.587 Fit side-chains REVERT: B 998 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7892 (t0) REVERT: B 1309 LYS cc_start: 0.9074 (tppt) cc_final: 0.8659 (tmtt) REVERT: B 1314 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6769 (mtmm) REVERT: B 1317 ASP cc_start: 0.7912 (m-30) cc_final: 0.7536 (m-30) REVERT: B 1687 ASN cc_start: 0.8193 (t0) cc_final: 0.7553 (t0) REVERT: B 1719 MET cc_start: 0.7481 (ppp) cc_final: 0.6419 (ppp) REVERT: B 1877 PHE cc_start: 0.8810 (t80) cc_final: 0.8478 (t80) REVERT: B 1947 MET cc_start: 0.7128 (mtp) cc_final: 0.6036 (mmm) REVERT: B 2167 ILE cc_start: 0.8129 (mm) cc_final: 0.7752 (mm) outliers start: 14 outliers final: 7 residues processed: 177 average time/residue: 0.1014 time to fit residues: 28.9488 Evaluate side-chains 165 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1306 PHE Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1776 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1093 ASN B1310 HIS B1437 ASN B1998 HIS B2391 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.176027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126479 restraints weight = 46636.168| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 5.02 r_work: 0.3417 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14538 Z= 0.122 Angle : 0.601 7.655 19670 Z= 0.305 Chirality : 0.044 0.148 2281 Planarity : 0.005 0.073 2489 Dihedral : 5.250 69.249 1929 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.61 % Favored : 90.33 % Rotamer: Outliers : 1.12 % Allowed : 8.68 % Favored : 90.19 % 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: 1782 helix: 0.20 (0.23), residues: 549 sheet: -0.72 (0.31), residues: 307 loop : -1.81 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1941 TYR 0.014 0.001 TYR B1898 PHE 0.017 0.001 PHE B 676 TRP 0.017 0.001 TRP B1742 HIS 0.006 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (14538) covalent geometry : angle 0.60113 / 0.30 (19670) hydrogen bonds : bond 0.03507 / 2.45 ( 482) hydrogen bonds : angle 4.79168 / 3.39 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.560 Fit side-chains REVERT: B 595 MET cc_start: 0.6036 (mtm) cc_final: 0.5831 (mtm) REVERT: B 998 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7951 (t0) REVERT: B 1309 LYS cc_start: 0.9104 (tppt) cc_final: 0.8749 (tmtt) REVERT: B 1314 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6950 (mtpt) REVERT: B 1317 ASP cc_start: 0.7883 (m-30) cc_final: 0.7543 (m-30) REVERT: B 1606 ILE cc_start: 0.6671 (tp) cc_final: 0.6240 (tp) REVERT: B 1687 ASN cc_start: 0.8235 (t0) cc_final: 0.7666 (t0) REVERT: B 1719 MET cc_start: 0.7316 (ppp) cc_final: 0.6602 (ppp) REVERT: B 1877 PHE cc_start: 0.8812 (t80) cc_final: 0.8449 (t80) REVERT: B 2058 SER cc_start: 0.8911 (t) cc_final: 0.8516 (m) REVERT: B 2167 ILE cc_start: 0.8115 (mm) cc_final: 0.7687 (mm) REVERT: B 2168 TRP cc_start: 0.7787 (m100) cc_final: 0.7461 (m100) outliers start: 18 outliers final: 13 residues processed: 174 average time/residue: 0.1084 time to fit residues: 29.7036 Evaluate side-chains 173 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1175 MET Chi-restraints excluded: chain B residue 1232 ILE Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1306 PHE Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1660 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 1776 LEU Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 0.0970 chunk 132 optimal weight: 0.0070 chunk 136 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1437 ASN B2391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.177888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129156 restraints weight = 46953.522| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 5.14 r_work: 0.3448 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14538 Z= 0.103 Angle : 0.583 10.571 19670 Z= 0.293 Chirality : 0.043 0.162 2281 Planarity : 0.004 0.064 2489 Dihedral : 5.025 63.575 1929 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 1.06 % Allowed : 9.62 % Favored : 89.32 % 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: -1.28 (0.20), residues: 1782 helix: 0.45 (0.24), residues: 539 sheet: -0.67 (0.31), residues: 304 loop : -1.73 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1412 TYR 0.009 0.001 TYR B2064 PHE 0.018 0.001 PHE B 676 TRP 0.015 0.001 TRP B1742 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (14538) covalent geometry : angle 0.58334 / 0.29 (19670) hydrogen bonds : bond 0.03139 / 2.18 ( 482) hydrogen bonds : angle 4.62280 / 3.26 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: B 998 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7924 (t0) REVERT: B 1317 ASP cc_start: 0.7899 (m-30) cc_final: 0.7460 (m-30) REVERT: B 1606 ILE cc_start: 0.6552 (tp) cc_final: 0.6144 (tp) REVERT: B 1687 ASN cc_start: 0.8176 (t0) cc_final: 0.7571 (t0) REVERT: B 1719 MET cc_start: 0.7104 (ppp) cc_final: 0.6770 (ppp) REVERT: B 1947 MET cc_start: 0.6443 (mmm) cc_final: 0.6223 (mmm) REVERT: B 2058 SER cc_start: 0.8931 (t) cc_final: 0.8537 (m) REVERT: B 2064 TYR cc_start: 0.9208 (t80) cc_final: 0.8998 (t80) REVERT: B 2167 ILE cc_start: 0.8143 (mm) cc_final: 0.7734 (mm) REVERT: B 2168 TRP cc_start: 0.7850 (m100) cc_final: 0.7506 (m100) outliers start: 17 outliers final: 13 residues processed: 192 average time/residue: 0.0987 time to fit residues: 30.6988 Evaluate side-chains 181 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1175 MET Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1387 ASP Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1660 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 1776 LEU Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 0.9980 chunk 154 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 102 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1437 ASN B2391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.177361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128056 restraints weight = 46916.643| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 5.06 r_work: 0.3448 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14538 Z= 0.108 Angle : 0.596 11.542 19670 Z= 0.297 Chirality : 0.043 0.152 2281 Planarity : 0.004 0.060 2489 Dihedral : 4.922 59.217 1929 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.44 % Favored : 90.50 % Rotamer: Outliers : 1.06 % Allowed : 10.43 % Favored : 88.51 % 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: -1.24 (0.20), residues: 1782 helix: 0.48 (0.23), residues: 546 sheet: -0.63 (0.31), residues: 304 loop : -1.72 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1412 TYR 0.009 0.001 TYR B1332 PHE 0.014 0.001 PHE B 676 TRP 0.014 0.001 TRP B1742 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14538) covalent geometry : angle 0.59569 / 0.30 (19670) hydrogen bonds : bond 0.03098 / 2.17 ( 482) hydrogen bonds : angle 4.53653 / 3.20 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.603 Fit side-chains REVERT: B 998 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7965 (t0) REVERT: B 1309 LYS cc_start: 0.9138 (tppt) cc_final: 0.8740 (tttt) REVERT: B 1317 ASP cc_start: 0.7884 (m-30) cc_final: 0.7451 (m-30) REVERT: B 1352 GLN cc_start: 0.8013 (tp40) cc_final: 0.7645 (tt0) REVERT: B 1606 ILE cc_start: 0.6452 (tp) cc_final: 0.6028 (tp) REVERT: B 1687 ASN cc_start: 0.8187 (t0) cc_final: 0.7595 (t0) REVERT: B 1719 MET cc_start: 0.7145 (ppp) cc_final: 0.6847 (ppp) REVERT: B 1877 PHE cc_start: 0.8824 (t80) cc_final: 0.8545 (t80) REVERT: B 2058 SER cc_start: 0.8947 (t) cc_final: 0.8544 (m) REVERT: B 2167 ILE cc_start: 0.8127 (mm) cc_final: 0.7723 (mm) REVERT: B 2168 TRP cc_start: 0.7870 (m100) cc_final: 0.7518 (m100) outliers start: 17 outliers final: 13 residues processed: 182 average time/residue: 0.1002 time to fit residues: 29.7160 Evaluate side-chains 179 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1175 MET Chi-restraints excluded: chain B residue 1232 ILE Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1387 ASP Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1660 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1437 ASN B2391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.173927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125779 restraints weight = 60685.819| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 6.66 r_work: 0.3317 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14538 Z= 0.153 Angle : 0.639 12.256 19670 Z= 0.318 Chirality : 0.044 0.149 2281 Planarity : 0.004 0.062 2489 Dihedral : 5.039 59.833 1929 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.12 % Favored : 89.83 % Rotamer: Outliers : 1.37 % Allowed : 10.43 % Favored : 88.19 % 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: -1.27 (0.20), residues: 1782 helix: 0.44 (0.23), residues: 549 sheet: -0.71 (0.30), residues: 314 loop : -1.71 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1412 TYR 0.012 0.001 TYR B1277 PHE 0.016 0.001 PHE B1026 TRP 0.014 0.001 TRP B1742 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (14538) covalent geometry : angle 0.63917 / 0.32 (19670) hydrogen bonds : bond 0.03419 / 2.41 ( 482) hydrogen bonds : angle 4.58859 / 3.24 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.584 Fit side-chains REVERT: B 636 TYR cc_start: 0.7092 (t80) cc_final: 0.6830 (t80) REVERT: B 998 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8097 (t0) REVERT: B 1309 LYS cc_start: 0.9143 (tppt) cc_final: 0.8695 (tttt) REVERT: B 1317 ASP cc_start: 0.7980 (m-30) cc_final: 0.7540 (m-30) REVERT: B 1606 ILE cc_start: 0.6643 (tp) cc_final: 0.6192 (tp) REVERT: B 1687 ASN cc_start: 0.8298 (t0) cc_final: 0.7728 (t0) REVERT: B 1719 MET cc_start: 0.7428 (ppp) cc_final: 0.6549 (ppp) REVERT: B 1877 PHE cc_start: 0.8931 (t80) cc_final: 0.8677 (t80) REVERT: B 2058 SER cc_start: 0.8981 (t) cc_final: 0.8600 (m) REVERT: B 2121 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: B 2167 ILE cc_start: 0.8194 (mm) cc_final: 0.7754 (mm) REVERT: B 2168 TRP cc_start: 0.7959 (m100) cc_final: 0.7574 (m100) outliers start: 22 outliers final: 13 residues processed: 180 average time/residue: 0.1054 time to fit residues: 30.2084 Evaluate side-chains 180 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1175 MET Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1232 ILE Chi-restraints excluded: chain B residue 1387 ASP Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1660 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 2121 GLU Chi-restraints excluded: chain B residue 2358 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 129 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 164 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1194 ASN B2391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.175506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127194 restraints weight = 60442.794| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 6.08 r_work: 0.3356 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14538 Z= 0.120 Angle : 0.619 12.532 19670 Z= 0.306 Chirality : 0.044 0.148 2281 Planarity : 0.004 0.059 2489 Dihedral : 4.880 55.178 1929 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.67 % Favored : 90.28 % Rotamer: Outliers : 1.06 % Allowed : 11.12 % Favored : 87.82 % 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: -1.22 (0.20), residues: 1782 helix: 0.49 (0.23), residues: 548 sheet: -0.68 (0.31), residues: 310 loop : -1.69 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1412 TYR 0.010 0.001 TYR B1332 PHE 0.014 0.001 PHE B 676 TRP 0.014 0.001 TRP B1742 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14538) covalent geometry : angle 0.61888 / 0.31 (19670) hydrogen bonds : bond 0.03200 / 2.26 ( 482) hydrogen bonds : angle 4.56762 / 3.22 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.574 Fit side-chains REVERT: B 636 TYR cc_start: 0.7104 (t80) cc_final: 0.6829 (t80) REVERT: B 998 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (t0) REVERT: B 1083 PRO cc_start: 0.8782 (Cg_endo) cc_final: 0.8479 (Cg_exo) REVERT: B 1309 LYS cc_start: 0.9125 (tppt) cc_final: 0.8692 (tttt) REVERT: B 1317 ASP cc_start: 0.7951 (m-30) cc_final: 0.7524 (m-30) REVERT: B 1352 GLN cc_start: 0.8064 (tp40) cc_final: 0.7609 (tt0) REVERT: B 1606 ILE cc_start: 0.6529 (tp) cc_final: 0.6080 (tp) REVERT: B 1687 ASN cc_start: 0.8307 (t0) cc_final: 0.7671 (t0) REVERT: B 1719 MET cc_start: 0.7244 (ppp) cc_final: 0.6574 (ppp) REVERT: B 1877 PHE cc_start: 0.8911 (t80) cc_final: 0.8640 (t80) REVERT: B 2058 SER cc_start: 0.8949 (t) cc_final: 0.8592 (m) REVERT: B 2167 ILE cc_start: 0.8165 (mm) cc_final: 0.7797 (mm) outliers start: 17 outliers final: 12 residues processed: 181 average time/residue: 0.1043 time to fit residues: 30.3184 Evaluate side-chains 179 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1175 MET Chi-restraints excluded: chain B residue 1232 ILE Chi-restraints excluded: chain B residue 1387 ASP Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1660 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 2358 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 167 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1437 ASN B2391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.175635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126773 restraints weight = 57651.630| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 5.95 r_work: 0.3366 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14538 Z= 0.121 Angle : 0.618 12.933 19670 Z= 0.307 Chirality : 0.043 0.150 2281 Planarity : 0.004 0.057 2489 Dihedral : 4.818 53.270 1929 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.39 % Favored : 90.56 % Rotamer: Outliers : 1.06 % Allowed : 10.93 % Favored : 88.01 % 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: -1.19 (0.20), residues: 1782 helix: 0.53 (0.23), residues: 548 sheet: -0.60 (0.31), residues: 306 loop : -1.70 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1412 TYR 0.010 0.001 TYR B1332 PHE 0.014 0.001 PHE B 676 TRP 0.013 0.001 TRP B1742 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14538) covalent geometry : angle 0.61788 / 0.31 (19670) hydrogen bonds : bond 0.03144 / 2.22 ( 482) hydrogen bonds : angle 4.53477 / 3.20 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.596 Fit side-chains REVERT: B 636 TYR cc_start: 0.7099 (t80) cc_final: 0.6842 (t80) REVERT: B 998 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8084 (t0) REVERT: B 1309 LYS cc_start: 0.9125 (tppt) cc_final: 0.8736 (tttt) REVERT: B 1317 ASP cc_start: 0.7937 (m-30) cc_final: 0.7509 (m-30) REVERT: B 1352 GLN cc_start: 0.8032 (tp40) cc_final: 0.7593 (tt0) REVERT: B 1606 ILE cc_start: 0.6456 (tp) cc_final: 0.6030 (tp) REVERT: B 1687 ASN cc_start: 0.8305 (t0) cc_final: 0.7669 (t0) REVERT: B 1719 MET cc_start: 0.7073 (ppp) cc_final: 0.6464 (ppp) REVERT: B 1877 PHE cc_start: 0.8900 (t80) cc_final: 0.8635 (t80) REVERT: B 2058 SER cc_start: 0.8932 (t) cc_final: 0.8574 (m) REVERT: B 2167 ILE cc_start: 0.8159 (mm) cc_final: 0.7796 (mm) outliers start: 17 outliers final: 14 residues processed: 174 average time/residue: 0.0998 time to fit residues: 28.1570 Evaluate side-chains 178 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1175 MET Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain B residue 1232 ILE Chi-restraints excluded: chain B residue 1306 PHE Chi-restraints excluded: chain B residue 1387 ASP Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1660 LEU Chi-restraints excluded: chain B residue 1676 HIS Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 1875 LEU Chi-restraints excluded: chain B residue 2358 VAL Chi-restraints excluded: chain B residue 2419 LEU Chi-restraints excluded: chain B residue 2489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 0.0010 chunk 153 optimal weight: 0.8980 chunk 82 optimal weight: 0.0270 chunk 113 optimal weight: 0.0170 chunk 154 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 overall best weight: 0.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1405 HIS B1437 ASN ** B1684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.181046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132058 restraints weight = 43607.677| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.73 r_work: 0.3511 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (15 function evaluations) r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14538 Z= 0.104 Angle : 0.611 12.873 19670 Z= 0.301 Chirality : 0.043 0.148 2281 Planarity : 0.004 0.052 2489 Dihedral : 4.451 44.705 1929 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 0.75 % Allowed : 11.24 % Favored : 88.01 % 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: -1.06 (0.20), residues: 1782 helix: 0.60 (0.23), residues: 553 sheet: -0.43 (0.32), residues: 297 loop : -1.65 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1412 TYR 0.008 0.001 TYR B1332 PHE 0.012 0.001 PHE B 676 TRP 0.014 0.001 TRP B1742 HIS 0.005 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (14538) covalent geometry : angle 0.61147 / 0.30 (19670) hydrogen bonds : bond 0.02757 / 1.92 ( 482) hydrogen bonds : angle 4.40463 / 3.09 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.593 Fit side-chains REVERT: B 605 LEU cc_start: 0.6778 (mp) cc_final: 0.6315 (tt) REVERT: B 680 SER cc_start: 0.8181 (p) cc_final: 0.7957 (m) REVERT: B 776 THR cc_start: 0.8519 (m) cc_final: 0.8251 (p) REVERT: B 1317 ASP cc_start: 0.7963 (m-30) cc_final: 0.7512 (m-30) REVERT: B 1646 MET cc_start: 0.6769 (mpp) cc_final: 0.6428 (mpp) REVERT: B 1687 ASN cc_start: 0.8114 (t0) cc_final: 0.7536 (t0) REVERT: B 1877 PHE cc_start: 0.8807 (t80) cc_final: 0.8543 (t80) REVERT: B 2058 SER cc_start: 0.8828 (t) cc_final: 0.8504 (m) REVERT: B 2167 ILE cc_start: 0.8048 (mm) cc_final: 0.7673 (mm) REVERT: B 2168 TRP cc_start: 0.7827 (m100) cc_final: 0.7522 (m100) REVERT: B 2523 ARG cc_start: 0.7424 (ttm170) cc_final: 0.7214 (ttm170) outliers start: 12 outliers final: 8 residues processed: 203 average time/residue: 0.1081 time to fit residues: 34.5145 Evaluate side-chains 186 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 1306 PHE Chi-restraints excluded: chain B residue 1387 ASP Chi-restraints excluded: chain B residue 1535 LEU Chi-restraints excluded: chain B residue 1758 HIS Chi-restraints excluded: chain B residue 2358 VAL Chi-restraints excluded: chain B residue 2419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 81 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1147 ASN ** B1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.130537 restraints weight = 42878.231| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 4.57 r_work: 0.3451 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14538 Z= 0.119 Angle : 0.632 11.724 19670 Z= 0.310 Chirality : 0.044 0.148 2281 Planarity : 0.004 0.051 2489 Dihedral : 4.486 45.240 1929 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.71 % Favored : 91.23 % Rotamer: Outliers : 0.69 % Allowed : 11.81 % Favored : 87.51 % 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: -1.06 (0.21), residues: 1782 helix: 0.61 (0.23), residues: 555 sheet: -0.50 (0.31), residues: 300 loop : -1.63 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1412 TYR 0.011 0.001 TYR B2064 PHE 0.018 0.001 PHE B 676 TRP 0.012 0.001 TRP B1791 HIS 0.006 0.001 HIS B1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14538) covalent geometry : angle 0.63180 / 0.31 (19670) hydrogen bonds : bond 0.02960 / 2.07 ( 482) hydrogen bonds : angle 4.39301 / 3.10 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.49 seconds wall clock time: 67 minutes 24.90 seconds (4044.90 seconds total)