Starting phenix.real_space_refine on Sat Sep 12 05:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y67_72555/09_2026/9y67_72555.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y67_72555/09_2026/9y67_72555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y67_72555/09_2026/9y67_72555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y67_72555/09_2026/9y67_72555.map" model { file = "/net/cci-nas-00/data/ceres_data/9y67_72555/09_2026/9y67_72555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y67_72555/09_2026/9y67_72555.cif" } resolution = 3.72 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= 0.017 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 78 5.16 5 C 8406 2.51 5 N 2250 2.21 5 O 2399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 13135 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1708, 13097 Classifications: {'peptide': 1708} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 72, 'TRANS': 1635} Chain breaks: 17 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 622 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 19, 'HIS:plan': 2, 'GLN:plan1': 13, 'TYR:plan': 5, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 289 Conformer: "B" Number of residues, atoms: 1708, 13097 Classifications: {'peptide': 1708} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 72, 'TRANS': 1635} Chain breaks: 17 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 622 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 19, 'HIS:plan': 2, 'GLN:plan1': 13, 'TYR:plan': 5, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 289 bond proxies already assigned to first conformer: 13321 Chain: "A" 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 AHIS A1039 " occ=0.84 ... (18 atoms not shown) pdb=" NE2BHIS A1039 " occ=0.16 Time building chain proxies: 4.04, per 1000 atoms: 0.31 Number of scatterers: 13135 At special positions: 0 Unit cell: (115.005, 111.265, 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 78 16.00 P 2 15.00 O 2399 8.00 N 2250 7.00 C 8406 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: 1.07 Conformation dependent library (CDL) restraints added in 995.7 milliseconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3258 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 33.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 584 through 596 removed outlier: 3.569A pdb=" N SER A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 603 through 612 removed outlier: 4.253A pdb=" N SER A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 643 through 658 removed outlier: 4.075A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 4.196A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 4.337A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.619A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.974A pdb=" N LEU A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 853 removed outlier: 4.605A pdb=" N GLU A 853 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.559A pdb=" N SER A1007 " --> pdb=" O CYS A1004 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A1008 " --> pdb=" O CYS A1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1004 through 1008' Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 4.148A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A1032 " --> pdb=" O GLN A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 3.927A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1245 Processing helix chain 'A' and resid 1261 through 1267 Processing helix chain 'A' and resid 1285 through 1291 Processing helix chain 'A' and resid 1315 through 1328 removed outlier: 3.620A pdb=" N ILE A1319 " --> pdb=" O ALA A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1355 Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.649A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1442 removed outlier: 4.212A pdb=" N LYS A1432 " --> pdb=" O VAL A1428 " (cutoff:3.500A) Proline residue: A1433 - end of helix Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1494 through 1507 Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1539 removed outlier: 4.115A pdb=" N LYS A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1560 Processing helix chain 'A' and resid 1568 through 1579 removed outlier: 3.769A pdb=" N ALA A1572 " --> pdb=" O GLU A1568 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS A1574 " --> pdb=" O PRO A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.776A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A1608 " --> pdb=" O CYS A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1656 Processing helix chain 'A' and resid 1703 through 1716 removed outlier: 4.088A pdb=" N ASN A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A1715 " --> pdb=" O ARG A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1791 removed outlier: 4.763A pdb=" N LEU A1776 " --> pdb=" O LYS A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1835 Processing helix chain 'A' and resid 1913 through 1922 removed outlier: 3.656A pdb=" N LEU A1917 " --> pdb=" O SER A1913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 Processing helix chain 'A' and resid 1963 through 1966 removed outlier: 3.786A pdb=" N LEU A1966 " --> pdb=" O LYS A1963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1963 through 1966' Processing helix chain 'A' and resid 1969 through 1985 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2053 through 2068 removed outlier: 3.628A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2077 Processing helix chain 'A' and resid 2079 through 2090 removed outlier: 4.797A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A2088 " --> pdb=" O ASP A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.668A pdb=" N GLU A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.683A pdb=" N SER A2134 " --> pdb=" O ASP A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2140 removed outlier: 3.587A pdb=" N CYS A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2394 Processing helix chain 'A' and resid 2499 through 2525 removed outlier: 3.932A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A2521 " --> pdb=" O LEU A2517 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A2523 " --> pdb=" O GLU A2519 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.632A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.904A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A1113 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1157 through 1159 removed outlier: 6.834A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A1202 " --> pdb=" O LEU A1178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1249 through 1251 Processing sheet with id=AA5, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA6, first strand: chain 'A' and resid 1376 through 1377 removed outlier: 3.775A pdb=" N MET A1335 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A1340 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A1447 " --> pdb=" O ASP A1484 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N HIS A1486 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A1449 " --> pdb=" O HIS A1486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1582 through 1583 Processing sheet with id=AA8, first strand: chain 'A' and resid 1733 through 1734 removed outlier: 6.883A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 removed outlier: 3.659A pdb=" N VAL A1841 " --> pdb=" O ILE A1850 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1850 " --> pdb=" O VAL A1841 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1894 through 1897 removed outlier: 7.468A pdb=" N MET A1944 " --> pdb=" O ALA A1938 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA A1938 " --> pdb=" O MET A1944 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A1946 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'A' and resid 2142 through 2145 removed outlier: 4.269A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2199 through 2205 removed outlier: 3.786A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A2203 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A2219 " --> pdb=" O THR A2223 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR A2223 " --> pdb=" O THR A2219 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU A2224 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2245 through 2249 removed outlier: 3.531A pdb=" N ALA A2273 " --> pdb=" O VAL A2265 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A2267 " --> pdb=" O LYS A2271 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A2274 " --> pdb=" O LYS A2289 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A2289 " --> pdb=" O ILE A2274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2300 through 2305 removed outlier: 3.765A pdb=" N CYS A2302 " --> pdb=" O GLY A2318 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY A2317 " --> pdb=" O PHE A2324 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A2324 " --> pdb=" O GLY A2317 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A2319 " --> pdb=" O LYS A2322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.419A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL A2359 " --> pdb=" O ALA A2362 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A2362 " --> pdb=" O VAL A2359 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A2387 " --> pdb=" O VAL A2373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2416 through 2419 removed outlier: 3.810A pdb=" N THR A2416 " --> pdb=" O GLY A2428 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A2427 " --> pdb=" O LEU A2435 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A2435 " --> pdb=" O ILE A2427 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A2436 " --> pdb=" O ARG A2446 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3975 1.34 - 1.46: 2259 1.46 - 1.58: 7022 1.58 - 1.70: 3 1.70 - 1.82: 116 Bond restraints: 13375 Sorted by residual: bond pdb=" C5 GDP A2601 " pdb=" C4 GDP A2601 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" N LEU A2140 " pdb=" CA LEU A2140 " ideal model delta sigma weight residual 1.457 1.511 -0.053 1.29e-02 6.01e+03 1.70e+01 bond pdb=" C5 GDP A2601 " pdb=" C6 GDP A2601 " ideal model delta sigma weight residual 1.490 1.412 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N CYS A2139 " pdb=" CA CYS A2139 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" N SER A1508 " pdb=" CA SER A1508 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.02e+01 ... (remaining 13370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 17682 2.73 - 5.46: 370 5.46 - 8.19: 59 8.19 - 10.92: 22 10.92 - 13.64: 3 Bond angle restraints: 18136 Sorted by residual: angle pdb=" N LEU A1509 " pdb=" CA LEU A1509 " pdb=" C LEU A1509 " ideal model delta sigma weight residual 110.80 97.16 13.64 2.13e+00 2.20e-01 4.10e+01 angle pdb=" C LEU A2140 " pdb=" N THR A2141 " pdb=" CA THR A2141 " ideal model delta sigma weight residual 121.54 112.05 9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" N PRO A2105 " pdb=" CA PRO A2105 " pdb=" C PRO A2105 " ideal model delta sigma weight residual 112.47 122.66 -10.19 2.06e+00 2.36e-01 2.45e+01 angle pdb=" C LYS A1906 " pdb=" N ILE A1907 " pdb=" CA ILE A1907 " ideal model delta sigma weight residual 121.97 130.86 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C ARG A1968 " pdb=" N THR A1969 " pdb=" CA THR A1969 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 ... (remaining 18131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7289 17.99 - 35.98: 700 35.98 - 53.97: 106 53.97 - 71.96: 19 71.96 - 89.94: 12 Dihedral angle restraints: 8126 sinusoidal: 3137 harmonic: 4989 Sorted by residual: dihedral pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta harmonic sigma weight residual -180.00 -139.16 -40.84 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CA SER A1091 " pdb=" C SER A1091 " pdb=" N TYR A1092 " pdb=" CA TYR A1092 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLU A2098 " pdb=" C GLU A2098 " pdb=" N TYR A2099 " pdb=" CA TYR A2099 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1765 0.069 - 0.138: 340 0.138 - 0.207: 36 0.207 - 0.276: 2 0.276 - 0.345: 1 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA LEU A1509 " pdb=" N LEU A1509 " pdb=" C LEU A1509 " pdb=" CB LEU A1509 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU A 708 " pdb=" N LEU A 708 " pdb=" C LEU A 708 " pdb=" CB LEU A 708 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CG LEU A1864 " pdb=" CB LEU A1864 " pdb=" CD1 LEU A1864 " pdb=" CD2 LEU A1864 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2141 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A2138 " 0.044 2.00e-02 2.50e+03 8.69e-02 7.55e+01 pdb=" C VAL A2138 " -0.150 2.00e-02 2.50e+03 pdb=" O VAL A2138 " 0.057 2.00e-02 2.50e+03 pdb=" N CYS A2139 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1856 " -0.095 5.00e-02 4.00e+02 1.44e-01 3.31e+01 pdb=" N PRO A1857 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A1857 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1857 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1541 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A1542 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A1542 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1542 " 0.047 5.00e-02 4.00e+02 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 964 2.74 - 3.28: 13175 3.28 - 3.82: 21126 3.82 - 4.36: 24462 4.36 - 4.90: 41415 Nonbonded interactions: 101142 Sorted by model distance: nonbonded pdb=" OG1 THR A2246 " pdb=" O LEU A2300 " model vdw 2.201 3.040 nonbonded pdb=" NE2 HIS A1929 " pdb=" OD1 ASP A1980 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU A1115 " pdb=" OG SER A1137 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASN A1089 " pdb=" OG SER A1091 " model vdw 2.291 3.040 nonbonded pdb=" O PRO A1433 " pdb=" ND2 ASN A1437 " model vdw 2.296 3.120 ... (remaining 101137 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=0.16 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 0.115 13375 Z= 0.212 Angle : 0.979 13.644 18136 Z= 0.487 Chirality : 0.053 0.345 2144 Planarity : 0.008 0.144 2288 Dihedral : 14.445 89.944 4868 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.23 % Favored : 89.11 % Rotamer: Outliers : 0.29 % Allowed : 0.36 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -2.76 (0.19), residues: 1675 helix: -1.25 (0.21), residues: 533 sheet: -1.31 (0.33), residues: 250 loop : -2.40 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2522 TYR 0.028 0.002 TYR A1739 PHE 0.033 0.002 PHE A1088 TRP 0.021 0.002 TRP A1295 HIS 0.013 0.002 HIS A1926 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (13375) covalent geometry : angle 0.97902 / 0.49 (18136) hydrogen bonds : bond 0.17492 / 12.15 ( 425) hydrogen bonds : angle 8.10114 / 5.78 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 200 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 721 ASN cc_start: 0.6340 (OUTLIER) cc_final: 0.6110 (p0) REVERT: A 1509 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7863 (tt) REVERT: A 1715 ILE cc_start: 0.8319 (tp) cc_final: 0.8023 (tp) REVERT: A 1774 CYS cc_start: 0.7890 (m) cc_final: 0.7487 (m) outliers start: 4 outliers final: 0 residues processed: 202 average time/residue: 0.0893 time to fit residues: 28.0373 Evaluate side-chains 156 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 1509 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1407 HIS A1757 ASN A1872 ASN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2391 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.138410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105154 restraints weight = 50538.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.107112 restraints weight = 23203.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.108284 restraints weight = 16745.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.108716 restraints weight = 14403.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.109987 restraints weight = 12335.256| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13375 Z= 0.127 Angle : 0.744 12.785 18136 Z= 0.368 Chirality : 0.047 0.230 2144 Planarity : 0.006 0.114 2288 Dihedral : 5.822 52.865 1812 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.45 % Favored : 90.19 % Rotamer: Outliers : 1.00 % Allowed : 7.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -2.46 (0.20), residues: 1675 helix: -0.74 (0.23), residues: 529 sheet: -1.51 (0.31), residues: 262 loop : -2.27 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2072 TYR 0.022 0.002 TYR A2099 PHE 0.025 0.002 PHE A1088 TRP 0.016 0.002 TRP A1734 HIS 0.013 0.001 HIS A2391 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (13375) covalent geometry : angle 0.74445 / 0.37 (18136) hydrogen bonds : bond 0.03998 / 2.81 ( 425) hydrogen bonds : angle 6.11587 / 4.38 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 724 MET cc_start: 0.8703 (mpp) cc_final: 0.7782 (ttp) REVERT: A 816 SER cc_start: 0.8595 (m) cc_final: 0.8293 (t) REVERT: A 1317 ASP cc_start: 0.8070 (m-30) cc_final: 0.7782 (m-30) REVERT: A 1715 ILE cc_start: 0.8550 (tp) cc_final: 0.8190 (tp) REVERT: A 1869 MET cc_start: 0.7728 (mmm) cc_final: 0.7054 (mmt) REVERT: A 2241 MET cc_start: 0.5144 (tpp) cc_final: 0.4608 (tpp) REVERT: A 2269 ASP cc_start: 0.7950 (p0) cc_final: 0.7669 (t70) REVERT: A 2315 MET cc_start: 0.6464 (tpp) cc_final: 0.6260 (tpp) REVERT: A 2449 TYR cc_start: 0.7959 (p90) cc_final: 0.7750 (p90) outliers start: 14 outliers final: 9 residues processed: 178 average time/residue: 0.0928 time to fit residues: 25.3738 Evaluate side-chains 160 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1757 ASN Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2388 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1741 ASN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2236 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097396 restraints weight = 50565.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099156 restraints weight = 23356.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100359 restraints weight = 16607.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100708 restraints weight = 14378.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.101305 restraints weight = 12630.509| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13375 Z= 0.234 Angle : 0.796 12.107 18136 Z= 0.397 Chirality : 0.049 0.221 2144 Planarity : 0.006 0.093 2288 Dihedral : 5.726 55.772 1810 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.12 % Favored : 88.52 % Rotamer: Outliers : 1.43 % Allowed : 10.71 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -2.46 (0.20), residues: 1675 helix: -0.62 (0.23), residues: 526 sheet: -1.66 (0.29), residues: 278 loop : -2.30 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2072 TYR 0.035 0.002 TYR A1053 PHE 0.016 0.002 PHE A1575 TRP 0.015 0.002 TRP A2104 HIS 0.008 0.002 HIS A1453 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (13375) covalent geometry : angle 0.79597 / 0.40 (18136) hydrogen bonds : bond 0.04050 / 2.87 ( 425) hydrogen bonds : angle 5.91462 / 4.24 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 MET cc_start: 0.8820 (mpp) cc_final: 0.7773 (ttt) REVERT: A 816 SER cc_start: 0.8694 (m) cc_final: 0.8394 (t) REVERT: A 1715 ILE cc_start: 0.8713 (tp) cc_final: 0.8323 (tp) REVERT: A 1745 GLU cc_start: 0.8143 (pp20) cc_final: 0.7922 (pp20) REVERT: A 1747 TYR cc_start: 0.8623 (p90) cc_final: 0.8333 (p90) REVERT: A 1894 TYR cc_start: 0.8435 (m-10) cc_final: 0.8091 (m-10) REVERT: A 2269 ASP cc_start: 0.8094 (p0) cc_final: 0.7594 (t70) REVERT: A 2449 TYR cc_start: 0.8116 (p90) cc_final: 0.7907 (p90) REVERT: A 2522 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8066 (ttp80) outliers start: 20 outliers final: 14 residues processed: 180 average time/residue: 0.0964 time to fit residues: 26.5082 Evaluate side-chains 165 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1477 ARG Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2246 THR Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 0.0870 chunk 83 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1879 GLN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.134414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101746 restraints weight = 53023.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103590 restraints weight = 22660.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104483 restraints weight = 16804.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104927 restraints weight = 13595.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.106429 restraints weight = 12028.754| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13375 Z= 0.123 Angle : 0.707 10.493 18136 Z= 0.349 Chirality : 0.046 0.180 2144 Planarity : 0.005 0.083 2288 Dihedral : 5.360 47.816 1810 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.69 % Favored : 89.95 % Rotamer: Outliers : 1.14 % Allowed : 12.86 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -2.22 (0.20), residues: 1675 helix: -0.38 (0.23), residues: 527 sheet: -1.40 (0.30), residues: 257 loop : -2.23 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1707 TYR 0.030 0.002 TYR A1053 PHE 0.011 0.001 PHE A1088 TRP 0.037 0.002 TRP A1295 HIS 0.006 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13375) covalent geometry : angle 0.70701 / 0.35 (18136) hydrogen bonds : bond 0.03419 / 2.43 ( 425) hydrogen bonds : angle 5.60823 / 4.02 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 724 MET cc_start: 0.8795 (mpp) cc_final: 0.7650 (ttt) REVERT: A 726 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: A 728 LEU cc_start: 0.9080 (tp) cc_final: 0.8695 (tp) REVERT: A 747 GLN cc_start: 0.9321 (mt0) cc_final: 0.8726 (mp10) REVERT: A 751 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8971 (tptt) REVERT: A 816 SER cc_start: 0.8624 (m) cc_final: 0.8316 (t) REVERT: A 1702 MET cc_start: 0.9066 (tpp) cc_final: 0.8664 (tpp) REVERT: A 1715 ILE cc_start: 0.8696 (tp) cc_final: 0.8328 (tp) REVERT: A 1747 TYR cc_start: 0.8578 (p90) cc_final: 0.8295 (p90) REVERT: A 1774 CYS cc_start: 0.8246 (m) cc_final: 0.7981 (m) REVERT: A 1894 TYR cc_start: 0.8407 (m-10) cc_final: 0.8036 (m-10) REVERT: A 2082 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: A 2225 LEU cc_start: 0.7024 (tt) cc_final: 0.6758 (mm) REVERT: A 2269 ASP cc_start: 0.8077 (p0) cc_final: 0.7551 (t70) REVERT: A 2449 TYR cc_start: 0.8050 (p90) cc_final: 0.7843 (p90) outliers start: 16 outliers final: 10 residues processed: 176 average time/residue: 0.0905 time to fit residues: 24.6437 Evaluate side-chains 163 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2447 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 145 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.134206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097653 restraints weight = 41152.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101097 restraints weight = 19487.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103354 restraints weight = 12458.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104799 restraints weight = 9470.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.105758 restraints weight = 7920.391| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13375 Z= 0.129 Angle : 0.700 10.045 18136 Z= 0.348 Chirality : 0.046 0.175 2144 Planarity : 0.005 0.072 2288 Dihedral : 5.259 49.370 1810 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.69 % Favored : 89.95 % Rotamer: Outliers : 1.21 % Allowed : 14.07 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -2.13 (0.20), residues: 1675 helix: -0.26 (0.24), residues: 526 sheet: -1.33 (0.30), residues: 262 loop : -2.21 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2522 TYR 0.027 0.002 TYR A1053 PHE 0.011 0.001 PHE A 691 TRP 0.037 0.002 TRP A1295 HIS 0.009 0.001 HIS A2206 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13375) covalent geometry : angle 0.69970 / 0.35 (18136) hydrogen bonds : bond 0.03307 / 2.34 ( 425) hydrogen bonds : angle 5.50186 / 3.95 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 MET cc_start: 0.8750 (mpp) cc_final: 0.7603 (ttt) REVERT: A 726 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: A 747 GLN cc_start: 0.9306 (mt0) cc_final: 0.8719 (mp10) REVERT: A 751 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8974 (tptt) REVERT: A 787 ILE cc_start: 0.8766 (mt) cc_final: 0.8389 (tt) REVERT: A 816 SER cc_start: 0.8618 (m) cc_final: 0.8288 (t) REVERT: A 1033 THR cc_start: 0.8055 (m) cc_final: 0.7730 (m) REVERT: A 1203 MET cc_start: 0.8085 (mmm) cc_final: 0.7565 (tpp) REVERT: A 1702 MET cc_start: 0.9068 (tpp) cc_final: 0.8756 (tpp) REVERT: A 1715 ILE cc_start: 0.8709 (tp) cc_final: 0.8338 (tp) REVERT: A 1747 TYR cc_start: 0.8419 (p90) cc_final: 0.8167 (p90) REVERT: A 1774 CYS cc_start: 0.8100 (m) cc_final: 0.7876 (m) REVERT: A 1894 TYR cc_start: 0.8360 (m-10) cc_final: 0.7926 (m-10) REVERT: A 2082 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 2168 TRP cc_start: 0.7471 (OUTLIER) cc_final: 0.7159 (t60) REVERT: A 2225 LEU cc_start: 0.7594 (tt) cc_final: 0.7274 (mm) REVERT: A 2269 ASP cc_start: 0.8213 (p0) cc_final: 0.7621 (t70) outliers start: 17 outliers final: 9 residues processed: 170 average time/residue: 0.0880 time to fit residues: 23.2203 Evaluate side-chains 161 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2168 TRP Chi-restraints excluded: chain A residue 2246 THR Chi-restraints excluded: chain A residue 2425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 169 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 136 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2450 ASN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099318 restraints weight = 60990.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101204 restraints weight = 24738.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102392 restraints weight = 18081.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103062 restraints weight = 13990.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105583 restraints weight = 12432.624| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13375 Z= 0.157 Angle : 0.716 10.630 18136 Z= 0.356 Chirality : 0.046 0.169 2144 Planarity : 0.005 0.067 2288 Dihedral : 5.170 29.393 1808 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.71 % Favored : 89.00 % Rotamer: Outliers : 1.36 % Allowed : 14.50 % Favored : 84.14 % 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: -2.17 (0.20), residues: 1675 helix: -0.29 (0.24), residues: 527 sheet: -1.36 (0.30), residues: 262 loop : -2.23 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2522 TYR 0.025 0.002 TYR A1053 PHE 0.021 0.002 PHE A1883 TRP 0.037 0.002 TRP A1295 HIS 0.009 0.001 HIS A2206 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (13375) covalent geometry : angle 0.71581 / 0.36 (18136) hydrogen bonds : bond 0.03308 / 2.36 ( 425) hydrogen bonds : angle 5.50276 / 3.96 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 MET cc_start: 0.8559 (mpp) cc_final: 0.7605 (ttt) REVERT: A 726 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: A 751 LYS cc_start: 0.9320 (mmmm) cc_final: 0.8983 (tptt) REVERT: A 787 ILE cc_start: 0.8803 (mt) cc_final: 0.8419 (tt) REVERT: A 816 SER cc_start: 0.8598 (m) cc_final: 0.8273 (t) REVERT: A 1033 THR cc_start: 0.8158 (m) cc_final: 0.7840 (m) REVERT: A 1168 MET cc_start: 0.8371 (mmm) cc_final: 0.7787 (mmm) REVERT: A 1203 MET cc_start: 0.8080 (mmm) cc_final: 0.7706 (tpp) REVERT: A 1715 ILE cc_start: 0.8762 (tp) cc_final: 0.8407 (tp) REVERT: A 1747 TYR cc_start: 0.8617 (p90) cc_final: 0.8328 (p90) REVERT: A 2082 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: A 2269 ASP cc_start: 0.8164 (p0) cc_final: 0.7570 (t70) outliers start: 19 outliers final: 11 residues processed: 170 average time/residue: 0.0929 time to fit residues: 24.7221 Evaluate side-chains 163 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2246 THR Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 158 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 164 optimal weight: 6.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1039 HIS A ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1757 ASN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.134745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101960 restraints weight = 49703.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103975 restraints weight = 21601.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105240 restraints weight = 16072.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105440 restraints weight = 13428.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106570 restraints weight = 11785.870| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13375 Z= 0.118 Angle : 0.701 10.790 18136 Z= 0.347 Chirality : 0.046 0.206 2144 Planarity : 0.005 0.065 2288 Dihedral : 5.041 28.560 1808 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.33 % Favored : 90.37 % Rotamer: Outliers : 1.50 % Allowed : 14.50 % Favored : 84.00 % 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: -2.11 (0.20), residues: 1675 helix: -0.27 (0.24), residues: 533 sheet: -1.35 (0.31), residues: 265 loop : -2.19 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2522 TYR 0.024 0.002 TYR A1053 PHE 0.038 0.001 PHE A 649 TRP 0.036 0.002 TRP A1295 HIS 0.007 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13375) covalent geometry : angle 0.70133 / 0.35 (18136) hydrogen bonds : bond 0.03129 / 2.23 ( 425) hydrogen bonds : angle 5.36774 / 3.85 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: A 751 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8953 (tptt) REVERT: A 767 ARG cc_start: 0.8455 (mmp-170) cc_final: 0.7994 (mmt90) REVERT: A 787 ILE cc_start: 0.8788 (mt) cc_final: 0.8431 (tt) REVERT: A 816 SER cc_start: 0.8658 (m) cc_final: 0.8368 (t) REVERT: A 1033 THR cc_start: 0.8089 (m) cc_final: 0.7775 (m) REVERT: A 1168 MET cc_start: 0.8300 (mmm) cc_final: 0.7666 (mmm) REVERT: A 1715 ILE cc_start: 0.8696 (tp) cc_final: 0.8339 (tp) REVERT: A 1747 TYR cc_start: 0.8552 (p90) cc_final: 0.8199 (p90) REVERT: A 1774 CYS cc_start: 0.8262 (m) cc_final: 0.7976 (m) REVERT: A 2082 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: A 2269 ASP cc_start: 0.8087 (p0) cc_final: 0.7507 (t70) REVERT: A 2426 TRP cc_start: 0.6775 (m-10) cc_final: 0.6574 (m-10) outliers start: 21 outliers final: 13 residues processed: 169 average time/residue: 0.0933 time to fit residues: 24.5585 Evaluate side-chains 166 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1757 ASN Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2246 THR Chi-restraints excluded: chain A residue 2425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.0040 chunk 22 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1757 ASN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102012 restraints weight = 46391.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104202 restraints weight = 21516.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105058 restraints weight = 14818.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.105374 restraints weight = 12622.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.105717 restraints weight = 11238.247| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13375 Z= 0.120 Angle : 0.707 11.084 18136 Z= 0.347 Chirality : 0.046 0.199 2144 Planarity : 0.005 0.065 2288 Dihedral : 5.023 27.963 1808 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.87 % Favored : 89.83 % Rotamer: Outliers : 1.29 % Allowed : 15.14 % Favored : 83.57 % 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: -2.07 (0.20), residues: 1675 helix: -0.23 (0.23), residues: 531 sheet: -1.39 (0.31), residues: 270 loop : -2.13 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2522 TYR 0.023 0.001 TYR A1053 PHE 0.054 0.001 PHE A 649 TRP 0.037 0.002 TRP A1295 HIS 0.007 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13375) covalent geometry : angle 0.70664 / 0.35 (18136) hydrogen bonds : bond 0.03092 / 2.20 ( 425) hydrogen bonds : angle 5.31341 / 3.83 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 MET cc_start: 0.8470 (mpp) cc_final: 0.7604 (ttt) REVERT: A 726 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: A 751 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8952 (tptt) REVERT: A 767 ARG cc_start: 0.8487 (mmp-170) cc_final: 0.8014 (mmt90) REVERT: A 787 ILE cc_start: 0.8796 (mt) cc_final: 0.8444 (tt) REVERT: A 816 SER cc_start: 0.8625 (m) cc_final: 0.8348 (t) REVERT: A 1033 THR cc_start: 0.8088 (m) cc_final: 0.7776 (m) REVERT: A 1168 MET cc_start: 0.8355 (mmm) cc_final: 0.7668 (mmm) REVERT: A 1715 ILE cc_start: 0.8696 (tp) cc_final: 0.8340 (tp) REVERT: A 1747 TYR cc_start: 0.8517 (p90) cc_final: 0.8171 (p90) REVERT: A 1774 CYS cc_start: 0.8204 (m) cc_final: 0.7900 (m) REVERT: A 2082 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 2269 ASP cc_start: 0.8106 (p0) cc_final: 0.7498 (t70) REVERT: A 2426 TRP cc_start: 0.6796 (m-10) cc_final: 0.6568 (m-10) outliers start: 18 outliers final: 15 residues processed: 171 average time/residue: 0.1047 time to fit residues: 27.3204 Evaluate side-chains 169 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1757 ASN Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2246 THR Chi-restraints excluded: chain A residue 2425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097600 restraints weight = 31686.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101407 restraints weight = 17368.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101486 restraints weight = 10455.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.102359 restraints weight = 10396.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.102205 restraints weight = 10478.613| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13375 Z= 0.167 Angle : 0.728 11.241 18136 Z= 0.361 Chirality : 0.047 0.211 2144 Planarity : 0.005 0.065 2288 Dihedral : 5.141 28.293 1808 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.65 % Favored : 89.06 % Rotamer: Outliers : 1.14 % Allowed : 15.79 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1675 helix: -0.16 (0.24), residues: 525 sheet: -1.36 (0.31), residues: 265 loop : -2.22 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2072 TYR 0.023 0.002 TYR A1053 PHE 0.053 0.002 PHE A 649 TRP 0.040 0.002 TRP A1295 HIS 0.007 0.001 HIS A1758 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13375) covalent geometry : angle 0.72790 / 0.36 (18136) hydrogen bonds : bond 0.03227 / 2.32 ( 425) hydrogen bonds : angle 5.37905 / 3.89 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 MET cc_start: 0.8640 (mpp) cc_final: 0.7642 (ttt) REVERT: A 726 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8680 (mt-10) REVERT: A 751 LYS cc_start: 0.9300 (mmmm) cc_final: 0.8983 (tptt) REVERT: A 816 SER cc_start: 0.8679 (m) cc_final: 0.8407 (t) REVERT: A 1033 THR cc_start: 0.8150 (m) cc_final: 0.7835 (m) REVERT: A 1168 MET cc_start: 0.8425 (mmm) cc_final: 0.7446 (mmm) REVERT: A 1715 ILE cc_start: 0.8749 (tp) cc_final: 0.8380 (tp) REVERT: A 1745 GLU cc_start: 0.8229 (pp20) cc_final: 0.7788 (pp20) REVERT: A 1747 TYR cc_start: 0.8522 (p90) cc_final: 0.8240 (p90) REVERT: A 2082 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: A 2269 ASP cc_start: 0.8313 (p0) cc_final: 0.7578 (t0) outliers start: 16 outliers final: 13 residues processed: 166 average time/residue: 0.1092 time to fit residues: 27.9173 Evaluate side-chains 167 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 43 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 0.0010 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 overall best weight: 0.7468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.133964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100611 restraints weight = 62164.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102608 restraints weight = 24522.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104169 restraints weight = 17857.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104674 restraints weight = 13505.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106239 restraints weight = 11895.467| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13375 Z= 0.126 Angle : 0.710 11.121 18136 Z= 0.350 Chirality : 0.046 0.204 2144 Planarity : 0.005 0.065 2288 Dihedral : 5.066 27.909 1808 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.75 % Favored : 89.95 % Rotamer: Outliers : 1.14 % Allowed : 15.79 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.20), residues: 1675 helix: -0.14 (0.24), residues: 525 sheet: -1.36 (0.31), residues: 272 loop : -2.16 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2522 TYR 0.023 0.001 TYR A1053 PHE 0.025 0.001 PHE A1883 TRP 0.038 0.002 TRP A1295 HIS 0.007 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13375) covalent geometry : angle 0.70998 / 0.35 (18136) hydrogen bonds : bond 0.03070 / 2.19 ( 425) hydrogen bonds : angle 5.30626 / 3.83 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 MET cc_start: 0.8690 (mpp) cc_final: 0.7733 (ttt) REVERT: A 726 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: A 751 LYS cc_start: 0.9289 (mmmm) cc_final: 0.8963 (tptt) REVERT: A 767 ARG cc_start: 0.8523 (mmp-170) cc_final: 0.8052 (mmt90) REVERT: A 787 ILE cc_start: 0.8835 (mt) cc_final: 0.8585 (tt) REVERT: A 816 SER cc_start: 0.8639 (m) cc_final: 0.8386 (t) REVERT: A 1033 THR cc_start: 0.8112 (m) cc_final: 0.7803 (m) REVERT: A 1168 MET cc_start: 0.8379 (mmm) cc_final: 0.7353 (mmm) REVERT: A 1715 ILE cc_start: 0.8718 (tp) cc_final: 0.8367 (tp) REVERT: A 1747 TYR cc_start: 0.8567 (p90) cc_final: 0.8226 (p90) REVERT: A 1774 CYS cc_start: 0.8280 (m) cc_final: 0.7993 (m) REVERT: A 2082 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: A 2269 ASP cc_start: 0.8158 (p0) cc_final: 0.7510 (t0) outliers start: 16 outliers final: 13 residues processed: 169 average time/residue: 0.1068 time to fit residues: 27.6184 Evaluate side-chains 171 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1790 GLU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2082 GLU Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 0.3980 chunk 168 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 96 optimal weight: 0.0980 chunk 1 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1045 ASN A1068 ASN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102761 restraints weight = 50010.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105062 restraints weight = 21872.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.106116 restraints weight = 15066.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.106352 restraints weight = 12266.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107720 restraints weight = 11240.829| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13375 Z= 0.115 Angle : 0.706 11.289 18136 Z= 0.347 Chirality : 0.046 0.223 2144 Planarity : 0.005 0.065 2288 Dihedral : 4.952 27.167 1808 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.45 % Favored : 90.31 % Rotamer: Outliers : 1.21 % Allowed : 16.07 % Favored : 82.71 % 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: -1.93 (0.20), residues: 1675 helix: -0.04 (0.24), residues: 519 sheet: -1.30 (0.31), residues: 272 loop : -2.09 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2522 TYR 0.023 0.001 TYR A1053 PHE 0.026 0.001 PHE A1883 TRP 0.038 0.002 TRP A1295 HIS 0.007 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (13375) covalent geometry : angle 0.70622 / 0.35 (18136) hydrogen bonds : bond 0.02980 / 2.13 ( 425) hydrogen bonds : angle 5.22833 / 3.77 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.69 seconds wall clock time: 43 minutes 46.32 seconds (2626.32 seconds total)